Science.gov

Sample records for earwig anisolabis maritima

  1. Asymmetric forceps increase fighting success among males of similar size in the maritime earwig

    PubMed Central

    Munoz, Nicole E.; Zink, Andrew G.

    2012-01-01

    Extreme asymmetric morphologies are hypothesized to serve an adaptive function that counteracts sexual selection for symmetry. However direct tests of function for asymmetries are lacking, particularly in the context of animal weapons. The weapon of the maritime earwig, Anisolabis maritima, exhibits sizeable variation in the extent of directional asymmetry within and across body sizes, making it an ideal candidate for investigating the function of asymmetry. In this study, we characterized the extent of weapon asymmetry, characterized the manner in which asymmetric weapons are used in contests, staged dyadic contests between males of different size classes and analyzed the correlates of fighting success. In contests between large males, larger individuals won more fights and emerged as the dominant male. In contests between small males, however, weapon asymmetry was more influential in predicting overall fighting success than body size. This result reveals an advantage of asymmetric weaponry among males that are below the mean size in the population. A forceps manipulation experiment suggests that asymmetry may be an indirect, correlate of a morphologically independent factor that affects fighting ability. PMID:22984320

  2. Management strategies in apple orchards influence earwig community.

    PubMed

    Malagnoux, Laure; Marliac, Gaëlle; Simon, Sylvaine; Rault, Magali; Capowiez, Yvan

    2015-04-01

    Our aim was to assess whether different apple orchard management strategies (low-input, organic, Integrated Pest Management (IPM)) would have an effect on earwigs, which are important natural enemies of apple pests. These commercial orchards were as well compared to abandoned orchards. The density of Forficula auricularia and Forficula pubescens was studied for three years in 74 orchards around Avignon. The pesticide usage, some orchard characteristics and two small-scale landscape parameters were characterized. Pesticide use was significantly different between low-input, organic and IPM orchards with particularly significant differences in the number of insecticide applications (2.2, 4.9 and 9.2 respectively). Pesticide use had a much stronger impact on earwig community than other characteristics. F. auricularia density was significantly lower in IPM orchards (0.47 individuals per tree) compared to organic, low-input and abandoned orchards (3.1, 4.5 and 1.6 individuals per tree, respectively). F. pubescens was almost absent from IPM orchards and its abundance was higher in abandoned or low-input orchards compared to organic orchards (1.5 and 2.8 vs 0.8 individuals per tree). The percentage of F. pubescens in the earwig community decreased from abandoned (52%) to low-input (40%), organic (15%) and IPM orchards (0.5%). These results were confirmed by LD50 assays showing that for the two pesticides causing mortality close to normal application rates (chlorpyrifos-ethyl and acetamiprid), F. pubescens was significantly more sensitive than F. auricularia. Since earwigs are also easy to capture and identify, they may be useful to estimate the effects of management strategies and their modification in pome fruit orchards. PMID:25577700

  3. Reassessing the phylogenetic position of the epizoic earwigs (Insecta: Dermaptera).

    PubMed

    Naegle, Michael A; Mugleston, Joseph D; Bybee, Seth M; Whiting, Michael F

    2016-07-01

    Dermaptera is a relatively small order of free-living insects that typically feed on detritus and other plant material. However, two earwig lineages - Arixeniidae and Hemimeridae - are epizoic on Cheiromeles bats and Beamys and Cricetomys rats respectively. Both of these epizoic families are comprised of viviparous species. The monophyly of these epizoic lineages and their placement within dermapteran phylogeny has remained unclear. A phylogenetic analyses was performed on a diverse sample of 47 earwig taxa for five loci (18S rDNA, 28S rDNA, COI, Histone 3, and Tubulin Alpha I). Our results support two independent origins of the epizoic lifestyle within Dermaptera, with Hemimeridae and Arixeniidae each derived from a different lineage of Spongiphoridae. Our analyses places Marava, a genus of spongiphorids that includes free-living but viviparous earwigs, as sister group to Arixeniidae, suggesting that viviparity evolved prior to the shift to the epizoic lifestyle. Additionally, our results support the monophyly of Forficulidae and Chelisochidae and the paraphyly of Labiduridae, Pygidicranidae, Spongiphoridae, and Anisolabididae. PMID:27033951

  4. European Earwig, Forficula auricularia L. (Dermaptera: Forficulidae) at the Hanford Reach National Monument, Washington State

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The European earwig, Forficula auricularia L., was surveyed using pitfall traps at three sites at the Hanford Reach National Monument in south central Washington state. Pitfall traps were collected weekly from April 2002 through April 2003. The earwig was consistently taken during all months of the...

  5. Detecting aphid predation by earwigs in organic citrus orchards using molecular markers.

    PubMed

    Romeu-Dalmau, C; Piol, J; Agust, N

    2012-10-01

    Aphids (Hemiptera: Aphidoidea) can damage citrus trees via direct damage to leaves and flowers or via the indirect transmission of viruses. Predators such as the European earwig, Forficula auricularia Linnaeus (Dermaptera: Forficulidae), may assist in keeping aphid populations under control in citrus orchards. Group-specific primers were developed to detect aphid DNA in earwigs, in order to determine earwig predation rates in aphids in Mediterranean organic citrus trees. These primers were designed in accordance with the alignment of comparable sequences of aphids and earwigs, and they amplified a 224 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) region. Following the consumption of three to five Aphis spiraecola Patch, aphid DNA was still detectable in 50% of earwigs one day after the ingestion. When predation was evaluated in the field, aphid DNA was detected in earwigs in May, June and July but not in April and August. The most interesting result is that of May, when aphid abundance was very low but 30% of the earwigs tested positive for aphid DNA. This finding suggests that earwigs are important aphid predators in citrus orchards, as they probably alter aphid dynamics as a result of early seasonal pressure on this pest. PMID:22414267

  6. Earwigs ( Labidura riparia) mimic rotting-flesh odor to deceive vertebrate predators

    NASA Astrophysics Data System (ADS)

    Byers, John A.

    2015-08-01

    Many insects repel predators with caustic chemicals, while insects mimicking odors of wastes/dead insects to fool predators have not been documented. We found that the shore earwig, Labidura riparia (Dermaptera: Labiduridae) when bitten by anole lizards, Anolis carolinenesus, spits a rotting-flesh odor that deceives these insectivores into rejecting prey. Once a lizard attacked and rejected an earwig, the lizard did not attack another earwig during several weeks despite consuming other prey, indicating associative learning after one trial. The fetid odor was found in the head-prothorax containing salivary glands of both male and female earwigs and was comprised of ˜100 ng dimethyl disulfide and ˜600 ng dimethyl trisulfide. Nymphs had <5 ng of either compound. Adults also spit odorous sulfides after prolonged attacks by harvester ants, Pogonomyrmex rugosus, who were only deterred by the earwig's forceps. Sulfides released by the earwig are similar to odors of carrion/feces, which may be innately repulsive to some vertebrate predators. The mean initial discharge percentage (IDP) of sulfides from a cohort of earwigs was 62 %; however, IDPs of individuals were highly variable (3-99 %; mean 57 %). The discharge refill time (DRT) to refill 50 % of the earwig's allomone reservoir was estimated at 13 h. A positive relationship in sulfide amounts with body weight was found only in females in 2009, suggesting metabolic cost tradeoffs were revealed when sulfide content was half that in 2010. This is the first report of insects releasing sulfur-containing compounds that may mimic carrion-fecal odors as a deceptive defense against vertebrate predators.

  7. Earwigs (Labidura riparia) mimic rotting-flesh odor to deceive vertebrate predators.

    PubMed

    Byers, John A

    2015-08-01

    Many insects repel predators with caustic chemicals, while insects mimicking odors of wastes/dead insects to fool predators have not been documented. We found that the shore earwig, Labidura riparia (Dermaptera: Labiduridae) when bitten by anole lizards, Anolis carolinenesus, spits a rotting-flesh odor that deceives these insectivores into rejecting prey. Once a lizard attacked and rejected an earwig, the lizard did not attack another earwig during several weeks despite consuming other prey, indicating associative learning after one trial. The fetid odor was found in the head-prothorax containing salivary glands of both male and female earwigs and was comprised of ∼ 100 ng dimethyl disulfide and ∼ 600 ng dimethyl trisulfide. Nymphs had <5 ng of either compound. Adults also spit odorous sulfides after prolonged attacks by harvester ants, Pogonomyrmex rugosus, who were only deterred by the earwig's forceps. Sulfides released by the earwig are similar to odors of carrion/feces, which may be innately repulsive to some vertebrate predators. The mean initial discharge percentage (IDP) of sulfides from a cohort of earwigs was 62 %; however, IDPs of individuals were highly variable (3-99 %; mean 57 %). The discharge refill time (DRT) to refill 50 % of the earwig's allomone reservoir was estimated at 13 h. A positive relationship in sulfide amounts with body weight was found only in females in 2009, suggesting metabolic cost tradeoffs were revealed when sulfide content was half that in 2010. This is the first report of insects releasing sulfur-containing compounds that may mimic carrion-fecal odors as a deceptive defense against vertebrate predators. PMID:26071006

  8. New earwigs in mid-Cretaceous amber from Myanmar (Dermaptera, Neodermaptera)

    PubMed Central

    Engel, Michael S.

    2011-01-01

    Abstract Two new earwigs (Dermaptera) recently discovered in mid-Cretaceous (latest Albian) amber from Myanmar are described and figured. Astreptolabis ethirosomatia gen. et sp. n. is represented by a peculiar pygidicranoid female, assigned to a new subfamily, Astreptolabidinae subfam. n., and differs from other protodermapterans in the structure of the head, pronotum, tegmina, and cercal forceps. Tytthodiplatys mecynocercus gen. et sp. n. is a distinctive form of first-instar nymph of the Diplatyidae, the earliest record for this basal earwig family. The taxon can be distinguished from other Early Cretaceous nymphs by the structure of the head, antennae, legs, and most notably its filamentous and annulate cerci. The character affinities of these taxa among Neodermaptera are generally discussed as is the identity of an enigmatic ‘earwig-like’ species from the Jurassic of China. PMID:22259272

  9. Simultaneous optimisation of earwig hindwings for flight and folding.

    PubMed

    Deiters, Julia; Kowalczyk, Wojciech; Seidl, Tobias

    2016-01-01

    Earwig wings are highly foldable structures that lack internal muscles. The behaviour and shape changes of the wings during flight are yet unknown. We assume that they meet a great structural challenge to control the occurring deformations and prevent the wing from collapsing. At the folding structures especially, the wing could easily yield to the pressure. Detailed microscopy studies reveal adaptions in the structure and material which are not relevant for folding purposes. The wing is parted into two structurally different areas with, for example, a different trend or stiffness of the wing veins. The storage of stiff or more flexible material shows critical areas which undergo great changes or stress during flight. We verified this with high-speed video recordings. These reveal the extent of the occurring deformations and their locations, and support our assumptions. The video recordings reveal a dynamical change of a concave flexion line. In the static unfolded state, this flexion line blocks a folding line, so that the wing stays unfolded. However, during flight it extends and blocks a second critical folding line and prevents the wing from collapsing. With these results, more insight in passive wing control, especially within high foldable structures, is gained. PMID:27113958

  10. Beta maritima: the Origin of Beets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Along the undisturbed shores, especially of the Mediterranean Sea and the European North Atlantic Ocean, is a widespread plant called Beta maritima (Beta vulgaris subspecies maritima) by the botanists, or more commonly sea beet. Nothing for the inexperienced observer's eye distinguishes it from surr...

  11. 75 FR 35990 - Endangered and Threatened Wildlife and Plants; Listing the Flying Earwig Hawaiian Damselfly and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-24

    ... FR 21664). Candidate species are those taxa for which the Service has sufficient information on their... FR 58804), whereas the Pacific Hawaiian damselfly retained its status as a candidate species. On November 15, 1994 (59 FR 58982), the flying earwig Hawaiian damselfly was added back onto the...

  12. A "spare" compensates for the risk of destruction of the elongated penis of earwigs (Insecta: Dermaptera)

    NASA Astrophysics Data System (ADS)

    Kamimura, Yoshitaka; Matsuo, Yoh

    2001-11-01

    Male animals in several groups have multiple intromittent organs that outnumber the corresponding female gonopore. In Dermaptera (earwigs), males of the family Anisolabididae have paired, elongated male intromittent organs (virgae), while females have a single sperm-storage organ (spermatheca). Several authors have assumed that one of the paired virgae is non-functional, because it points in the "wrong" direction. We investigated the mating success of handicapped males of Euborellia plebeja in which one of their paired virgae was removed experimentally. These handicapped males succeeded in inseminating a mate. Males with genital damage are found in the field, suggesting that the "spare" functions under natural conditions. Based on phylogenetic information on earwigs, we discuss possible evolutionary scenarios for this genital peculiarity.

  13. When the body hides the ancestry: phylogeny of morphologically modified epizoic earwigs based on molecular evidence.

    PubMed

    Kocarek, Petr; John, Vaclav; Hulva, Pavel

    2013-01-01

    Here, we present a study regarding the phylogenetic positions of two enigmatic earwig lineages whose unique phenotypic traits evolved in connection with ectoparasitic relationships with mammals. Extant earwigs (Dermaptera) have traditionally been divided into three suborders: the Hemimerina, Arixeniina, and Forficulina. While the Forficulina are typical, well-known, free-living earwigs, the Hemimerina and Arixeniina are unusual epizoic groups living on molossid bats (Arixeniina) or murid rodents (Hemimerina). The monophyly of both epizoic lineages is well established, but their relationship to the remainder of the Dermaptera is controversial because of their extremely modified morphology with paedomorphic features. We present phylogenetic analyses that include molecular data (18S and 28S ribosomal DNA and histone-3) for both Arixeniina and Hemimerina for the first time. This data set enabled us to apply a rigorous cladistics approach and to test competing hypotheses that were previously scattered in the literature. Our results demonstrate that Arixeniidae and Hemimeridae belong in the dermapteran suborder Neodermaptera, infraorder Epidermaptera, and superfamily Forficuloidea. The results support the sister group relationships of Arixeniidae+Chelisochidae and Hemimeridae+Forficulidae. This study demonstrates the potential for rapid and substantial macroevolutionary changes at the morphological level as related to adaptive evolution, in this case linked to the utilization of a novel trophic niche based on an epizoic life strategy. Our results also indicate that the evolutionary consequences of the transition to an ectoparazitic mode of living, which is extremely rare in earwigs, have biased previous morphology-based hypotheses regarding the phylogeny of this insect group. PMID:23826171

  14. De Novo Transcriptome Hybrid Assembly and Validation in the European Earwig (Dermaptera, Forficula auricularia)

    PubMed Central

    Pichon, Samuel; Arbore, Roberto; Kühn-Bühlmann, Simone; Kölliker, Mathias; Walser, Jean-Claude

    2014-01-01

    Background The European earwig (Forficula auricularia) is an established system for studies of sexual selection, social interactions and the evolution of parental care. Despite its scientific interest, little knowledge exists about the species at the genomic level, limiting the scope of molecular studies and expression analyses of genes of interest. To overcome these limitations, we sequenced and validated the transcriptome of the European earwig. Methodology and Principal Findings To obtain a comprehensive transcriptome, we sequenced mRNA from various tissues and developmental stages of female and male earwigs using Roche 454 pyrosequencing and Illumina HiSeq. The reads were de novo assembled independently and screened for possible microbial contamination and repeated elements. The remaining contigs were combined into a hybrid assembly and clustered to reduce redundancy. A comparison with the eukaryotic core gene dataset indicates that we sequenced a substantial part of the earwig transcriptome with a low level of fragmentation. In addition, a comparative analysis revealed that more than 8,800 contigs of the hybrid assembly show significant similarity to insect-specific proteins and those were assigned for Gene Ontology terms. Finally, we established a quantitative PCR test for expression stability using commonly used housekeeping genes and applied the method to five homologs of known sex-biased genes of the honeybee. The qPCR pilot study confirmed sex specific expression and also revealed significant expression differences between the brain and antenna tissue samples. Conclusions By employing two different sequencing approaches and including samples obtained from different tissues, developmental stages, and sexes, we were able to assemble a comprehensive transcriptome of F. auricularia. The transcriptome presented here offers new opportunities to study the molecular bases and evolution of parental care and sociality in arthropods. PMID:24722757

  15. When the Body Hides the Ancestry: Phylogeny of Morphologically Modified Epizoic Earwigs Based on Molecular Evidence

    PubMed Central

    Kocarek, Petr; John, Vaclav; Hulva, Pavel

    2013-01-01

    Here, we present a study regarding the phylogenetic positions of two enigmatic earwig lineages whose unique phenotypic traits evolved in connection with ectoparasitic relationships with mammals. Extant earwigs (Dermaptera) have traditionally been divided into three suborders: the Hemimerina, Arixeniina, and Forficulina. While the Forficulina are typical, well-known, free-living earwigs, the Hemimerina and Arixeniina are unusual epizoic groups living on molossid bats (Arixeniina) or murid rodents (Hemimerina). The monophyly of both epizoic lineages is well established, but their relationship to the remainder of the Dermaptera is controversial because of their extremely modified morphology with paedomorphic features. We present phylogenetic analyses that include molecular data (18S and 28S ribosomal DNA and histone-3) for both Arixeniina and Hemimerina for the first time. This data set enabled us to apply a rigorous cladistics approach and to test competing hypotheses that were previously scattered in the literature. Our results demonstrate that Arixeniidae and Hemimeridae belong in the dermapteran suborder Neodermaptera, infraorder Epidermaptera, and superfamily Forficuloidea. The results support the sister group relationships of Arixeniidae+Chelisochidae and Hemimeridae+Forficulidae. This study demonstrates the potential for rapid and substantial macroevolutionary changes at the morphological level as related to adaptive evolution, in this case linked to the utilization of a novel trophic niche based on an epizoic life strategy. Our results also indicate that the evolutionary consequences of the transition to an ectoparazitic mode of living, which is extremely rare in earwigs, have biased previous morphology-based hypotheses regarding the phylogeny of this insect group. PMID:23826171

  16. Advanced morphology and behaviour of extinct earwig-like cockroaches (Blattida: Fuziidae fam. nov.)

    NASA Astrophysics Data System (ADS)

    Vršanský, Peter; Liang, Jun-Hui; Ren, Dong

    2009-12-01

    We describe the extinct cockroach family Fuziidae fam. nov., represented by Fuzia dadao gen. et sp. nov. from the ?Bathonian (168 Ma) Middle Jurassic sediments of Daohugou, Inner Mongolia, China. Males are characterized by unique, long and narrow bodies with a notch on forceps of earwig-like cerci, which attaches to the long external ovipositor during courtship. In a combination with the presence of male tergal glands, it appears the most advanced form of reproduction in the nearly 300 Myr history of long external ovipositor-bearing cockroaches. Its advanced morphology significantly supports attribution of living and fossil cockroaches within a single order Blattida.

  17. The Halophyte Cakile maritima Reduces Phenanthrene Phytotoxicity.

    PubMed

    Shiri, Moez; Rabhi, Mokded; El Amrani, Abdelhak; Abdelly, Chedly

    2015-01-01

    In a previous study, we showed that the halophyte plant model Thellungiella salsuginea was more tolerant to phenanthrene (Polycyclic Aromatic Hydrocarbon: PAH) than its relative glycophyte Arabidopsis thaliana. In the present work, we investigated the potential of another halophyte with higher biomass production, Cakile maritma, to reduce phenanthrene phytotoxicity. Sand was used instead of arable soil with the aim to avoid pollutant degradation by microorganisms or their interaction with the plant. After 6 weeks of treatment by 500 ppm phenanthrene (Phe), stressed plants showed a severe reduction (-73%) in their whole biomass, roots being more affected than leaves and stems. In parallel, Guaiacol peroxidase (GPX) activity was increased by 185 and 62% in leaves and roots, respectively. Non-enzymatic antioxidant capacity (assayed by ABTS test) was maintained unchanged in all plant organs. The model halophytic plant Thellungiella salsuginea was used as a biomarker of phenanthrene stress severity and was grown at 0 (control), 125, 250, and 375 ppm. T. salsuginea plants grown on the sand previously contaminated by 500 ppm Phe then treated by C. maritma culture (phytoremediation culture) showed similar biomass production as plants subjected to 125 ppm Phe. This suggests that the phytotoxic effects of phenanthrene were reduced by 75% by the 6-week treatment by C. maritima. Our findings indicate that C. maritima can constitute a potentially good candidate for PAH phytoremediation. PMID:25581445

  18. The Temperature Dependent Proteomic Analysis of Thermotoga maritima

    PubMed Central

    Wang, Quanhui; Bai, Xue; Chen, Zhen; Zhao, Jingjing; Xu, Ningzhi; Liu, Siqi

    2012-01-01

    Thermotoga maritima (T. maritima) is a typical thermophile, and its proteome response to environmental temperature changes has yet to be explored. This study aims to uncover the temperature-dependent proteins of T. maritima using comparative proteomic approach. T. maritima was cultured under four temperatures, 60°C, 70°C, 80°C and 90°C, and the bacterial proteins were extracted and electrophoresed in two-dimensional mode. After analysis of gel images, a total of 224 spots, either cytoplasm or membrane, were defined as temperature-dependent. Of these spots, 75 unique bacterial proteins were identified using MALDI TOF/TOF MS. As is well known, the chaperone proteins such as heat shock protein 60 and elongation factor Tu, were up-regulated in abundance due to increased temperature. However, several temperature-dependent proteins of T. maritima responded very differently when compared to responses of the thermophile T. tengcongensis. Intriguingly, a number of proteins involved in central carbohydrate metabolism were significantly up-regulated at higher temperature. Their corresponding mRNA levels were elevated accordingly. The increase in abundance of several key enzymes indicates that a number of central carbohydrate metabolism pathways of T. maritima are activated at higher temperatures. PMID:23071576

  19. Sibling cooperation in earwig families provides insights into the early evolution of social life.

    PubMed

    Falk, Joachim; Wong, Janine W Y; Kölliker, Mathias; Meunier, Joël

    2014-04-01

    The evolutionary transition from solitary to social life is driven by direct and indirect fitness benefits of social interactions. Understanding the conditions promoting the early evolution of social life therefore requires identification of these benefits in nonderived social systems, such as animal families where offspring are mobile and able to disperse and will survive independently. Family life is well known to provide benefits to offspring through parental care, but research on sibling interactions generally focused on fitness costs to offspring due to competitive behaviors. Here we show experimentally that sibling interactions also reflect cooperative behaviors in the form of food sharing in nonderived families of the European earwig, Forficula auricularia. Food ingested by individual offspring was transferred to their siblings through mouth-to-anus contacts and active allo-coprophagy. These transfers occurred in both the presence and the absence of the tending mothers, even though the direct contact with the mothers limited sibling food sharing. Neither food deprivation or relatedness influenced the total amount of transferred food, but relatedness affected frass release and the behavioral mechanisms mediating food sharing. Related offspring obtained food predominately through allo-coprophagy, whereas unrelated offspring obtained food through mouth-to-anus contacts. Overall, this study emphasizes that sibling cooperation may be a key process promoting the early evolution of social life. PMID:24642498

  20. Abiotic modulation of Spartina maritima photobiology in different latitudinal populations

    NASA Astrophysics Data System (ADS)

    Duarte, B.; Couto, T.; Freitas, J.; Valentim, J.; Silva, H.; Marques, J. C.; Dias, J. M.; Caçador, I.

    2013-09-01

    Spartina maritima has a very wide distribution in the northern hemisphere salt marshes crossing a wide variety of climatic environments. Therefore, it is not strange that some differences arise when observing the photosynthetic mechanisms of different populations inhabiting different latitudes. During this study it could be observed that climate is the most important factor controlling the photosynthetic traits of different populations distributed along a climatic gradient, namely the air temperature, humidity and light environment. Also some sediment physicochemical parameters such as pH and pore water salinity showed important influences driving the photosynthetic mechanisms in S. maritima. Furthermore S. maritima is one of the most abundant halophytes colonizing the Portuguese salt marshes. These facts have greater importance if one considers the large abundance of this halophytic species and how climate change will affect their metabolism and thus the ecosystem services provided by this species to the estuarine system.

  1. The Complete Mitochondrial Genome of the Geophilomorph Centipede Strigamia maritima

    PubMed Central

    Rhodes, Adelaide C.; Telford, Maximilian J.

    2015-01-01

    Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard ‘cloverleaf’ secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia. PMID:25794168

  2. The complete mitochondrial genome of the geophilomorph centipede Strigamia maritima.

    PubMed

    Robertson, Helen E; Lapraz, François; Rhodes, Adelaide C; Telford, Maximilian J

    2015-01-01

    Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard 'cloverleaf' secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia. PMID:25794168

  3. ROOT-EXUDED OXYGEN IN THE AQUATIC ANGIOSPERM 'RUPPIA MARITIMA'

    EPA Science Inventory

    The potential impact of oxygen from roots on the source of inorganic nitrogen for Ruppia maritima L. (Potamogetonales) was investigated in laboratory experiments. Roots released oxygen at an average rate of 2 to 3 micrograms O2 (mg dry wt)/hr. A distinctive oxygenated zone with a...

  4. Wigeongrass (Ruppia maritima L.): a literature review

    USGS Publications Warehouse

    Kantrud, H.A.

    1991-01-01

    Wigeongrass (Ruppia maritima L.) is a submersed macrophyte of nearly cosmopolitan distribution and worldwide importance as a waterfowl food. Unfortunately, the plant no longer inhabits vast areas disturbed by human activities. Taxonomic status of the plant is uncertain, especially in North America. In mild climates, in habitats subject to environmental extremes, the plant behaves as an annual (vegetation perishes), or as a perennial in deeper, more stable habitats (some vegetative parts grow year round). Drupelets (seeds) provide a mechanism for wigeongrass to survive periods of drought and excessive water salinity. These sexual propagules can be washed ashore or carried by birds or fish for long distances.Wigeongrass mostly occurs in temporarily to permanently flooded mesohaline-hyperhaline estuarine wetlands, but it also occurs inland in fresh to hypersaline palustrine and lacustrine wetlands. Most populations inhabit warm, relatively unpolluted, and well lit waters 2S conditions. Turbidity frequently limits wigeongrass growth in waters overlying easily suspendible bottom substrates.Wigeongrass often occurs in monotypic stands, yet grows with many other submersed and emergent macrophytes. Dominance in certain wetlands sometimes alternates with dominance by other submersed macrophytes as salinities, seasonal temperature cycles, or other environmental factors change. The shading effect of metaphytic, planktonic, or epiphytic algae often reduces production.Wigeongrass and its detritus provide food and cover for a large invertebrate biota, although direct consumption of the living plants is minimal. Wigeongrass beds in coastal wetlands are heavily used by fish. The plant is recognized worldwide as an important food of migrant and wintering waterfowl, wading birds, and shorebirds. In subtropical climates, wintering waterfowl can quickly consume entire stands.Propagation and management of wigeongrass has occurred for nearly 60 years in the southern and eastern United States. During the seventies and eighties, sophisticated water level and salinity management techniques have been developed to encourage growth of the plant.Future research should concentrate on determining the means to reduce light-limiting turbidity in many wetland types; understanding the ways in which human activities on and near wetlands affect wigeongrass production; and developing reliable and predictable techniques to stimulate wigeongrass production by water level manipulations and other means in different environmental settings. Trophic interactions and the effects of biomanipulation of fish populations in managed wigeongrass habitat--now little understood--also require more study.

  5. Characterization of the Earwig, Doru lineare, as a Predator of Larvae of the Fall Armyworm, Spodoptera frugiperda: A Functional Response Study

    PubMed Central

    Sueldo, Mabel Romero; Bruzzone, Octavio A.; Virla, Eduardo G.

    2010-01-01

    Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) is considered as the most important pest of maize in almost all tropical America. In Argentina, the earwig Doru lineare Eschscholtz (Dermaptera: Forficulidae) has been observed preying on S. frugiperda egg masses in corn crops, but no data about its potential role as a biocontrol agent of this pest have been provided. The predation efficiency of D. lineare on newly emerged S. frugiperda larva was evaluated through a laboratory functional response study. D. lineare showed type II functional response to S. frugiperda larval density, and disc equation estimations of searching efficiency and handling time were (a) = 0.374 and (t) = 182.9 s, respectively. Earwig satiation occurred at 39.4 S. frugiperda larvae. PMID:20575739

  6. NUTRITIONAL REQUIREMENTS OF THE SUBMERGED ANGIO-SPERM 'RUPPIA MARITIMA' IN ALGAE-FREE CULTURE

    EPA Science Inventory

    Ruppia maritima has the potential to become a model laboratory organism for studies with submerged aquatic vascular plants. The present study demonstrated that algae-free R. maritima grew well in a defined medium without sediment. Growth was a linear response to photon flux densi...

  7. Complete Mitochondrial Genome of the Free-Living Earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and Phylogeny of Polyneoptera

    PubMed Central

    Wan, Xinlong; Kim, Man Il; Kim, Min Jee; Kim, Iksoo

    2012-01-01

    The insect order Dermaptera, belonging to Polyneoptera, includes ∼2,000 extant species, but no dermapteran mitochondrial genome has been sequenced. We sequenced the complete mitochondrial genome of the free-living earwig, Challia fletcheri, compared its genomic features to other available mitochondrial sequences from polyneopterous insects. In addition, the Dermaptera, together with the other known polyneopteran mitochondrial genome sequences (protein coding, ribosomal RNA, and transfer RNA genes), were employed to understand the phylogeny of Polyneoptera, one of the least resolved insect phylogenies, with emphasis on the placement of Dermaptera. The complete mitochondrial genome of C. fletcheri presents the following several unusual features: the longest size in insects is 20,456 bp; it harbors the largest tandem repeat units (TRU) among insects; it displays T- and G-skewness on the major strand and A- and C-skewness on the minor strand, which is a reversal of the general pattern found in most insect mitochondrial genomes, and it possesses a unique gene arrangement characterized by a series of gene translocations and/or inversions. The reversal pattern of skewness is explained in terms of inversion of replication origin. All phylogenetic analyses consistently placed Dermaptera as the sister to Plecoptera, leaving them as the most basal lineage of Polyneoptera or sister to Ephemeroptera, and placed Odonata consistently as the most basal lineage of the Pterygota. PMID:22879905

  8. Trends in codon and amino acid usage in Thermotoga maritima.

    PubMed

    Zavala, Alejandro; Naya, Hugo; Romero, Héctor; Musto, Héctor

    2002-05-01

    The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino acid in this species) was detected as the second most prominent source of variation. However, this result is probably an artifact due to the very low frequency of Cys together with the nonbiased composition of this genome. The third trend was related to the preferential usage of a subset of codons among highly expressed genes, and these triplets are presumed to be translationally optimal. Concerning the amino acid usage, the hydropathy level of each protein (and therefore the frequency of charged residues) was the main trend, while the second factor was related to the frequency of usage of the smaller residues, suggesting that the cell economy strongly influences the architecture of the proteins. The third axis of the analysis discriminated the usage of Phe, Tyr, Trp (aromatic residues) plus Cys, Met, and His. These six residues have in common the property of being the preferential targets of reactive oxygen species, and therefore the anaerobic condition of T. maritima is an important factor for the amino acid frequencies. Finally, the Cys content of each protein was the fourth trend. PMID:11965430

  9. Data on the abundance of the banana weevil Cosmopolites sordidus and of the earwig Euborellia caraibea in bare soil and cover crop plots

    PubMed Central

    Carval, Dominique; Resmond, Rémi; Achard, Raphaël; Tixier, Philippe

    2016-01-01

    The data presented in this article are related to the research article entitled “Cover cropping reduces the abundance of the banana weevil Cosmopolites sordidus but does not reduce its damage to the banana plants” (Carval et al., in press) [1]. This article describes how the abundance of the banana weevil, Cosmopolites sordidus, and the abundance of the earwig Euborellia caraibea were affected by the addition of a cover crop. The field data set is made publicly available to enable critical or extended analyzes. PMID:27222854

  10. Effect of Oxygen and Redox Potential on Glucose Fermentation in Thermotoga maritima under Controlled Physicochemical Conditions

    PubMed Central

    Lakhal, Raja; Auria, Richard; Davidson, Sylvain; Ollivier, Bernard; Dolla, Alain; Hamdi, Moktar; Combet-Blanc, Yannick

    2010-01-01

    Batch cultures of Thermotoga maritima were performed in a bioreactor equipped with instruments adapted for experiments performed at 80°C to mimic the fluctuating oxidative conditions in the hot ecosystems it inhabits. When grown anaerobically on glucose, T. maritima was shown to significantly decrease the redox potential (Eh) of the culture medium down to about −480 mV, as long as glucose was available. Addition of oxygen into T. maritima cultures during the stationary growth phase led to a drastic reduction in glucose consumption rate. However, although oxygen was toxic, our experiment unambiguously proved that T. maritima was able to consume it during a 12-hour exposure period. Furthermore, a shift in glucose metabolism towards lactate production was observed under oxidative conditions. PMID:21461371

  11. Volatile composition of oyster leaf (Mertensia maritima (L.) Gray).

    PubMed

    Delort, Estelle; Jaquier, Alain; Chapuis, Christian; Rubin, Mark; Starkenmann, Christian

    2012-11-28

    Oyster leaf (Mertensia maritima), also called vegetarian oyster, has a surprising oyster-like aroma. Its volatile composition was investigated here for the first time. In total, 109 compounds were identified by gas chromatography-mass spectrometry (GC-MS) and quantified by GC-FID. The use of GC-olfactometry on both polar and nonpolar columns allowed the detection of the molecules having an oyster-like, marine odor. Four compounds were identified and confirmed by synthesis: (Z)-3-nonenal, (Z)-1,5-octadien-3-ol, (Z,Z)-3,6-nonadienal, and (Z)-1,5-octadien-3-one. After evaluation of freshly prepared reference samples, these compounds were confirmed to be reminiscent of the oyster-like marine notes perceived in the tasting of cut leaves. PMID:23140514

  12. Quinone- and nitroreductase reactions of Thermotoga maritima thioredoxin reductase.

    PubMed

    Valiauga, Benjaminas; Rouhier, Nicolas; Jacquot, Jean-Pierre; Čėnas, Narimantas

    2015-01-01

    The Thermotoga maritima NADH:thioredoxin reductase (TmTR) contains FAD and a catalytic disulfide in the active center, and uses a relatively poorly studied physiological oxidant Grx-1-type glutaredoxin. In order to further assess the redox properties of TmTR, we used series of quinoidal and nitroaromatic oxidants with a wide range of single-electron reduction potentials (E(1)7, -0.49-0.09 V). We found that TmTR catalyzed the mixed single- and two-electron reduction of quinones and nitroaromatic compounds, which was much faster than the reduction of Grx-1. The reactivity of both groups of oxidants increased with an increase in their E(1)7, thus pointing to the absence of their structural specificity. The maximal rates of quinone reduction in the steady-state reactions were lower than the maximal rates of reduction of FAD by NADH, obtained in presteady-state experiments. The mixed-type reaction inhibition by NAD(+) was consistent with its competition for a NADH binding site in the oxidized enzyme form, and also with the reoxidation of the reduced enzyme form. The inhibition data yielded a value of the standard potential for TmTR of -0.31±0.03 V at pH 7.0, which may correspond to the FAD/FADH2 redox couple. Overall, the mechanism of quinone- and nitroreductase reactions of T. maritima TR was similar to the previously described mechanism of Arabidopsis thaliana TR, and points to their prooxidant and possibly cytotoxic role. PMID:26098718

  13. The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

    SciTech Connect

    Latif, Haythem; Lerman, Joshua A.; Portnoy, Vasiliy A.; Tarasova, Yekaterina; Nagarajan, Harish; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Lee, Dae-Hee; Qiu, Yu; Zengler, Karsten

    2013-04-25

    Recent studies have revealed that microbial genomes have many more organizational features than previously thought. Here, an integrated approach utilizing multiple ‘omics’ datasets and bioinformatics tools is established that elucidates genomic features spanning various levels of cellular organization. This methodology produces gene annotation improvements and includes the definition of transcription units. These enhancements to the annotation enable identification of a set of genetic elements instrumental to gene expression and regulation including promoters, ribosome binding sites (RBSs) and untranslated regions (UTRs). This was applied to characterize the genome organization of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium with a small 1.86 Mb genome. Analysis derived from this multiomics approach in combination with bioinformatics tools demonstrate that the genome organization of T. maritima reflects its lifestyle, both with respect to its extreme growth temperature and compact genome. Comparative analysis of genome features suggests that thermodynamic limitations on binding kinetics for RNA polymerase and the ribosome necessitate increased sequence conservation of promoters and RBSs. Thus, restricting the sequences capable of initiating transcription and translation. Furthermore, this organism has uncharacteristically short 5’UTRs (11-17 nucleotides), which reduce the potential for 5’UTR regulatory interactions. The short intergenic distances in the T. maritima genome (5 bp on average) leave little space for regulation through transcription factor binding. The net effect of these constraints, temperature and genomic space, is a reduced ability to tune gene expression. This effect is readily apparent in global gene expression patterns, which show a high fraction of genes expressed independent of growth state with a tight, linear mRNA/protein correlation (Pearson r = 0.62, p < 2.2 x 10-16 t-test). This methodology for characterizing the genome organization is applicable to any culturable bacteria, and as similar studies are completed in diverse taxa, comparative analysis of genome features may provide insights into microbial evolution.

  14. Description and biology of Euborellia arcanum sp. nov., an alien earwig           occupying greenhouses in Germany and Austria (Dermaptera: Anisolabididae).

    PubMed

    Matzke, Danilo; Kocarek, Petr

    2015-01-01

    Greenhouses in botanical or zoological gardens are home to dozens of species of invertebrates that were introduced alongside plants or potting soil. Our study presents the description of an alien species of earwig, Euborellia arcanum sp. nov., found in tropical greenhouses in Leipzig and Potsdam (Germany) and in Vienna (Austria), including information about its biology in breeding culture. The species was most likely introduced into Europe by way of plants or plant matter from Florida, but the region of its natural habitat is unknown. The sequence of the mitochondrial gene cytochrome c oxidase subunit I (COI) was also evaluated and added to GenBank as a DNA barcode for further identification. PMID:26248909

  15. Diversity and Versatility of the Thermotoga maritima Sugar Kinome

    PubMed Central

    Rodionova, Irina A.; Yang, Chen; Li, Xiaoqing; Kurnasov, Oleg V.; Best, Aaron A.

    2012-01-01

    Sugar phosphorylation is an indispensable committed step in a large variety of sugar catabolic pathways, which are major suppliers of carbon and energy in heterotrophic species. Specialized sugar kinases that are indispensable for most of these pathways can be utilized as signature enzymes for the reconstruction of carbohydrate utilization machinery from microbial genomic and metagenomic data. Sugar kinases occur in several structurally distinct families with various partially overlapping as well as yet unknown substrate specificities that often cannot be accurately assigned by homology-based techniques. A subsystems-based metabolic reconstruction combined with the analysis of genome context and followed by experimental testing of predicted gene functions is a powerful approach of functional gene annotation. Here we applied this integrated approach for functional mapping of all sugar kinases constituting an extensive and diverse sugar kinome in the thermophilic bacterium Thermotoga maritima. Substrate preferences of 14 kinases mainly from the FGGY and PfkB families were inferred by bioinformatics analysis and biochemically characterized by screening with a panel of 45 different carbohydrates. Most of the analyzed enzymes displayed narrow substrate preferences corresponding to their predicted physiological roles in their respective catabolic pathways. The observed consistency supports the choice of kinases as signature enzymes for genomics-based identification and reconstruction of sugar utilization pathways. Use of the integrated genomic and experimental approach greatly speeds up the identification of the biochemical function of unknown proteins and improves the quality of reconstructed pathways. PMID:22885293

  16. Cytotoxic constituents from the stems of Diospyros maritima.

    PubMed

    Kuo, Y H; Chang, C I; Li, S Y; Chou, C J; Chen, C F; Kuo, Y H; Lee, K H

    1997-08-01

    One novel coumaric acid ester of lupeol, dioslupecin A (1), three naphthoquinones, 8'-hydroxyisodiospyrin (2), isodiospyrin (3), and plumbagin (4), three triterpenes, lupeol, lupenone and taraxerone, and four sterols, beta-sitosterol, stigmasterol, stigmast-4-en-3-one and ergosta-4,6,8(14),22-tetraen-3-one were isolated from the n-hexane extract of the stems of Diospyros maritima Blume. The structural determination of 1 was based on 1D and 2D NMR spectra (including 1H-1H COSY, 1H-13C COSY, and HMBC). All compounds were evaluated for in vitro cytotoxicity in 4 cancer cell lines. Compound 2 showed similar cytotoxicity against hepatoma (HEPA-3B, ED50 = 1.72 micrograms/ml), nasopharynx carcinoma (KB, ED50 = 1.85 micrograms/ml), colon carcinoma (COLO-205, ED50 = 2.24 micrograms/ml) and cervical carcinoma (HELA, ED50 = 1.92 micrograms/ml). Compounds 3 and 4 exhibited strong cytotoxicity against HEPA-3B, KB, COLO-205 and HELA (ED50 = 0.25, 1.81, 0.13 and 0.27 micrograms/ml for 3; ED50 = 0.87, 3.27, 0.56 and 0.35 micrograms/ml for 4, respectively. PMID:9270382

  17. Contribution of Spartina maritima to the reduction of eutrophication in estuarine systems.

    PubMed

    Sousa, Ana I; Lillebø, Ana I; Caçador, Isabel; Pardal, Miguel A

    2008-12-01

    Salt marshes are among the most productive ecosystems in the world, performing important ecosystem functions, particularly nutrient recycling. In this study, a comparison is made between Mondego and Tagus estuaries in relation to the role of Spartina maritima in nitrogen retention capacity and cycling. Two mono-specific S. maritima stands per estuary were studied during 1yr (biomass, nitrogen (N) pools, litter production, decomposition rates). Results showed that the oldest Tagus salt marsh population presented higher annual belowground biomass and N productions, and a slower decomposition rate for litter, contributing to the higher N accumulation in the sediment, whereas S. maritima younger marshes had higher aboveground biomass production. Detritus moved by tides represented a huge amount of aboveground production, probably significant when considering the N balance of these salt marshes. Results reinforce the functions of salt marshes as contributing to a reduction of eutrophication in transitional waters, namely through sedimentation processes. PMID:18684544

  18. POLYMERIZATION PROPERTIES OF THE T. MARITIMA ACTIN, MreB

    PubMed Central

    Bean, Greg J.; Amann, Kurt J.

    2008-01-01

    MreB is a bacterial ortholog of actin that affects cell shape, polarity and chromosome segregation. Although a significant body of work has explored its cellular functions, we know very little about the biochemical behavior of MreB. We have cloned, overexpressed in E. coli, and purified untagged MreB1 from Thermotoga maritima. We have characterized the conditions that regulate its monomer-to-polymer assembly reaction, the critical concentrations of that reaction, the manner in which MreB uses nucleotides, its stability, and the structure of the assembled polymer. MreB requires a bound purine nucleotide for polymerization and rapidly hydrolyzes it following assembly. MreB assembly contains two distinct components, one that does not require divalent cations and one that does, which may comprise the nucleation and elongation phases of assembly, respectively. MreB assembly is strongly favored by increasing temperature or protein concentration but inhibited differentially by high concentrations of monovalent salts. Polymerization rate increases and bulk critical concentration decreases with increasing temperature, but in contrast to previous reports, MreB is capable of polymerizing across a broad range of temperatures. MreB polymers are shorter, stiffer, and scatter more light than eukaryotic actin filaments. Due to rapid ATP hydrolysis and phosphate release, we suggest that most assembled MreB in cells is in the ADP-bound state. Because of only moderate differences between the ATP and ADP critical concentrations, treadmilling may occur, but we do not predict dynamic instability in cells. Because of the relatively low cellular concentration of MreB and the observed structural properties of the polymer, a single MreB assembly may exist in cells. PMID:18095710

  19. Draft Genome Sequence of a Heterotrophic Facultative Anaerobic Thermophilic Bacterium, Ardenticatena maritima Strain 110ST

    PubMed Central

    Yoshida, Takashi; Nakamura, Ryuhei

    2015-01-01

    Ardenticatena maritima strain 110ST is a filamentous bacterium isolated from an iron-rich coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the draft genome sequence comprising 3,569,367 bp, containing 3,355 predicted coding sequences (CDSs). PMID:26430053

  20. IMPACTS OF SALINITY AND NUTRIENT STRESS TO RUPPIA MARITIMA AND ZOSTERA MARINA: A MESOCOSM EXPERIMENT

    EPA Science Inventory

    Healthy seagrass beds were once found throughout the shallow areas of Narragansett Bay, R.I. but have disappeared due to infilling, pollution and disease. In Greenwich Bay, a highly developed embayment within Narragansett Bay, Ruppia maritima has colonized an area on the norther...

  1. ASSESSING THE IMPACTS OF SALINITY AND NUTRIENT STRESS TO RUPPIA MARITIMA AND ZOSTERA MARINA

    EPA Science Inventory

    Healthy seagrass beds were once found throughout the shallow areas of Narragansett Bay, R.I. but have disappeared due to infilling, pollution and disease. In Greenwich Bay, a highly developed embayment within Narragansett Bay, Ruppia maritima has colonized an area on the norther...

  2. GENETIC STRUCTURE AND PATTERNS OF SELECTION IN NATURAL POPULATIONS OF BETA VULGARIS SSP. MARITIMA.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty one accessions, including one sugar beet (Beta vulgaris ssp. vulgaris) 30 wild beet (29 Beta vulgaris ssp. maritima and 1 Beta macrocarpa) were included in this study. 29 Accessions were collected from wild populations along the coast of France (Atlantic and Mediterranean) and have associate...

  3. Characterization of the Thermotoga maritima Chemotaxis Methylation System that Lacks Methyltransferase CheR:MCP Tethering

    PubMed Central

    Perez, Eduardo; Stock, Ann M.

    2013-01-01

    Summary Sensory adaptation in bacterial chemotaxis is mediated by covalent modifications of specific glutamate and glutamine residues within the cytoplasmic domains of methyl-accepting proteins (MCPs). In Escherichia coli and Salmonella enterica, efficient methylation of MCPs depends on the localization of methyltransferase CheR to MCP clusters through an interaction between the CheR ?-subdomain and a pentapeptide sequence (NWETF or NWESF) at the C terminus of the MCP. In vitro methylation analyses utilizing S. enterica and Thermotoga maritima CheR proteins and MCPs indicate that MCP methylation in T. maritima occurs independently of a pentapeptide-binding motif. Kinetic and binding measurements demonstrate that despite efficient methylation, the interaction between T. maritima CheR and T. maritima MCPs is of relatively low affinity. Comparative protein sequence analyses of CheR ?-subdomains from organisms having MCPs that contain and/or lack pentapeptide-binding motifs identified key similarities and differences in residue conservation, suggesting the existence of two distinct classes of CheR proteins: pentapeptide-dependent and pentapeptide-independent methyltransferases. Analysis of MCP C-terminal ends showed that only ~10% of MCPs contain a putative C-terminal binding motif, the majority of which are restricted to the different proteobacteria classes (?, ?, ?, ?). These findings suggest that tethering of CheR to MCPs is a relatively recent event in evolution and that the pentapeptide-independent methylation system is more common than the well characterized pentapeptide-dependent methylation system. PMID:17163981

  4. EFFECTS OF SALINITY AND BOTTOM SUBSTRATE COMPOSITION ON THE GROWTH AND PROLIFERATION OF WIDGEONGRASS (RUPPIA MARITIMA)

    EPA Science Inventory

    The preliminary work for these experiments has been conducted, and the data will be collected during the next 6-8 months. We will collect R. maritima samples from different environments along the Gulf Coast and compare the genetic diversity using the ITRS reg...

  5. The Thermotoga maritima Phenotype Is Impacted by Syntrophic Interaction with Methanococcus jannaschii in Hyperthermophilic Coculture†

    PubMed Central

    Johnson, M. R.; Conners, S. B.; Montero, C. I.; Chou, C. J.; Shockley, K. R.; Kelly, R. M.

    2006-01-01

    Significant growth phase-dependent differences were noted in the transcriptome of the hyperthermophilic bacterium Thermotoga maritima when it was cocultured with the hyperthermophilic archaeon Methanococcus jannaschii. For the mid-log-to-early-stationary-phase transition of a T. maritima monoculture, 24 genes (1.3% of the genome) were differentially expressed twofold or more. In contrast, methanogenic coculture gave rise to 292 genes differentially expressed in T. maritima at this level (15.5% of the genome) for the same growth phase transition. Interspecies H2 transfer resulted in three- to fivefold-higher T. maritima cell densities than in the monoculture, with concomitant formation of exopolysaccharide (EPS)-based cell aggregates. Differential expression of specific sigma factors and genes related to the ppGpp-dependent stringent response suggests involvement in the transition into stationary phase and aggregate formation. Cell aggregation was growth phase dependent, such that it was most prominent during mid-log phase and decayed as cells entered stationary phase. The reduction in cell aggregation was coincidental with down-regulation of genes encoding EPS-forming glycosyltranferases and up-regulation of genes encoding β-specific glycosyl hydrolases; the latter were presumably involved in hydrolysis of β-linked EPS to release cells from aggregates. Detachment of aggregates may facilitate colonization of new locations in natural environments where T. maritima coexists with other organisms. Taken together, these results demonstrate that syntrophic interactions can impact the transcriptome of heterotrophs in methanogenic coculture, and this factor should be considered in examining the microbial ecology in anaerobic environments. PMID:16391122

  6. The aquatic vascular plant Ruppia maritima as an indicator organisms for contaminated sediments

    SciTech Connect

    Tagliabue, M.D.; Thursby, G.B.; Walker, H.A.; Johnston, R.K.

    1994-12-31

    An ongoing estuarine ecological risk assessment case study for the Portsmouth Naval Shipyard in the Great Bay (Kittery, ME, Portsmouth, NH) has been the catalyst for continued methods development with a rooted aquatic plant for a sediment toxicity test. A test using the aquatic vascular plant Ruppia maritima would be similar in it`s utility to the Algal (Champia parvula) Reproduction Test, an accepted, short term test (US EPA Short term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Waters to Marine and Estuarine Organisms). Laboratory studies were conducted to evaluate effects of lead, the primary site contaminant on R. maritima in the Great Bay. Morphology and life cycle of R. maritima are similar to that of the aquatic vascular plant Zostra marina which comprises up to 46% of the Great Bay habitat (Short 1992). R. maritima`s reduced size makes it a practical laboratory organism and Ruppia`s effects may offer useful insights into potential effects on Zostra or other aquatic vascular plants. Presently rooted vascular plants are not found in the site of concern (Clark Cove). This can be contributed to either of two factors; the physical parameters of the site, i.e., a depositional zone or the chemical parameters, i.e., metals contamination, specifically lead. Exposure of bedded and nonbedded plants occurred over a four day and ten day period using lead sulfate. Concentrations for bedded exposures were as follows, 0.3, 0.5, 0.8, 1.0 simultaneously extracted metal/acid volatile sulfide (SEM/AVS) molar ratios, and 0.1, 1.0, 10.0 and 100.0mg/l Pb for water only exposures. Some reduction in cumulative leaf growth was observed in the site samples as well as the spiked samples as compared to site controls. Results of this study and associated research which focuses on the further development of the Ruppia test methods will be presented.

  7. Transcriptional Analysis of Biofilm Formation Processes in the Anaerobic, Hyperthermophilic Bacterium Thermotoga maritima

    PubMed Central

    Pysz, Marybeth A.; Conners, Shannon B.; Montero, Clemente I.; Shockley, Keith R.; Johnson, Matthew R.; Ward, Donald E.; Kelly, Robert M.

    2004-01-01

    Thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80°C. A whole-genome cDNA microarray was used to examine differential expression patterns between biofilm and planktonic populations. Mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the genome), over a third of which were initially annotated as hypothetical proteins in the T. maritima genome. Among the previously annotated genes in the T. maritima genome, which showed expression changes during biofilm growth, were several that corresponded to biofilm formation genes identified in mesophilic bacteria (i.e., Pseudomonas species, Escherichia coli, and Staphylococcus epidermidis). Most notably, T. maritima biofilm-bound cells exhibited increased transcription of genes involved in iron and sulfur transport, as well as in biosynthesis of cysteine, thiamine, NAD, and isoprenoid side chains of quinones. These findings were all consistent with the up-regulation of iron-sulfur cluster assembly and repair functions in biofilm cells. Significant up-regulation of several β-specific glycosidases was also noted in biofilm cells, despite the fact that maltose was the primary carbon source fed to the chemostat. The reasons for increased β-glycosidase levels are unclear but are likely related to the processing of biofilm-based polysaccharides. In addition to revealing insights into the phenotype of sessile T. maritima communities, the methodology developed here can be extended to study other anaerobic biofilm formation processes as well as to examine aspects of microbial ecology in hydrothermal environments. PMID:15466556

  8. Early effects of salt stress on the physiological and oxidative status of Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte).

    PubMed

    Ellouzi, Hasna; Hamed, Karim Ben; Cela, Jana; Munné-Bosch, Sergi; Abdelly, Chedly

    2011-06-01

    Early changes in physiological and oxidative status induced by salt stress were monitored in two Brassicaceae plants differing in their tolerance to salinity, Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte). Growth response and antioxidant defense of C. maritima under 400 mM NaCl were compared with those of A. thaliana exposed to 100 mM NaCl. Salinity induced early growth reduction that is less pronounced in C. maritima than in A. thaliana. Maximum hydrogen peroxide (H₂O₂) level occurred in the leaves of both species 4 h after the onset of salt treatment. A rapid decline in H₂O₂ concentration was observed thereafter in C. maritima, whereas it remained high in A. thaliana. Correlatively, superoxide dismutase, catalase and peroxidase activities increased at 4 h of treatment in C. maritima and decreased thereafter. However, the activity of these enzymes remained higher in treated plants than that in controls, regardless of the duration of treatment, in A. thaliana. The concentrations of malondialdehyde (MDA) reached maximum values at 24 h of salt stress in both species. Again, MDA levels decreased later in C. maritima, but remained high in A. thaliana. The contents of α-tocopherol remained constant during salt stress in C. maritima and decreased during the first 24 h of salt stress and then remained low in A. thaliana. The results clearly showed that C. maritima, in contrast to A. thaliana, can rapidly evolve physiological and antioxidant mechanisms to adapt to salt and manage the oxidative stress. This may explain, at least partially, the difference in salt tolerance between halophytes and glycophytes. PMID:21288246

  9. Crystallization, preliminary X-ray diffraction and structure analysis of Thermotoga maritima mannitol dehydrogenase

    SciTech Connect

    Puttick, Jennifer; Vieille, Claire; Song, Seung H.; Fodje, Michel N.; Grochulski, Pawel; Delbaere, Louis T. J.

    2007-04-01

    T. maritima mannitol dehydrogenase has been crystallized in space group P2{sub 1}2{sub 1}2{sub 1} with a = 84.43, b = 120.61, c = 145.76 Å. The crystals diffracted to 3.3 Å resolution at the Canadian Light Source. Diffraction data have been collected from a crystal of Thermotoga maritima mannitol dehydrogenase at the Canadian Light Source. The crystal diffracted to 3.3 Å resolution and belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 83.43, b = 120.61, c = 145.76 Å. The structure is likely to be solved by molecular replacement.

  10. Crystallization and preliminary X-ray analysis of cytosolic α-mannosidase from Thermotoga maritima

    SciTech Connect

    Nakajima, Masahiro; Fushinobu, Shinya Imamura, Hiromi; Shoun, Hirofumi; Wakagi, Takayoshi

    2006-02-01

    Cytosolic class II α-mannosidase from T. maritima (TM1851), a family 38 glycoside hydrolase, was crystallized. A diffraction data set was collected to 2.9 Å resolution. Class II α-mannosidase cleaves off α-1,2-, α-1,3- and α-1,6-mannose residues. In this paper, the crystallization and preliminary X-ray analysis of cytosolic class II α-mannosidase from Thermotoga maritima (TM1851), a family 38 glycoside hydrolase, is described. The crystal of recombinant TM1851 belongs to the C-centred monoclinic space group C2, with unit-cell parameters a = 244.7, b = 87.4, c = 166.6 Å, β = 124.7°. X-ray diffraction data were collected to a resolution of 2.9 Å.

  11. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T)

    PubMed Central

    Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Mavromatis, Konstantinos

    2011-01-01

    Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH2T is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21886857

  12. Structures of and Interactions Between Domains of Trigger Factor from Thermotoga maritima

    SciTech Connect

    Martinez-Hackert,E.; Hendrickson, W.

    2007-01-01

    Trigger factor (TF) is a eubacterial chaperone that associates with ribosomes at the peptide-exit tunnel and also occurs in excess free in the cytosol. TF is a three-domain protein that appears to exist in a dynamic equilibrium of oligomerization states and interdomain conformations. X-ray crystallography and chemical cross-linking were used to study the roles of the N- and C-terminal domains of Thermotoga maritima TF in TF oligomerization and chaperone activity. The structural conservation of both the N- and C-terminal TF domains was unambiguously established. The biochemical and crystallographic data reveal a tendency for these domains to partake in diverse and apparently nonspecific protein-protein interactions. It is found that the T. maritima and Escherichia coli TF surfaces lack evident exposed hydrophobic patches. Taken together, these data suggest that TF chaperones could interact with nascent proteins via hydrophilic surfaces.

  13. Complete genome sequence of Hippea maritima type strain (MH2T)

    SciTech Connect

    Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, K

    2011-01-01

    Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome se- quencing because of its isolated phylogenetic location, as a distant next neighbor of the ge- nus Desulfurella. Strain MH2T is the first type strain from the order Desulfurellales with a com- pletely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein- coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Draft Genome Sequence of a Heterotrophic Facultative Anaerobic Thermophilic Bacterium, Ardenticatena maritima Strain 110ST.

    PubMed

    Kawaichi, Satoshi; Yoshida, Takashi; Sako, Yoshihiko; Nakamura, Ryuhei

    2015-01-01

    Ardenticatena maritima strain 110S(T) is a filamentous bacterium isolated from an iron-rich coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the draft genome sequence comprising 3,569,367 bp, containing 3,355 predicted coding sequences (CDSs). PMID:26430053

  15. Sediment and plant dynamics in saltmarshes pioneer zone: Puccinellia maritima as a key species?

    NASA Astrophysics Data System (ADS)

    Langlois, E.; Bonis, A.; Bouzillé, J. B.

    2003-02-01

    Low saltmarshes are subjected to variability between sites and tidal cycles in terms of erosive forces by current and waves, the frequency and duration of flooding and soil salinity. The establishment of vegetation in pioneer zones is directly related to sedimentary dynamics but few data are available concerning the effects of plants on sediment dynamics. In the Mont Saint Michel Bay (France), the low saltmarshes, including pioneer zones, are characterized by a micro-topography composed of hummocks with vegetation dominated by Puccinellia maritima, mudflats with a low sparse vegetation of Spartina anglica, Salicornia fragilis and Puccinellia maritima and a few erosion zones. The aim of this study was to (1) investigate the sediment deposition and soil elevation patterns, between tidal cycles and between sites; (2) look for a relationship between the development and dynamics of the micro-topography and the different plant species; and (3) evaluate whether Puccinellia maritima plays any role in enhancing sediment deposition and therefore plant succession in these lower marshes. The three study sites were situated in a system where accretion prevailed and soil substrate was essentially fine sand. The amount of sediment deposited varied between tidal cycles as well as between sites. The soil level changes, measured by a Sediment Erosion Bar, underlined the importance of Puccinellia maritima in stabilising sediment deposition. When the soil was covered with Puccinellia, the increase in soil level is almost doubled compared with bare sediment when the site was relatively sheltered. In more disturbed sites, such as site 1, the presence of Puccinellia was critical for the increase in soil level as it was eroded on bare soil. The presence of Puccinellia appeared to be strongly linked with the installation of hummocks and the micro-topography. In 2 to 3 years, Puccinellia cover increased and species typical of higher levels of the saltmarsh became established on the higher and more stable parts of the micro-topography (the 'hummocks'), which led to an increase in the succession rate.

  16. The aquatic vascular plant Ruppia maritima as an indicator organism for contaminated sediments

    SciTech Connect

    Tagliabue, M.D.; Thursby, G.B.; Walker, H.A.; Johnston, R.K.

    1995-12-31

    An ongoing estuarine ecological risk assessment case study for the Portsmouth Naval Shipyard in the Great Bay Estuary (New Hampshire, Maine) was the catalyst to continue development a rooted aquatic plant sediment toxicity test. Laboratory studies were conducted to evaluate effects of lead, the primary site contaminant on R. maritima in the Great Bay. Although the aquatic vascular plant Zostra marina comprises up to 46% of the Great Bay subtidal habitat, R. maritima`s much smaller size makes it a more practical laboratory organism. Effects on Ruppia may offer useful insights into potential effects on Zostra or other aquatic vascular plants. Presently rooted vascular plants are not found in Clark Cove located adjacent to a landfill disposal site on the shipyard. The absence of rooted vegetation can be contributed to, physical parameters of the site (turbidity, grain size, texture) or chemical parameters (heavy metal/Pb contamination, redox potential). Exposure of bedded and nonbedded plants occurred over a four day and ten day period using lead sulfate. Concentrations for bedded exposures were as follows, 0.3, 0.5, 0.8, 1.0 simultaneously extracted metal/acid volatile sulfide (SEM/AVS) molar ratios, and 0.1, 1.0, 10.0 and 100.0mg/l Pb for water only exposures. Reduction in cumulative leaf growth was observed for the Clark Cove sediments as well as the spiked sediments as compared to reference sediments.

  17. Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions.

    PubMed

    Velez, Patricia; Alejandri-Ramírez, Naholi D; González, María C; Estrada, Karel J; Sanchez-Flores, Alejandro; Dinkova, Tzvetanka D

    2015-09-01

    Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat. PMID:26116293

  18. Complexes of Thermotoga maritima S-adenosylmethionine decarboxylase provide insights into substrate specificity

    SciTech Connect

    Bale, Shridhar; Baba, Kavita; McCloskey, Diane E.; Pegg, Anthony E.; Ealick, Steven E.

    2010-06-25

    The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5{prime}-deoxy-5{prime}-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues from both chains of the homodimer. The complexes provide insights into the substrate specificity and ligand binding of AdoMetDC in prokaryotes. The conservation of the ligand-binding mode and the active-site residues between human and T. maritima AdoMetDC provides insight into the evolution of AdoMetDC.

  19. Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions

    PubMed Central

    Velez, Patricia; Alejandri-Ramírez, Naholi D.; González, María C.; Estrada, Karel J.; Sanchez-Flores, Alejandro; Dinkova, Tzvetanka D.

    2015-01-01

    Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat. PMID:26116293

  20. Ecophysiological response of Crambe maritima to airborne and soil-borne salinity

    PubMed Central

    de Vos, Arjen C.; Broekman, Rob; Groot, Maartje P.; Rozema, Jelte

    2010-01-01

    Background and Aims There is a need to evaluate the salt tolerance of plant species that can be cultivated as crops under saline conditions. Crambe maritima is a coastal plant, usually occurring on the driftline, with potential use as a vegetable crop. The aim of this experiment was to determine the growth response of Crambe maritima to various levels of airborne and soil-borne salinity and the ecophysiological mechanisms underlying these responses. Methods In the greenhouse, plants were exposed to salt spray (400 mm NaCl) as well as to various levels of root-zone salinity (RZS) of 0, 50, 100, 200 and 300 mm NaCl during 40 d. The salt tolerance of Crambe maritima was assessed by the relative growth rate (RGR) and its components. To study possible salinity effects on the tissue and cellular level, the leaf succulence, tissue Na+ concentrations, Na+ : K+ ratio, net K+/Na+ selectivity, N, P, K+, Ca2+, Mg2+, proline, soluble sugar concentrations, osmotic potential, total phenolics and antioxidant capacity were measured. Key Results Salt spray did not affect the RGR of Crambe maritima. However, leaf thickness and leaf succulence increased with salt spray. Root zone salinities up to 100 mm NaCl did not affect growth. However, at 200 mm NaCl RZS the RGR was reduced by 41 % compared with the control and by 56 % at 300 mm NaCl RZS. The reduced RGR with increasing RZS was largely due to the reduced specific leaf area, which was caused by increased leaf succulence as well as by increased leaf dry matter content. No changes in unit leaf rate were observed but increased RZS resulted in increased Na+ and proline concentrations, reduced K+, Ca2+ and Mg2+ concentrations, lower osmotic potential and increased antioxidant capacity. Proline concentrations of the leaves correlated strongly (r = 0·95) with RZS concentrations and not with plant growth. Conclusions Based on its growth response, Crambe maritima can be classified as a salt spray tolerant plant that is sensitive to root zone salinities exceeding 100 mm NaCl. PMID:20354071

  1. Moving closer towards restoration of contaminated estuaries: Bioaugmentation with autochthonous rhizobacteria improves metal rhizoaccumulation in native Spartina maritima.

    PubMed

    Mesa, Jennifer; Rodríguez-Llorente, Ignacio David; Pajuelo, Eloisa; Piedras, José María Barcia; Caviedes, Miguel Angel; Redondo-Gómez, Susana; Mateos-Naranjo, Enrique

    2015-12-30

    Spartina maritima is an ecosystem engineer that has shown to be useful for phytoremediation purposes. A glasshouse experiment using soil from a metal-contaminated estuary was designed to investigate the effect of a native bacterial consortium, isolated from S. maritima rizhosphere and selected owing to their plant growth promoting properties and multiresistance to heavy metals, on plant growth and metal accumulation. Plants of S. maritima were randomly assigned to three soil bioaugmentation treatments (without inoculation, one inoculation and repeated inoculations) for 30 days. Growth parameters and photosynthetic traits, together with total concentrations of several metals were determined in roots and/or leaves. Bacterial inoculation improved root growth, through a beneficial effect on photosynthetic rate (AN) due to its positive impact on functionality of PSII and chlorophyll concentration. Also, favoured intrinsic water use efficiency of S. maritima, through the increment in AN, stomatal conductance and in root-to-shoot ratio. Moreover, this consortium was able to stimulate plant metal uptake specifically in roots, with increases of up to 19% for As, 65% for Cu, 40% for Pb and 29% for Zn. Thus, bioaugmentation of S. maritima with the selected bacterial consortium can be claimed to enhance plant adaptation and metal rhizoaccumulation during marsh restoration programs. PMID:26188869

  2. Differential responses of antioxidative enzymes and lipid peroxidation to salt stress in salt-tolerant Plantago maritima and salt-sensitive Plantago media.

    PubMed

    Sekmen, Aşkim Hediye; Türkan, Ismail; Takio, Susumu

    2007-11-01

    The changes in plant growth, relative water content (RWC), stomatal conductance, lipid peroxidation and antioxidant system in relation to the tolerance to salt stress were investigated in salt-tolerant Plantago maritima and salt-sensitive Plantago media. The 60 days old P. maritima and P. media seedlings were subjected to 0, 100 and 200 mM NaCl for 7 days. Reduction in shoot length was higher in P. media than in P. maritima after exposure to 200 mM NaCl, but 100 mM NaCl treatment did not show any effect on shoot length of P. maritima. Shoot dry weight decreased in P. media and did not change in P. maritima. Two hundred millimolar NaCl treatment had no effect on leaf RWC in P. maritima, but it was reduced in P. media. Salt stress caused reduction in stomatal conductance being more pronounced in P. media than in P. maritima. Activities of superoxide dismutase (SOD; EC 1.15.1.1), catalase (CAT; EC 1.11.1.6), glutathione reductase (GR; EC 1.6.4.2) decreased in P. media with increasing salinity. Ascorbate peroxidase (APX; EC 1.11.1.11) activity in leaves of P. media was increased and showed no change under 100 and 200 mM NaCl, respectively. However, activities of CAT, APX and GR increased under 200 mM NaCl while their activities did not change under 100 mM NaCl in P. maritima. SOD activity in leaves of P. maritima increased with increasing salinity. Concomitant with this, four SOD activity bands were identified in leaves of P. maritima, two bands only were observed in P. media. Peroxidase (POX; EC 1.11.1.7) activity increased under both salt concentrations in P. maritima, but only under 200 mM NaCl in P. media. Confirming this, five POX activity bands were identified in leaves of P. maritima, but only two bands were determined in P. media. Malondialdehyde levels in the leaves increased under salt stress in P. media but showed no change and decreased in P. maritima at 100 and 200 mM NaCl, respectively. These results suggest that the salt-tolerant P. maritima showed a better protection mechanism against oxidative damage caused by salt stress by its higher induced activities of antioxidant enzymes than the salt-sensitive P. media. PMID:18251879

  3. Structural Insight inot the low Affinity Between Thermotoga maritima CheA and CheB Compared to their Escherichia coli/Salmonella typhimurium Counterparts

    SciTech Connect

    S Park; B Crane

    2011-12-31

    CheA-mediated CheB phosphorylation and the subsequent CheB-mediated demethylation of the chemoreceptors are important steps required for the bacterial chemotactic adaptation response. Although Escherichia coli CheB has been reported to interact with CheA competitively against CheY, we have observed that Thermotoga maritima CheB has no detectable CheA-binding. By determining the CheY-like domain crystal structure of T. maritima CheB, and comparing against the T. maritima CheY and Salmonella typhimurium CheB structures, we propose that the two consecutive glutamates in the {beta}4/{alpha}4 loop of T. maritima CheB that is absent in T. maritima CheY and in E. coli/S. typhimurium CheB may be one factor contributing to the low CheA affinity.

  4. Scouting contaminated estuaries: heavy metal resistant and plant growth promoting rhizobacteria in the native metal rhizoaccumulator Spartina maritima.

    PubMed

    Mesa, J; Mateos-Naranjo, E; Caviedes, M A; Redondo-Gómez, S; Pajuelo, E; Rodríguez-Llorente, I D

    2015-01-15

    Spartina maritima is a native endangered heavy metal rhizoaccumulator cordgrass naturally growing in southwest coasts of Spain, where is used as a biotool to rehabilitate degraded salt marshes. Fifteen bacterial strains were isolated from the rhizosphere of S. maritima growing in the estuary of the Tinto River, one of the most polluted areas in the world. A high proportion of bacteria were resistant towards several heavy metals. They also exhibited multiple plant growth promoting (PGP) properties, in the absence and the presence of Cu. Bacillus methylotrophicus SMT38, Bacillusaryabhattai SMT48, B. aryabhattai SMT50 and Bacilluslicheniformis SMT51 were selected as the best performing strains. In a gnobiotic assay, inoculation of Medicago sativa seeds with the selected isolates induced higher root elongation. The inoculation of S. maritima with these indigenous metal-resistant PGP rhizobacteria could be an efficient method to increase plant adaptation and growth in contaminated estuaries during restoration programs. PMID:25467875

  5. Seed germination responses to varying environmental conditions and provenances in Crucianella maritima L., a threatened coastal species.

    PubMed

    Del Vecchio, Silvia; Mattana, Efisio; Acosta, Alicia T R; Bacchetta, Gianluigi

    2012-01-01

    Seed germination (effects of light, temperature, NaCl and KNO(3)) of the coastal endangered species Crucianella maritima was investigated by testing seeds from three different populations. Data were analyzed by means of Generalized Linear Mixed Model (GLMM). The principal results showed that germination of C. maritima seeds was characterized by photoinhibition, absence of primary dormancy and salt-induced secondary dormancy, with no need for high nutrient availability (KNO(3)). Intraspecific differences in germination pattern emerged, apparently due to a different seed mass. These results show important germination traits of C. maritima which should be taken into account in possible reintroduction attempts aimed at restoring threatened populations of this species. PMID:22226161

  6. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

    PubMed Central

    Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S. T.; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C. J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J. P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H. L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen

    2014-01-01

    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. PMID:25423365

  7. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

    PubMed

    Chipman, Ariel D; Ferrier, David E K; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S T; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C; Alonso, Claudio R; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C J; Blankenburg, Kerstin P; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K; Du Pasquier, Louis; Duncan, Elizabeth J; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D; Extavour, Cassandra G; Francisco, Liezl; Gabaldón, Toni; Gillis, William J; Goodwin-Horn, Elizabeth A; Green, Jack E; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J P; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H L; Hunn, Julia P; Hunnekuhl, Vera S; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N; Jiggins, Francis M; Jones, Tamsin E; Kaiser, Tobias S; Kalra, Divya; Kenny, Nathan J; Korchina, Viktoriya; Kovar, Christie L; Kraus, F Bernhard; Lapraz, François; Lee, Sandra L; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C; Robertson, Helen E; Robertson, Hugh M; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E; Schurko, Andrew M; Siggens, Kenneth W; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M; Willis, Judith H; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M; Worley, Kim C; Gibbs, Richard A; Akam, Michael; Richards, Stephen

    2014-11-01

    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. PMID:25423365

  8. Computational prediction and experimental validation of a novel miRNA in Suaeda maritima, a halophyte.

    PubMed

    Gharat, S A; Shaw, B P

    2016-01-01

    The lack of available transcriptome data for plants of no economic or agronomic importance limits the identification of miRNAs in many species. Considering the possible similarity of the transcriptome between related species, the present study used expressed sequence tags (ESTs) of Suaeda salsa and Suaeda glauca to identify conserved miRNAs, which were validated in a halophyte, Suaeda maritima, with the aim of identifying salt-responsive miRNAs from naturally salt-tolerant plants, information on which is limited. In this study, computational analysis predicted three miRNA sequences by mapping non-redundant miRNA sequences from miRBase 16.0 on 1534 ESTs of S. salsa and S. glauca. The expression of one could be validated in S. maritima, and was named sma-miR1867. This miRNA was downregulated in response to NaCl treatment. It was predicted to target ferredoxin-thioredoxin reductase (FTR), cell division control protein 6 (CDC6), and ubiquitin-protein ligase (UPL) in S. salsa and/or S. glauca. However, only UPL could be amplified in S. maritima, and RT-qPCR showed that it was upregulated in response to NaCl treatment. These results indicate that, in halophytes, FTR and CDC6 may promote carbon metabolism and cell division, respectively, in the presence of salt, while UPL may regulate the abundance of proteins that are important for salt tolerance in halophytes. Thus, sma-miR1867 could be an essential component of salt resistance in halophytes. PMID:26909919

  9. Effects of Oil-Contaminated Sediments on Submerged Vegetation: An Experimental Assessment of Ruppia maritima

    PubMed Central

    Martin, Charles W.; Hollis, Lauris O.; Turner, R. Eugene

    2015-01-01

    Oil spills threaten the productivity of ecosystems through the degradation of coastal flora and the ecosystem services these plants provide. While lab and field investigations have quantified the response of numerous species of emergent vegetation to oil, the effects on submerged vegetation remain uncertain. Here, we discuss the implications of oil exposure for Ruppia maritima, one of the most common species of submerged vegetation found in the region affected by the recent Deepwater Horizon oil spill. We grew R. maritima in a range of manipulated sediment oil concentrations: 0, 0.26, 0.53, and 1.05 mL oil /L tank volume, and tracked changes in growth (wet weight and shoot density/length), reproductive activity (inflorescence and seed production), root characteristics (mass, length, diameter, and area), and uprooting force of plants. While no statistical differences were detected in growth, plants exhibited significant changes to reproductive output, root morphology, and uprooting force. We found significant reductions in inflorescences and fruiting bodies at higher oil concentrations. In addition, the roots growing in the high oil were shorter and wider. Plants in medium and high oil required less force to uproot. A second experiment was performed to separate the effects of root morphology and oiled sediment properties and indicated that there were also changes to sediment cohesion that contributed to a reduction in uprooting forces in medium and high oil. Given the importance of sexual reproduction for these plants, oil contamination may have substantial population-level effects. Moreover, areas containing buried oil may be more susceptible to high energy storm events due to the reduction in uprooting force of foundation species such as R. maritima. PMID:26430971

  10. Effects of Oil-Contaminated Sediments on Submerged Vegetation: An Experimental Assessment of Ruppia maritima.

    PubMed

    Martin, Charles W; Hollis, Lauris O; Turner, R Eugene

    2015-01-01

    Oil spills threaten the productivity of ecosystems through the degradation of coastal flora and the ecosystem services these plants provide. While lab and field investigations have quantified the response of numerous species of emergent vegetation to oil, the effects on submerged vegetation remain uncertain. Here, we discuss the implications of oil exposure for Ruppia maritima, one of the most common species of submerged vegetation found in the region affected by the recent Deepwater Horizon oil spill. We grew R. maritima in a range of manipulated sediment oil concentrations: 0, 0.26, 0.53, and 1.05 mL oil /L tank volume, and tracked changes in growth (wet weight and shoot density/length), reproductive activity (inflorescence and seed production), root characteristics (mass, length, diameter, and area), and uprooting force of plants. While no statistical differences were detected in growth, plants exhibited significant changes to reproductive output, root morphology, and uprooting force. We found significant reductions in inflorescences and fruiting bodies at higher oil concentrations. In addition, the roots growing in the high oil were shorter and wider. Plants in medium and high oil required less force to uproot. A second experiment was performed to separate the effects of root morphology and oiled sediment properties and indicated that there were also changes to sediment cohesion that contributed to a reduction in uprooting forces in medium and high oil. Given the importance of sexual reproduction for these plants, oil contamination may have substantial population-level effects. Moreover, areas containing buried oil may be more susceptible to high energy storm events due to the reduction in uprooting force of foundation species such as R. maritima. PMID:26430971

  11. The role of Spartina maritima and Sarcocornia fruticosa on trace metals retention in Ria Formosa, Portugal

    NASA Astrophysics Data System (ADS)

    Moreira da Silva, Manuela; Duarte, Duarte; Isidoro, Jorge; Chícharo, Luís

    2013-04-01

    Over the last years, phytoremediation has become an increasingly recognized pathway for contaminant removal from water and shallow soils. Assessing the phytoremediation potential of wetlands is complex due to variable conditions of hydrology, soil/sediment types, plant species diversity, growing season and water chemistry. Physico-chemical properties of wetlands provide many positive attributes for remediating contaminants. Saltmarsh plants can sequestrate and inherently tolerate high metal concentrations found in saltmarsh sediments. An increasing number of studies have been carried out to understand the role of halophyte vegetation on retention, biovailability and remediation of the pollutants in coastal areas (estuaries and lagoons). It is already known that the accumulation capacity and the pattern of metal distribution in the plant tissues vary among plant species, namely monocotyledonous and dicotyledonous, and with sediment characteristics. During the last decades, there has been a large increase in urbanization and industrialization of the area surrounding Ria Formosa. Due to this reality, anthropogenic contaminants, including trace metals, are transported via untreated sewage and agricultural effluents to several parts of the lagoon. The dominant producers are Spartina maritima (Poales: Poaceae) and Sarcocornia fruticosa (Caryophyllales: Chenopodiaceae), appearing in pure stands respectively in the lower and in the upper saltmarshes. The aim of this work was to survey, comparatively, the role of S. maritima and S. fruticosa on minor and trace element (Ag, Cd, Cu, Cr, Mo, Ni, Pb and Zn), contents and distribution amongst sediment and plant tissues. Both S. maritima and S. fruticosa could fix metals from the surrounding belowground environment and accumulate metals, mainly in roots (also in rhizomes in the case of the former). Metal translocation to aerial parts of the plants was, in general, residual.

  12. Extracts from Alternanthera maritima as natural photosensitizers in photodynamic antimicrobial chemotherapy (PACT).

    PubMed

    Gasparetto, Adriana; Lapinski, Tadia F; Zamuner, Stella R; Khouri, Sonia; Alves, Leandro P; Munin, Egberto; Salvador, Marcos J

    2010-04-01

    This study investigated the effect of photodynamic antimicrobial chemotherapy (PACT) using extracts from Alternanthera maritima on the viability of Candida dubliniensis. Human infections constitute a great health problem. Several antifungal drugs are currently available, but their uses are limited by a number of factors, such as low potency, poor solubility, microbial resistance, and drug toxicity. Therefore, the search for new and more effective antimicrobial agents and the development of alternative therapies, such as PACT, are necessary. Crude hexane and ethanol extracts of A. maritima were produced. The prepared extracts presented absorption at 650-700 nm. For bioassays, 50 microL of culture medium, 50 microL of extract (25 mg/mL) or control, and 5 microL of a suspension of the microorganism to be tested (C. dubliniensis ATCC 778157 or ATCC 777, 10(7)CFU/mL) were placed in a sterile 96-well microtiter plate (well cross section=0.38 cm(2)). The contents of each well were irradiated with a 685-nm diode laser with an output power of 35 mW, which was distributed through the well cross section yielding an energy dosage of 28 J/cm(2). In each assay (n=6), one plate was subjected to irradiation, and one was not. For each active sample, the number of colony-forming units per milliliter (CFU/mL) was obtained, and data were analyzed by the Tukey test. The chemical compositions of the extracts were determined by chromatographic and spectroscopic techniques. The results suggest inhibition of the growth of C. dubliniensis when irradiated with a diode laser in the presence of hexane and ethanol extracts from A. maritima as photosensitizers. Laser irradiation alone or crude extracts at 25mg/mL did not significantly reduce the number of CFU/mL. Steroids, triterpenes, and flavonoids were identified in the analyzed extracts. In conclusion, the photoactivation of crude hexane and ethanol extracts of A. maritima by red laser radiation at 685 nm promoted an antimicrobial effect, showing that these natural products can be used as photosensitizers in PACT. PMID:20172737

  13. The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating.

    PubMed

    Rousseau-Gueutin, M; Bellot, S; Martin, G E; Boutte, J; Chelaifa, H; Lima, O; Michon-Coudouel, S; Naquin, D; Salmon, A; Ainouche, K; Ainouche, M

    2015-12-01

    The history of many plant lineages is complicated by reticulate evolution with cases of hybridization often followed by genome duplication (allopolyploidy). In such a context, the inference of phylogenetic relationships and biogeographic scenarios based on molecular data is easier using haploid markers like chloroplast genome sequences. Hybridization and polyploidization occurred recurrently in the genus Spartina (Poaceae, Chloridoideae), as illustrated by the recent formation of the invasive allododecaploid S. anglica during the 19th century in Europe. Until now, only a few plastid markers were available to explore the history of this genus and their low variability limited the resolution of species relationships. We sequenced the complete chloroplast genome (plastome) of S. maritima, the native European parent of S. anglica, and compared it to the plastomes of other Poaceae. Our analysis revealed the presence of fast-evolving regions of potential taxonomic, phylogeographic and phylogenetic utility at various levels within the Poaceae family. Using secondary calibrations, we show that the tetraploid and hexaploid lineages of Spartina diverged 6-10 my ago, and that the two parents of the invasive allopolyploid S. anglica separated 2-4 my ago via long distance dispersal of the ancestor of S. maritima over the Atlantic Ocean. Finally, we discuss the meaning of divergence times between chloroplast genomes in the context of reticulate evolution. PMID:26182838

  14. Essential Oils from Anthemis maritima Flowers: Infraspecific Variability along the Adriatic Coast (Italy).

    PubMed

    Ciccarelli, Daniela; Giovanelli, Silvia; Pistelli, Luisa

    2016-05-01

    The hydrodistilled essential oils (EOs) from flowers of five Adriatic populations of Anthemis maritima were analyzed by GC-FID and GC/MS. Anthemis maritima is a psammophilous plant living generally on coastal sand dunes but occasionally on sea cliffs and shingle beaches. A total of 163 chemical compounds were identified, accounting for 90.5% of the oils. The main classes of compounds represented in the EOs were monoterpene hydrocarbons, oxygenated monoterpenes, sesquiterpene hydrocarbons, oxygenated sesquiterpenes, and terpene esters.The multivariate chemometric techniques, in particular cluster analysis and principal coordinate analysis, used to classify the samples, highlighted three different chemotypes linked to a geographic origin. One group living in northern Italy was characterized by the highest content of β-pinene, γ-terpinene, and β-caryophyllene, a second chemotype was in central Italy with the highest amount of trans-chrysanthenyl acetate and a third group living in southern Italy with a more heterogeneous volatile profile was characterized by the highest values of cis-chrysanthenyl acetate, trans-chrysanthenyl isobutyrate, cis-carveol propionate, α-zingiberene, and cubenol. Moreover, the comparison of the Adriatic populations with the Tyrrhenian samples, analyzed in a previous research, showed that cubenol (absent in all the Tyrrhenian populations) and (E)-β-farnesene (absent in all the Adriatic samples) play a crucial role in discriminating the Italian populations. PMID:27114258

  15. An auto-inhibited state in the structure of Thermotoga maritima NusG

    PubMed Central

    Drgemller, Johanna; Stegmann, Christian M.; Mandal, Angshuman; Steiner, Thomas; Burmann, Bjrn M.; Gottesman, Max E.; Whrl, Birgitta M.; Rsch, Paul; Wahl, Markus C.; Schweimer, Kristian

    2013-01-01

    Summary NusG is a conserved regulatory protein interacting with RNA polymerase (RNAP) and other proteins to form multi-component complexes that modulate transcription. The crystal structure of Thermotoga maritima NusG (TmNusG) shows a three-domain architecture, comprising well conserved amino-terminal (NTD) and carboxy-terminal (CTD) domains with an additional, species-specific domain inserted into the NTD. NTD and CTD directly contact each other, occluding a surface of the NTD for binding to RNAP and a surface on the CTD interacting either with transcription termination factor Rho or transcription anti-termination factor NusE. NMR spectroscopy confirmed the intra-molecular NTD-CTD interaction up to the optimal growth temperature of Thermotoga maritima. The domain interaction involves a dynamic equilibrium between open and closed states and contributes significantly to the overall fold stability of the protein. Wild type TmNusG and deletion variants could not replace for endogenous Escherichia coli NusG, suggesting that the NTD-CTD interaction of TmNusG represents an auto-inhibited state. PMID:23415559

  16. Biophysical probing of Spartina maritima photo-system II changes during prolonged tidal submersion periods.

    PubMed

    Duarte, B; Santos, D; Marques, J C; Caçador, I

    2014-04-01

    Submergence is one of the major constrains affecting wetland plants, with inevitable impacts on their physiology and productivity. Global warming as a driving force of sea level rise, tend to increase the submersion periods duration. Photosynthesis biophysical probing arise as an important tool to understand the energetics underlying plant feedback to these constrains. As in previous studies with Spartina maritima, there was no inhibition of photosynthetic activity in submerged individuals. Comparing both donor and acceptor sides of the PSII, the first was more severely affected during submersion, driven by the inactivation of the OEC with consequent impairment of the ETC. Although this apparent damage in the PSII donor side, the electron transport per active reaction centre was not substantially affected, indicating that this reduction in the electron flow is accompanied by a proportional increase in the number of active reaction centres. These conditions lead to the accumulation of excessive reducing power, source of damaging ROS, counteracted by efficient energy dissipation processes and anti-oxidant enzymatic defences. This way, S. maritima appears as a well-adapted species with an evident photochemical plasticity towards submersion, allowing it to maintain its photosynthetic activity even during prolonged submersion periods. PMID:24630362

  17. Anthemis maritima L. in different coastal habitats: A tool to explore plant plasticity

    NASA Astrophysics Data System (ADS)

    Spanò, Carmelina; Balestri, Mirko; Bottega, Stefania; Grilli, Isa; Forino, Laura Maria Costantina; Ciccarelli, Daniela

    2013-09-01

    Anthemis maritima, a plant which has the ability to colonise different stressful coastal environments, sand dunes and rocky cliff ecosystems, exhibits a high degree of leaf trait plasticity. The key parameters are the regulation of stomatal density and size, the succulence index and the specific antioxidant response. With the aim to explore plant plasticity, we analysed various morphological and physiological traits of the leaves of A. maritima populations dwelling in three different coastal areas of Italy. The highest values of stomatal density, leaf thickness, and succulence index were found in plants living in a sub-arid climate, on rocky cliffs, with the highest soil pH and salinity. Although this population exhibited the highest concentration of oxygen reactive species (hydrogen peroxide), it also had the lowest value of lipid peroxidation, an indicator of oxidative stress. Ascorbate was the main protective molecule in this population, while phenols appeared to carry out this role in plants living on soils with the lowest salinity and highest annual rainfall.

  18. Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima

    SciTech Connect

    Awwad, Khaldeyah; Desai, Anna; Smith, Clyde; Sommerhalter, Monika

    2013-02-01

    A 2.15 Å resolution crystal structure of TM0159 with bound IMP and enzyme-kinetic data are presented. This noncanonical nucleoside triphosphatase from T. maritima helps to maintain a correct pool of DNA and RNA precursor molecules. The hyperthermophilic bacterium Thermotoga maritima has a noncanonical nucleoside triphosphatase that catalyzes the conversion of inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) into inosine monophosphate (IMP), deoxyinosine monophosphate (IMP) and xanthosine monophosphate (XMP), respectively. The k{sub cat}/K{sub m} values determined at 323 and 353 K fall between 1.31 × 10{sup 4} and 7.80 × 10{sup 4} M{sup −1} s{sup −1}. ITP and dITP are slightly preferred over XTP. Activity towards canonical nucleoside triphosphates (ATP and GTP) was not detected. The enzyme has an absolute requirement for Mg{sup 2+} as a cofactor and has a preference for alkaline conditions. A protein X-ray structure of the enzyme with bound IMP was obtained at 2.15 Å resolution. The active site houses a well conserved network of residues that are critical for substrate recognition and catalysis. The crystal structure shows a tetramer with two possible dimer interfaces. One of these interfaces strongly resembles the dimer interface that is found in the structures of other noncanonical nucleoside pyrophosphatases from human (human ITPase) and archaea (Mj0226 and PhNTPase)

  19. Salinity effects on polyphenol content and antioxidant activities in leaves of the halophyte Cakile maritima.

    PubMed

    Ksouri, Riadh; Megdiche, Wided; Debez, Ahmed; Falleh, Hanen; Grignon, Claude; Abdelly, Chedly

    2007-01-01

    Cakile maritima is a local oilseed halophyte exhibiting potential for secondary metabolite production. In the present study, plant growth, leaf polyphenol content and antioxidant activity were comparatively analyzed in two C. maritima Tunisian accessions (Jerba and Tabarka, respectively sampled from arid and humid bioclimatic stages) under salt constraint. Three-week-old plants were subjected to 0, 100, and 400 mM NaCl for 28 days under glasshouse conditions. A significant variability in salt response was found between both accessions: while Tabarka growth (shoot biomass, leaf expansion) was significantly restricted at 100 and 400 mM NaCl, compared to the control, Jerba growth increased at 100mM before declining at 400 mM NaCl. The better behaviour of Jerba salt-challenged plants, compared to those of Tabarka, may be related to their higher polyphenol content (1.56- and 1.3-fold the control, at 100 and 400 mM NaCl respectively) and antioxidant activity (smaller IC(50) values for both 1,1-diphenyl-2-picrylhydrazyl and superoxide scavenging), associated with lower leaf MDA accumulation (ca. -66% of the control at 100mM NaCl). Taken together, our findings suggest that halophytes may be interesting for production of antioxidant compounds, and that the accession-dependent capacity to induce antioxidative mechanisms in response to salt, may result in a corresponding variability for growth sustainability. PMID:17408958

  20. Chemical composition and biological effects of Artemisia maritima and Artemisia nilagirica essential oils from wild plant of Western Himalaya

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Artemisia species possess pharmacological properties that are used for medical purposes worldwide. In this paper, the essential oils from the aerial parts of A. nilagirica and A. maritima from the western Indian Himalaya region are described. The main compounds analyzed by simultaneous GC/MS and GC/...

  1. Comparison of NaCl-induced programmed cell death in the obligate halophyte Cakile maritima and the glycophyte Arabidospis thaliana.

    PubMed

    Ben Hamed-Laouti, Ibtissem; Arbelet-Bonnin, Delphine; De Bont, Linda; Biligui, Bernadette; Gakière, Bertrand; Abdelly, Chedly; Ben Hamed, Karim; Bouteau, François

    2016-06-01

    Salinity represents one of the most important constraints that adversely affect plants growth and productivity. In this study, we aimed at determining possible differences between salt tolerant and salt sensitive species in early salt stress response. To this purpose, we subjected suspension-cultured cells from the halophyte Cakile maritima and the glycophyte Arabidopsis thaliana, two Brassicaceae, to salt stress and compared their behavior. In both species we could observe a time and dose dependent programmed cell death requiring an active metabolism, a dysfunction of mitochondria and caspase-like activation although C. maritima cells appeared less sensitive than A. thaliana cells. This capacity to mitigate salt stress could be due to a higher ascorbate pool that could allow C. maritima reducing the oxidative stress generated in response to NaCl. It further appeared that a higher number of C. maritima cultured cells when compared to A. thaliana could efficiently manage the Na(+) accumulation into the cytoplasm through non selective cation channels allowing also reducing the ROS generation and the subsequent cell death. PMID:27095399

  2. Structure of a periplasmic glucose-binding protein from Thermotoga maritima

    PubMed Central

    Palani, Kandavelu; Kumaran, Desigan; Burley, Stephen K.; Swaminathan, Subramanyam

    2012-01-01

    ABC transport systems have been characterized in organisms ranging from bacteria to humans. In most bacterial systems, the periplasmic component is the primary determinant of specificity of the transport complex as a whole. Here, the X-ray crystal structure of a periplasmic glucose-binding protein (GBP) from Thermotoga maritima determined at 2.4 Å resolution is reported. The molecule consists of two similar α/β domains connected by a three-stranded hinge region. In the current structure, a ligand (β-d-glucose) is buried between the two domains, which have adopted a closed conformation. Details of the substrate-binding sites revealed features that determine substrate specificity. In toto, ten residues from both domains form eight hydrogen bonds to the bound sugar and four aromatic residues (two from each domain) stabilize the substrate through stacking interactions. PMID:23192024

  3. Structure of a periplasmic glucose-binding protein from Thermotoga maritima.

    PubMed

    Palani, Kandavelu; Kumaran, Desigan; Burley, Stephen K; Swaminathan, Subramanyam

    2012-12-01

    ABC transport systems have been characterized in organisms ranging from bacteria to humans. In most bacterial systems, the periplasmic component is the primary determinant of specificity of the transport complex as a whole. Here, the X-ray crystal structure of a periplasmic glucose-binding protein (GBP) from Thermotoga maritima determined at 2.4 Å resolution is reported. The molecule consists of two similar α/β domains connected by a three-stranded hinge region. In the current structure, a ligand (β-D-glucose) is buried between the two domains, which have adopted a closed conformation. Details of the substrate-binding sites revealed features that determine substrate specificity. In toto, ten residues from both domains form eight hydrogen bonds to the bound sugar and four aromatic residues (two from each domain) stabilize the substrate through stacking interactions. PMID:23192024

  4. Structural characterization of the putative ABC–type 2 transporter from Thermotoga maritima MSB8

    PubMed Central

    Filippova, Ekaterina V.; Tkaczuk, Karolina L.; Chruszcz, Maksymilian; Xu, Xiaohui; Savchenko, Alexei; Edwards, Aled; Minor, Wladek

    2014-01-01

    This study describes the structure of the putative ABC-type 2 transporter TM0543 from Thermotoga maritima MSB8 determined at a resolution of 2.3 Å. In comparative sequence-clustering analysis, TM0543 displays similarity to NatAB-like proteins, which are components of the ABC-type Na+ efflux pump permease. However, the overall structure fold of the predicted nucleotide-binding domain reveals that it is different from any known structure of ABC-type efflux transporters solved to date. The structure of the putative TM0543 domain also exhibits different dimer architecture and topology of its presumed ATP binding pocket, which may indicate that it does not bind nucleotide at all. Structural analysis of calcium ion binding sites found at the interface between TM0543 dimer subunits suggests that protein may be involved in ion-transporting activity. A detailed analysis of the protein sequence and structure is presented and discussed. PMID:25306867

  5. Isolation and characterization of 28 microsatellite loci for a Korean endemic, Lespedeza maritima (Fabaceae)1

    PubMed Central

    Jin, Dong-Pil; Cho, Won-Bum; Choi, In-Su; Choi, Byoung-Hee

    2016-01-01

    Premise of the study: We developed microsatellite primers for Lespedeza maritima (Fabaceae), a Korean endemic shrub, and conducted cross-amplifications for closely related species. Methods and Results: We produced 28 polymorphic microsatellite markers through reference mapping of 300-bp paired-end reads obtained from Illumina MiSeq data. For 47 individual plants from two populations, the total alleles numbered two to 13, and observed and expected heterozygosities ranged from 0.067 to 0.867 and from 0.064 to 0.848, respectively. Most of these markers were well amplified in closely related species. Conclusions: In future research, the microsatellite markers described here will help reveal the taxonomic entity of this species. PMID:26819860

  6. Crystallization and preliminary X-ray diffraction analysis of a lectin from Canavalia maritima seeds

    PubMed Central

    de Almeida Gadelha, Carlos Alberto; Moreno, Frederico Bruno Mendes Batista; Santi-Gadelha, Tatiane; Cajazeiras, João Batista; da Rocha, Bruno Anderson M.; Rustiguel, Joane Kathelen Rodrigues; Freitas, Beatriz Tupinamba; Canduri, Fernanda; Delatorre, Plínio; de Azevedo, Walter Filgueira; Cavada, Benildo S.

    2005-01-01

    A lectin from Canavalia maritima seeds (ConM) was purified and submitted to crystallization experiments. The best crystals were obtained using the vapour-diffusion method at a constant temperature of 293 K and grew in 7 d. A complete structural data set was collected to 2.1 Å resolution using a synchrotron-radiation source. The ConM crystal belongs to the orthorhombic space group P21212, with unit-cell parameters a = 67.15, b = 70.90, c = 97.37 Å. A molecular-replacement search found a solution with a correlation coefficient of 69.2% and an R factor of 42.5%. Crystallographic refinement is under way. PMID:16508099

  7. Purification and characterization of Thermotoga maritima homoserine transsuccinylase indicates it is a transacetylase.

    PubMed

    Goudarzi, Maryam; Born, Timothy L

    2006-10-01

    The methionine biosynthetic pathway found in bacteria is controlled at the first step, acylation of the gamma-hydroxyl of homoserine. This reaction is catalyzed by one of two unique enzymes, homoserine transacetylase or homoserine transsuccinylase, which have no amino acid sequence similarity. We cloned, expressed, and purified homoserine transsuccinylase from the thermophilic bacterium Thermotoga maritima. Substrate specificity experiments demonstrated that acetyl-coenzyme A (CoA) is the preferred acyl donor and is used at least 30-fold more efficiently than succinyl-CoA. Steady-state kinetic experiments confirm that the enzyme utilizes a ping-pong kinetic mechanism in which the acetate group of acetyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine. The maximal velocity, V/K (acetyl-CoA) and V/K (homoserine), all exhibited bell-shaped pH curves with apparent pKs of 6.0-6.9 and 8.2-8.8. The enzyme was inactivated by iodoacetamide in a pH-dependent manner, with an apparent pK of 6.3, suggesting the presence of an active-site cysteine residue which forms an acetyl-enzyme thioester intermediate during catalytic turnover, similar to observations with other transsuccinylases. In addition, the enzyme is highly stable at elevated temperatures, maintaining full activity at 70 degrees C. Taken together, these data suggest that the T. maritima enzyme functions biochemically as a transacetylase, despite having the sequence of a transsuccinylase. PMID:16708165

  8. Proteomic and metabolic profiles of Cakile maritima Scop. Sea Rocket grown in the presence of cadmium.

    PubMed

    Taamalli, Manel; D'Alessandro, Angelo; Marrocco, Cristina; Gevi, Federica; Timperio, Anna Maria; Zolla, Lello

    2015-04-01

    Recent physiological reports have documented how Cakile maritima Scop. Sea Rocket could accumulate high doses of Cd without altering its physiological parameters. In the present study, we performed an integrated proteomics (2DE) and metabolomics (HPLC-MS) investigation to determine the molecular mechanisms underlying cadmium (Cd) tolerance of this halophyte. Peculiar features were observed: (i) up-regulation of thiol compound anabolism, including glutathione and phytochelatin homeostasis, which allows an intracellular chelation of Cd and its compartmentalization into vacuole by a significant up-regulation of vacuolar transporters; (ii) up-regulation of the PPP and Calvin cycle (both at the enzyme and metabolite level), which utterly promoted the maintenance of NADPH/NADP(+) homeostasis, other than the accumulation of triose-phosphates (serving as anabolic intermediates for triacylglycerol biosynthesis) and the glyoxylate precursor phosphoglycolate, to promote photorespiration and consequently CO2 release. An up-regulation of carbonic anhydrase was also observed. This halophyte is also correlated with a highly efficient antioxidant system, especially a high up-regulation of SOD1, resulting more efficient in coping with heavy metals stress than common plants. Interestingly, exposure to high Cd concentrations partly affected photosystem integrity and metabolic activity, through the up-regulation of enzymes from the Calvin cycle and glutathione-ascorbate homeostasis and PAP3 which stabilizes thylakoid membrane structures. In addition, up-regulation of Peptidyl-prolyl isomerase CYP38 increases stability and biogenesis of PSII. Finally, metabolomics results confirmed proteomics and previous physiological evidence, also suggesting that osmoprotectants, betaine and proline, together with plant hormones, methyl jasmonate and salicylic acid, might be involved in mediating responses to Cd-induced stress. Taken together, these peculiar features confirm that Cakile maritima Scop. Sea Rocket seemed to be naturally equipped to withstand even high doses of Cd pollution. PMID:25639878

  9. cDNA cloning of Batis maritima methyl chloride transferase and purification of the enzyme

    PubMed Central

    Ni, Xinhai; Hager, Lowell P.

    1998-01-01

    Methyl chloride transferase catalyzes the synthesis of methyl chloride from S-adenosine-l-methionine and chloride ion. This enzyme has been purified 2,700-fold to homogeneity from Batis maritima, a halophytic plant that grows abundantly in salt marshes. The purification of the enzyme was accomplished by a combination of ammonium sulfate fractionation, column chromatography on Sephadex G100 and adenosine-agarose, and TSK-250 size-exclusion HPLC. The purified enzyme exhibits a single band on SDS/PAGE with a molecular mass of approximately 22.5 kDa. The molecular mass of the purified enzyme was 22,474 Da as determined by matrix-associated laser desorption ionization mass spectrometry. The methylase can function in either a monomeric or oligomeric form. A 32-aa sequence of an internal fragment of the methylase was determined (GLVPGCGGGYDVVAMANPER FMVGLDIXENAL, where X represents unknown residue) by Edman degradation, and a full-length cDNA of the enzyme was obtained by rapid amplification of cDNA ends–PCR amplification of cDNA oligonucleotides. The cDNA gene contains an ORF of 690 bp encoding an enzyme of 230 aa residues having a predicted molecular mass of 25,761 Da. The disparity between the observed and calculated molecular mass suggests that the methylase undergoes posttranslational cleavage, possibly during purification. Sequence homologies suggest that the B. maritima methylase defines a new family of plant methyl transferases. A possible function for this novel methylase in halophytic plants is discussed. PMID:9789006

  10. Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.

    PubMed

    Latif, Haythem; Sahin, Merve; Tarasova, Janna; Tarasova, Yekaterina; Portnoy, Vasiliy A; Nogales, Juan; Zengler, Karsten

    2015-08-15

    Thermotoga maritima is a hyperthermophilic anaerobe that utilizes a vast network of ABC transporters to efficiently metabolize a variety of carbon sources to produce hydrogen. For unknown reasons, this organism does not metabolize glucose as readily as it does glucose di- and polysaccharides. The leading hypothesis implicates the thermolability of glucose at the physiological temperatures at which T. maritima lives. After a 25-day laboratory evolution, phenotypes were observed with growth rates up to 1.4 times higher than and glucose utilization rates exceeding 50% those of the wild type. Genome resequencing revealed mutations in evolved cultures related to glucose-responsive ABC transporters. The native glucose ABC transporter, GluEFK, has more abundant transcripts either as a result of gene duplication-amplification or through mutations to the operator sequence regulating this operon. Conversely, BglEFGKL, a transporter of beta-glucosides, is substantially downregulated due to a nonsense mutation to the solute binding protein or due to a deletion of the upstream promoter. Analysis of the ABC2 uptake porter families for carbohydrate and peptide transport revealed that the solute binding protein, often among the transcripts detected at the highest levels, is predominantly downregulated in the evolved cultures, while the membrane-spanning domain and nucleotide binding components are less varied. Similar trends were observed in evolved strains grown on glycerol, a substrate that is not dependent on ABC transporters. Therefore, improved growth on glucose is achieved through mutations favoring GluEFK expression over BglEFGKL, and in lieu of carbon catabolite repression, the ABC transporter network is modulated to achieve improved growth fitness. PMID:26048924

  11. High phenotypic plasticity of Suaeda maritima observed under hypoxic conditions in relation to its physiological basis

    PubMed Central

    Wetson, Anne M.; Zörb, Christian; John, Elizabeth A.; Flowers, Timothy J.

    2012-01-01

    Background and Aims Phenotypic plasticity, the potential of specific traits of a genotype to respond to different environmental conditions, is an important adaptive mechanism for minimizing potentially adverse effects of environmental fluctuations in space and time. Suaeda maritima shows morphologically different forms on high and low areas of the same salt marsh. Our aims were to examine whether these phenotypic differences occurred as a result of plastic responses to the environment. Soil redox state, indicative of oxygen supply, was examined as a factor causing the observed morphological and physiological differences. Methods Reciprocal transplantation of seedlings was carried out between high and low marsh sites on a salt marsh and in simulated tidal-flow tanks in a glasshouse. Plants from the same seed source were grown in aerated or hypoxic solution, and roots were assayed for lactate dehydrogenase (LDH) and alcohol dehydrogenase, and changes in their proteome. Key Results Transplanted (away) seedlings and those that remained in their home position developed the morphology characteristic of the home or away site. Shoot Na+, Cl− and K+ concentrations were significantly different in plants in the high and low marsh sites, but with no significant difference between home and away plants at each site. High LDH activity in roots of plants grown in aeration and in hypoxia indicated pre-adaptation to fluctuating root aeration and could be a factor in the phenotypic plasticity and growth of S. maritima over the full tidal range of the salt marsh environment. Twenty-six proteins were upregulated under hypoxic conditions. Conclusions Plasticity of morphological traits for growth form at extremes of the soil oxygenation spectrum of the tidal salt marsh did not correlate with the lack of physiological plasticity in the constitutively high LDH found in the roots. PMID:22316572

  12. Molecular cloning and characterization of novel cystatin gene in leaves Cakile maritima halophyte.

    PubMed

    Megdiche, Wided; Passaquet, Chantal; Zourrig, Walid; Zuily Fodil, Yasmine; Abdelly, Chedly

    2009-05-01

    Cakile maritima (Brassicaceae) is a halophyte that thrives on dunes along Mediterranean seashores, with high tolerance to salty and dry environments. We have previously shown that there is great morphological and physiological diversity between ecotypes. We investigated the expression of cysteine protease inhibitor (cystatin) genes in the response to hydric and saline constraints, as cystatins are known to participate in the response to environmental constraints in plants. We isolated, from C. maritime, a new cystatin cDNA (CmC) that encodes a 221 amino acid protein with a calculated molecular mass of 25 kDa. It displays a moderate-to-high amino acid sequence similarity with previously reported phytocystatin genes. The predicted protein is hydrophilic, with only one hydrophobic region, just at its N-terminus, and a calculated isoelectric point of 6.7. Sequence analysis revealed a monocystatin structure with one cystatin-like domain. The predicted protein CmC contains the main conserved motifs characteristic of the plant cystatins, and a putative site of phosphorylation by casein kinase II (TPSD). As some cystatins, it contains a C-terminal extension of 106 amino acid residues, with several conserved cystatin motifs. The expression was constitutive in non-stressed plants, with different levels between the ecotypes, and without apparent relation to the climatic area of origin. Augmented expression was observed under severe salinity except in the ecotype from the arid region. Water deficit also increased CmC expression in two ecotypes, with the highest value observed in the ecotype from the humid region. These results indicate that C. maritima responds to high salinity and water deficit by expressing a cystatin gene that is a known component of defense against abiotic constraints or biotic aggression and survival machinery. PMID:19042057

  13. Genome-Wide Transcriptional Variation within and between Steady States for Continuous Growth of the Hyperthermophile Thermotoga Maritima

    PubMed Central

    Shockley, Keith R.; Scott, Kevin L.; Pysz, Marybeth A.; Conners, Shannon B.; Johnson, Matthew R.; Montero, Clemente I.; Wolfinger, Russell D.; Kelly, Robert M.

    2005-01-01

    Maltose-limited, continuous growth of the hyperthermophile Thermotoga maritima at different temperatures and dilution rates (80°C/0.25 h−1, 80°C/0.17 h−1, and 85°C/0.25 h−1) showed that transcriptome-wide variation in gene expression within mechanical steady states was minimal compared to that between steady states, supporting the efficacy of chemostat-based approaches for functional genomics studies. PMID:16151150

  14. The influence of Spartina maritima on carbon retention capacity in salt marshes from warm-temperate estuaries.

    PubMed

    Sousa, Ana I; Lillebø, Ana I; Pardal, Miguel A; Caçador, Isabel

    2010-01-01

    Salt marshes constitute highly productive systems playing an important role on ecosystem functions. The aim of this study is to compare the role of Spartina maritima salt marshes on carbon cycling. Thus, four salt marshes located in two mesotidal estuarine systems (Tagus and Mondego, two salt marshes per estuary) were studied. The S. maritima above- and belowground biomass, carbon production, decomposition rates (through a litterbag experiment) and carbon content in the sediment were estimated for a one year period in both systems and compared. In Corroios (located at the Tagus estuary) S. maritima salt marsh had the highest belowground production (1008 gC m(-2) y(-1)), slower decomposition rate (k=0.0024 d(-1)), and the highest carbon content in sediments (750 gC m(-2) y(-1)); and thus, the highest carbon retention capacity. The other three salt marshes had comparatively higher aboveground productions, higher decomposition rates and lower carbon retention capacity. Therefore, Corroios had the most important carbon cycling characteristics. As a whole, results show that differences in carbon cycling in salt marshes depend mostly on its own characteristics and maturity, rather than the system itself. The intrinsic characteristics of the salt marshes, namely the physicochemical conditions determined by the maturity of the system, are more important factors affecting the role of warm-temperate mesotidal salt marshes as carbon sinks. PMID:20304438

  15. Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions

    SciTech Connect

    Tomanicek, Stephen J.; Hughes, Ronny C.; Ng, Joseph D.; Coates, Leighton

    2010-10-05

    The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5{prime}-phosphodiester bond at an AP site to generate a free 3{prime}-hydroxyl group and a 5{prime}-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

  16. Characterization of two genes encoding metal tolerance proteins from Beta vulgaris subspecies maritima that confers manganese tolerance in yeast.

    PubMed

    Erbasol, Isil; Bozdag, Gonensin Ozan; Koc, Ahmet; Pedas, Pai; Karakaya, Huseyin Caglar

    2013-10-01

    Manganese (Mn(2+)) is an essential micronutrient in plants. However increased Mn(2+) levels are toxic to plant cells. Metal tolerance proteins (MTPs), member of cation diffusion facilitator protein (CDF) family, have important roles in metal homeostatis in different plant species and catalyse efflux of excess metal ions. In this study, we identified and characterized two MTP genes from Beta vulgaris spp. maritima (B. v. ssp. maritima). Overexpression of these two genes provided Mn tolerance in yeast cells. Sequence analyses displayed BmMTP10 and BmMTP11 as members of the Mn-CDF family. Functional analyses of these proteins indicated that they are specific to Mn(2+) with a role in reducing excess cellular Mn(2+) levels when expressed in yeast. GFP-fusion constructs of both proteins localized to the Golgi apparatus as a punctuated pattern. Finally, Q-RT-PCR results showed that BmMTP10 expression was induced threefold in response to the excess Mn(2+) treatment. On the other hand BmMTP11 expression was not affected in response to excess Mn(2+) levels. Thus, our results suggest that the BmMTP10 and BmMTP11 proteins from B. v. ssp. maritima have non-redundant functions in terms of Mn(2+) detoxification with a similar in planta localization and function as the Arabidopsis Mn-CDF homolog AtMTP11 and this conservation shows the evolutionary importance of these vesicular proteins in heavy metal homeostatis among plant species. PMID:23864431

  17. Endophytic Cultivable Bacteria of the Metal Bioaccumulator Spartina maritima Improve Plant Growth but Not Metal Uptake in Polluted Marshes Soils

    PubMed Central

    Mesa, Jennifer; Mateos-Naranjo, Enrique; Caviedes, Miguel A.; Redondo-Gómez, Susana; Pajuelo, Eloisa; Rodríguez-Llorente, Ignacio D.

    2015-01-01

    Endophytic bacterial population was isolated from Spartina maritima tissues, a heavy metal bioaccumulator cordgrass growing in the estuaries of Tinto, Odiel, and Piedras River (south west Spain), one of the most polluted areas in the world. Strains were identified and ability to tolerate salt and heavy metals along with plant growth promoting and enzymatic properties were analyzed. A high proportion of these bacteria were resistant toward one or several heavy metals and metalloids including As, Cu, and Zn, the most abundant in plant tissues and soil. These strains also exhibited multiple enzymatic properties as amylase, cellulase, chitinase, protease and lipase, as well as plant growth promoting properties, including nitrogen fixation, phosphates solubilization, and production of indole-3-acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The best performing strains (Micrococcus yunnanensis SMJ12, Vibrio sagamiensis SMJ18, and Salinicola peritrichatus SMJ30) were selected and tested as a consortium by inoculating S. maritima wild plantlets in greenhouse conditions along with wild polluted soil. After 30 days, bacterial inoculation improved plant photosynthetic traits and favored intrinsic water use efficiency. However, far from stimulating plant metal uptake, endophytic inoculation lessened metal accumulation in above and belowground tissues. These results suggest that inoculation of S. maritima with indigenous metal-resistant endophytes could mean a useful approach in order to accelerate both adaption and growth of this indigenous cordgrass in polluted estuaries in restorative operations, but may not be suitable for rhizoaccumulation purposes. PMID:26733985

  18. Thermostable uracil-DNA glycosylase from Thermotoga maritima a member of a novel class of DNA repair enzymes.

    PubMed

    Sandigursky, M; Franklin, W A

    1999-05-20

    Uracil-DNA glycosylase (UDG) is a ubiquitous enzyme found in eukaryotes and prokaryotes [1][2][3]. This enzyme removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP [4] [5], and it is the primary activity in the DNA base excision repair pathway. Although UDG activities have been shown to be present in several thermophiles [6][7][8], no sequences have been found that are complementary to the Escherichia coli ung gene, which encodes UDG [9]. Here, we describe a UDG from the thermophile Thermotoga maritima. The T. maritima UDG gene has a low level of homology to the E. coli G-T/U mismatch-specific DNA glycosylase gene (mug). The expressed protein is capable of removing uracil from DNA containing either a U-A or a U-G base pair and is heat-stable up to 75 degrees C. The enzyme is also active on single-stranded DNA containing uracil. Analogous genes appear to be present in several prokaryotic organisms, including thermophilic and mesophilic eubacteria as well as archaebacteria, the human-disease pathogens Treponema palladium and Rickettsia prowazekii, and the extremely radioresistant organism Deinococcus radiodurans. These findings suggest that the T. maritima UDG is a member of a new class of DNA repair enzymes. PMID:10339434

  19. Expression and Characterization of a Novel Nitrilase from Hyperthermophilic Bacterium Thermotoga maritima MSB8.

    PubMed

    Chen, Zhi; Chen, Huayou; Ni, Zhong; Tian, Rui; Zhang, Tianxi; Jia, Jinru; Yang, Shengli

    2015-10-28

    The present study describes the gene cloning, overexpression and characterization of a novel nitrilase from hyperthermophilic bacterium Thermotoga maritima MSB8. The nitrilase gene consisted of 804 base pairs, encoding a protein of 268 amino acid residues with a molecular mass of 30.07 kDa after SDS-PAGE analysis. The optimal temperature and pH of the purified enzyme were 45°C and 7.5, respectively. The enzyme demonstrated good temperature tolerance, with 40% residual activity after 60 min of heat treatment at 75°C. The kinetic constants Vmax and Km of this nitrilase toward 3-cyanopyridine were 3.12 μmol/min/mg and 7.63 mM, respectively. Furthermore, this novel nitrilase exhibited a broad spectrum toward the hydrolysis of the aliphatic nitriles among the tested substrates, and particularly was specific to aliphatic dinitriles like succinonitrile, which was distinguished from most nitrilases ever reported. The catalytic efficiency kcat/Km was 0.44 /mM/s toward succinonitrile. This distinct characteristic might enable this nitrilase to be a potential candidate for industrial applications for biosynthesis of carboxylic acid. PMID:26059515

  20. Germ cells of the centipede Strigamia maritima are specified early in embryonic development

    PubMed Central

    Green, Jack E.; Akam, Michael

    2014-01-01

    We provide the first systematic description of germ cell development with molecular markers in a myriapod, the centipede Strigamia maritima. By examining the expression of Strigamia vasa and nanos orthologues, we find that the primordial germ cells are specified from at least the blastoderm stage. This is a much earlier embryonic stage than previously described for centipedes, or any other member of the Myriapoda. Using these genes as markers, and taking advantage of the developmental synchrony of Strigamia embryos within single clutches, we are able to track the development of the germ cells throughout embryogenesis. We find that the germ cells accumulate at the blastopore; that the cells do not internalize through the hindgut, but rather through the closing blastopore; and that the cells undergo a long-range migration to the embryonic gonad. This is the first evidence for primordial germ cells displaying these behaviours in any myriapod. The myriapods are a phylogenetically important group in the arthropod radiation for which relatively little developmental data is currently available. Our study provides valuable comparative data that complements the growing number of studies in insects, crustaceans and chelicerates, and is important for the correct reconstruction of ancestral states and a fuller understanding of how germ cell development has evolved in different arthropod lineages. PMID:24930702

  1. XX/XY System of Sex Determination in the Geophilomorph Centipede Strigamia maritima.

    PubMed

    Green, Jack E; Dalíková, Martina; Sahara, Ken; Marec, František; Akam, Michael

    2016-01-01

    We show that the geophilomorph centipede Strigamia maritima possesses an XX/XY system of sex chromosomes, with males being the heterogametic sex. This is, to our knowledge, the first report of sex chromosomes in any geophilomorph centipede. Using the recently assembled Strigamia genome sequence, we identified a set of scaffolds differentially represented in male and female DNA sequence. Using quantitative real-time PCR, we confirmed that three candidate X chromosome-derived scaffolds are present at approximately twice the copy number in females as in males. Furthermore, we confirmed that six candidate Y chromosome-derived scaffolds contain male-specific sequences. Finally, using this molecular information, we designed an X chromosome-specific DNA probe and performed fluorescent in situ hybridization against mitotic and meiotic chromosome spreads to identify the Strigamia XY sex-chromosome pair cytologically. We found that the X and Y chromosomes are recognizably different in size during the early pachytene stage of meiosis, and exhibit incomplete and delayed pairing. PMID:26919730

  2. Germ cells of the centipede Strigamia maritima are specified early in embryonic development.

    PubMed

    Green, Jack E; Akam, Michael

    2014-08-15

    We provide the first systematic description of germ cell development with molecular markers in a myriapod, the centipede Strigamia maritima. By examining the expression of Strigamia vasa and nanos orthologues, we find that the primordial germ cells are specified from at least the blastoderm stage. This is a much earlier embryonic stage than previously described for centipedes, or any other member of the Myriapoda. Using these genes as markers, and taking advantage of the developmental synchrony of Strigamia embryos within single clutches, we are able to track the development of the germ cells throughout embryogenesis. We find that the germ cells accumulate at the blastopore; that the cells do not internalize through the hindgut, but rather through the closing blastopore; and that the cells undergo a long-range migration to the embryonic gonad. This is the first evidence for primordial germ cells displaying these behaviours in any myriapod. The myriapods are a phylogenetically important group in the arthropod radiation for which relatively little developmental data is currently available. Our study provides valuable comparative data that complements the growing number of studies in insects, crustaceans and chelicerates, and is important for the correct reconstruction of ancestral states and a fuller understanding of how germ cell development has evolved in different arthropod lineages. PMID:24930702

  3. The centipede Strigamia maritima possesses a large complement of Wnt genes with diverse expression patterns.

    PubMed

    Hayden, Luke; Arthur, Wallace

    2014-05-01

    The genes of the Wnt family play important roles in the development of many animals. In the arthropods, these genes are known to have multiple functions, including roles in posterior development and segmentation. Despite this, secondary loss of Wnt genes is common among the Arthropoda. Unlike many arthropods, Strigamia maritima, a geophilomorph centipede, possesses a large complement of Wnt ligands, with 11 Wnt genes present. In this study, the expression of each of these genes was examined across a range of stages during embryonic development. The expression of Wnt genes in Strigamia displays much variability. Most Wnt genes are expressed in segmental stripes in the trunk; near the proctodeum; and in the head region. However, despite this overall broad similarity, there are many differences between the various Wnt genes in their exact patterns of expression. These data should be considered in the context of different hypotheses regarding the functional relationships between the Wnt genes and the degree of redundancy present in this system. The findings of this study are consistent with one particular model of Wnt activity, the combinatorial model, whereby the combination of Wnt ligands present in a particular region defines its identity. These findings should also be useful in attempts to reconstruct the evolutionary history of Wnt signaling in arthropods. PMID:24754405

  4. XX/XY System of Sex Determination in the Geophilomorph Centipede Strigamia maritima

    PubMed Central

    Green, Jack E.; Dalíková, Martina; Sahara, Ken; Marec, František; Akam, Michael

    2016-01-01

    We show that the geophilomorph centipede Strigamia maritima possesses an XX/XY system of sex chromosomes, with males being the heterogametic sex. This is, to our knowledge, the first report of sex chromosomes in any geophilomorph centipede. Using the recently assembled Strigamia genome sequence, we identified a set of scaffolds differentially represented in male and female DNA sequence. Using quantitative real-time PCR, we confirmed that three candidate X chromosome-derived scaffolds are present at approximately twice the copy number in females as in males. Furthermore, we confirmed that six candidate Y chromosome-derived scaffolds contain male-specific sequences. Finally, using this molecular information, we designed an X chromosome-specific DNA probe and performed fluorescent in situ hybridization against mitotic and meiotic chromosome spreads to identify the Strigamia XY sex-chromosome pair cytologically. We found that the X and Y chromosomes are recognizably different in size during the early pachytene stage of meiosis, and exhibit incomplete and delayed pairing. PMID:26919730

  5. Food and feeding ecology of purple sandpipers Calidris maritima on rocky intertidal habitats (Helgoland, German Bight)

    NASA Astrophysics Data System (ADS)

    Dierschke, Volker

    On the island of Helgoland (German Bight) Purple Sandpipers Calidris maritima feed mainly in the intertidal of piers and rocky shores. The main prey species are Littorina saxatilis and Mytilus edulis, complemented by crustaceans, polychaetes, other molluscs and green algae. Beach habitats are used as alternative feeding sites during storms. Feeding sites seem to be selected according to rates of assimilated energy intake. The most profitable habitat (wrack beds on the high-tide line with kelp-fly larvae, 16.8 W) is used after arrival in October but is not available during winter. Because of high intake rates in rocky habitats (13.1 W on piers, 5.5 W on mussel beds), which allow short daily feeding times, and available alternative feeding sites during storms, Purple Sandpipers do not need to carry fat reserves in winter like other waders wintering in central and Western Europe. This, and the ever accessible food supply of epibenthic macrofauna on rocky shores, may enable Purple Sandpipers to winter further north than other wader species.

  6. Bioconversion of Stemodia maritima diterpenes and derivatives by Cunninghamella echinulata var. elegans and Phanerochaete chrysosporium.

    PubMed

    Lamm, Andrew S; Reynolds, William F; Reese, Paul B

    2006-06-01

    Stemodane and stemarane diterpenes isolated from the plant Stemodia maritima and their dimethylcarbamate derivatives were fed to growing cultures of the fungi Cunninghamella echinulata var. elegans ATCC 8688a and Phanerochaete chrysosporium ATCC 24725. C. echinulata transformed stemodin (1) to its 7alpha-hydroxy- (2), 7beta-hydroxy- (3) and 3beta-hydroxy- (4) analogues. 2alpha-(N,N-Dimethylcarbamoxy)-13-hydroxystemodane (6) gave 2alpha-(N,N-dimethylcarbamoxy)-6alpha,13-dihydroxystemodane (7) and 2alpha-(N,N-dimethylcarbamoxy)-7alpha,13-dihydroxystemodane (8). Stemodinone (9) yielded 14-hydroxy-(10) and 7beta-hydroxy- (11) congeners along with 1, 2 and 3. Stemarin (13) was converted to the hitherto unreported 6alpha,13-dihydroxystemaran-19-oic acid (18). 19-(N,N-Dimethylcarbamoxy)-13-hydroxystemarane (14) yielded 13-hydroxystemaran-19-oic acid (17) along with the two metabolites: 19-(N,N-dimethylcarbamoxy)-2beta,13-dihydroxystemarane (15) and 19-(N,N-dimethylcarbamoxy)-2beta,8,13-trihydroxystemarane (16). P. chrysosporium converted 1 into 3, 4 and 2alpha,11beta,13-trihydroxystemodane (5). The dimethylcarbamate (6) was not transformed by this microorganism. Stemodinone (9) was hydroxylated at C-19 to give 12. Both stemarin (13) and its dimethylcarbamate (14) were recovered unchanged after incubation with Phanerochaete. PMID:16725164

  7. High-resolution structure of RNase P protein from Thermotoga maritima

    PubMed Central

    Kazantsev, Alexei V.; Krivenko, Angelika A.; Harrington, Daniel J.; Carter, Richard J.; Holbrook, Stephen R.; Adams, Paul D.; Pace, Norman R.

    2003-01-01

    The structure of RNase P protein from the hyperthermophilic bacterium Thermotoga maritima was determined at 1.2-Å resolution by using x-ray crystallography. This protein structure is from an ancestral-type RNase P and bears remarkable similarity to the recently determined structures of RNase P proteins from bacteria that have the distinct, Bacillus type of RNase P. These two types of protein span the extent of bacterial RNase P diversity, so the results generalize the structure of the bacterial RNase P protein. The broad phylogenetic conservation of structure and distribution of potential RNA-binding elements in the RNase P proteins indicate that all of these homologous proteins bind to their cognate RNAs primarily by interaction with the phylogenetically conserved core of the RNA. The protein is found to dimerize through an extensive, well-ordered interface. This dimerization may reflect a mechanism of thermal stability of the protein before assembly with the RNA moiety of the holoenzyme. PMID:12799461

  8. Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling

    PubMed Central

    Rudolph, Markus G.; del Toro Duany, Yoandris; Jungblut, Stefan P.; Ganguly, Agneyo; Klostermeier, Dagmar

    2013-01-01

    Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presented. PMID:23209025

  9. A simple assay for determining activities of phosphopentomutase from a hyperthermophilic bacterium Thermotoga maritima.

    PubMed

    Moustafa, Hanan M A; Zaghloul, Taha I; Zhang, Y-H Percival

    2016-05-15

    Phosphopentomutase (PPM) catalyzes the interconversion of α-d-(deoxy)-ribose 1-phosphate and α-d-(deoxy)-ribose 5-phosphate. We developed a coupled or uncoupled enzymatic assay with an enzyme nucleoside phosphorylase for determining PPM activities on d-ribose 5-phosphate at a broad temperature range from 30 to 90 °C. This assay not only is simple and highly sensitive but also does not require any costly special instrument. Via this technology, an open reading frame TM0167 from a thermophilic bacterium Thermotoga maritima putatively encoding PPM was cloned. The recombinant PPM was overexpressed in Escherichia coli Rosetta. This enzyme has the highest activity at 90 °C. MnCl2 (0.1 mM) and 50 μM α-d-glucose 1,6-bisphosphate are cofactors. The kinetic parameters of Km and kcat are 1.2 mM and 185 s(-1) at 90 °C, respectively. The enzyme has a half-life time of up to 156 min at 90 °C. This enzyme is the most active and thermostable PPM reported to date. PMID:26924489

  10. Urgineaglyceride A: a new monoacylglycerol from the Egyptian Drimia maritima bulbs.

    PubMed

    Mohamed, Gamal A; Ibrahim, Sabrin R M; Shaala, Lamiaa A; Alshali, Khalid Z; Youssef, Diaa T A

    2014-01-01

    One new compound, (2S)-1-O-(Z)-tetracos-6-enoate glycerol (1) named urgineaglyceride A, along with six known compounds, 3,5,7,3',5'-pentahydroxydihydroflavonol (2), stigmasterol (3), (25S)-5β-furostane-3β-22α-26-triol (4), scillaridin A (5), (2S)-(+)-2-hydroxynaringenin-4'-O-β-D-glucopyranoside (6) and quercetin-3'-O-β-D-glucopyranoside (7), were isolated from the EtOAc fraction of Drimia maritima (L.) Stearn bulbs. Their structures were secured based on their IR, UV, 1D and 2D NMR data, in addition to HR-MS data and comparison with the literature data. The isolated compounds were evaluated for their in vitro growth inhibitory activity against A549 non-small cell lung cancer (NSCLC), U373 glioblastoma (GBM) and PC-3 prostate cancer cell lines. Compounds 2 and 3 displayed variable activities against the tested cancer cell lines. Compound 2 was a selective inhibitor of the NSCLC cell line with an IC₅₀ of 2.3 μM, whereas 3 was selective against GBM with IC₅₀ of 0.5 μM and against PC-3 with 2.0 μM. PMID:24938488

  11. Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima.

    PubMed

    Shin, Dong Hae; Roberts, Anne; Jancarik, Jaru; Yokota, Hisao; Kim, Rosalind; Wemmer, David E; Kim, Sung-Hou

    2003-07-01

    We have determined the crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima, TM0651 (gi 4981173), at 2.2 A resolution by selenomethionine single-wavelength anomalous diffraction (SAD) techniques. TM0651 is a member of the haloacid dehalogenase (HAD) superfamily, with sequence homology to trehalose-6-phosphate phosphatase and sucrose-6(F)-phosphate phosphohydrolase. Selenomethionine labeled TM0651 crystallized in space group C2 with three monomers per asymmetric unit. Each monomer has approximate dimensions of 65 x 40 x 35 A(3), and contains two domains: a domain of known hydrolase fold characteristic of the HAD family, and a domain with a new tertiary fold consisting of a six-stranded beta-sheet surrounded by four alpha-helices. There is one disulfide bond between residues Cys35 and Cys265 in each monomer. One magnesium ion and one sulfate ion are bound in the active site. The superposition of active site residues with other HAD family members indicates that TM0651 is very likely a phosphatase that acts through the formation of a phosphoaspartate intermediate, which is supported by both NMR titration data and a biochemical assay. Structural and functional database searches and the presence of many aromatic residues in the interface of the two domains suggest the substrate of TM0651 is a carbohydrate molecule. From the crystal structure and NMR data, the protein likely undergoes a conformational change upon substrate binding. PMID:12824492

  12. Flow cytometry and GISH reveal mixed ploidy populations and Spartina nonaploids with genomes of S. alterniflora and S. maritima origin

    PubMed Central

    Renny-Byfield, Simon; Ainouche, Malika; Leitch, Ilia J.; Lim, K. Yoong; Le Comber, Steven C.; Leitch, Andrew R.

    2010-01-01

    Background The genus Spartina exhibits extensive hybridization and includes classic examples of recent speciation by allopolyploidy. In the UK there are two hexaploid species, S. maritima and S. alterniflora, as well as the homoploid hybrid S. townsendii (2n = 60) and a derived allododecaploid S. anglica (2n = 120, 122, 124); the latter two are considered to have originated in Hythe, southern England at the end of the 19th century. Methods Genomic in situ hybridization (GISH) and flow cytometry were used to characterize the genomic composition and distribution of these species and their ploidy levels at Eling Marchwood and Hythe, both near Southampton, southern England. Key Results GISH identified approx. 60 chromosomes each of S. maritima and S. alterniflora origin in S. anglica and 62 chromosomes from S. alterniflora and 30 chromosomes from S. maritima in a nonaploid individual from Eling Marchwood, UK. GISH and flow cytometry also revealed that most (94 %) individuals examined at Hythe were hexaploid (the remaining two individuals (6 %) were dodedcaploid; n = 34), whereas hexaploid (approx. 36 % of plants), nonaploid (approx. 27 %) and dodecaploid (approx. 36 %) individuals were found at Eling Marchwood (n = 22). Conclusions Nonaploid individuals indicate the potential for introgression between hexaploid and dodecaploid species, complicating the picture of polyploid-induced speciation within the genus. Despite the aggressive ecological habit of S. anglica, it has not out-competed S. townsendii at Hythe (homoploid hybrids at a frequency of 94 %, n = 34), despite >100 years of coexistence. The success of GISH opens up the potential for future studies of polyploid-induced genome restructuring in this genus. PMID:20150197

  13. Phosphoglycerate kinase and triosephosphate isomerase from the hyperthermophilic bacterium Thermotoga maritima form a covalent bifunctional enzyme complex.

    PubMed Central

    Schurig, H; Beaucamp, N; Ostendorp, R; Jaenicke, R; Adler, E; Knowles, J R

    1995-01-01

    Phosphoglycerate kinase (PGK) from the hyperthermophilic bacterium Thermotoga maritima has been purified to homogeneity. A second larger enzyme with PGK activity and identical N-terminal sequence was also found. Surprisingly, this enzyme displayed triosephosphate isomerase (TIM) activity. No other TIM is detectable in T. maritima crude extracts. As shown by ultracentrifugal analysis, PGK is a 43 kDa monomer, whereas the bifunctional PGK-TIM fusion protein is a homotetramer of 240-285 kDa. SDS-PAGE indicated a subunit size of 70 kDa for the fusion protein. Both enzymes show high thermostability. Measurements of the catalytic properties revealed no extraordinary results. pH optima, Km values and activation energies were found to be in the range observed for other PGKs and TIMs investigated so far. The corresponding pgk and tpi genes are part of the apparent gap operon of T. maritima. This gene segment contains two overlapping reading frames, where the 43 kDa PGK is encoded by the upstream open reading frame, the pgk gene. On the other hand, the 70 kDa PGK-TIM fusion protein is encoded jointly by the pgk gene and the overlapping downstream open reading frame of the tpi gene. A programmed frameshift may be responsible for this fusion. A comparison of the amino acid sequence of both the PGK and the TIM parts of the fusion protein with those of known PGKs and TIMs reveals high similarity to the corresponding enzymes from different procaryotic and eucaryotic organisms. Images PMID:7859734

  14. Development and cross-species amplification of microsatellite loci for Puccinellia maritima, an important engineer saltmarsh species.

    PubMed

    Rouger, R; Vallejo-Marin, M; Jump, A S

    2014-01-01

    The grass Puccinellia maritima is an important saltmarsh ecosystem engineer exhibiting wide morphological variation, which is partially genetically determined. Nevertheless, nothing is known about its population genetics or how neutral genetic variation is distributed throughout its geographical range. Here, we describe 12 polymorphic microsatellites pooled into two multiplexes for this octoploid species. Assessment of 24 samples from three populations revealed 4 to 29 alleles per locus, with variation in allele presence and abundance between populations. The transferability of these markers is reported based on their cross-amplification in six other Puccinellia species of different ploidy levels. PMID:24841787

  15. Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima: Structural Insights into Complex Formation

    SciTech Connect

    Morar, Mariya; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E.

    2008-10-02

    In the fourth step of the purine biosynthetic pathway, formyl glycinamide ribonucleotide (FGAR) amidotransferase, also known as PurL, catalyzes the conversion of FGAR, ATP, and glutamine to formyl glycinamidine ribonucleotide (FGAM), ADP, P{sub i}, and glutamate. Two forms of PurL have been characterized, large and small. Large PurL, present in most Gram-negative bacteria and eukaryotes, consists of a single polypeptide chain and contains three major domains: the N-terminal domain, the FGAM synthetase domain, and the glutaminase domain, with a putative ammonia channel located between the active sites of the latter two. Small PurL, present in Gram-positive bacteria and archaea, is structurally homologous to the FGAM synthetase domain of large PurL, and forms a complex with two additional gene products, PurQ and PurS. The structure of the PurS dimer is homologous with the N-terminal domain of large PurL, while PurQ, whose structure has not been reported, contains the glutaminase activity. In Bacillus subtilis, the formation of the PurLQS complex is dependent on glutamine and ADP and has been demonstrated by size-exclusion chromatography. In this work, a structure of the PurLQS complex from Thermotoga maritima is described revealing a 2:1:1 stoichiometry of PurS:Q:L, respectively. The conformational changes observed in TmPurL upon complex formation elucidate the mechanism of metabolite-mediated recruitment of PurQ and PurS. The flexibility of the PurS dimer is proposed to play a role in the activation of the complex and the formation of the ammonia channel. A potential path for the ammonia channel is identified.

  16. Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima

    PubMed Central

    Levisson, Mark; Han, Gye Won; Deller, Marc C.; Xu, Qingping; Biely, Peter; Hendriks, Sjon; Ten Eyck, Lynn F.; Flensburg, Claus; Roversi, Pietro; Miller, Mitchell D.; McMullan, Daniel; von Delft, Frank; Kreusch, Andreas; Deacon, Ashley M.; van der Oost, John; Lesley, Scott A.; Elsliger, Marc-André; Kengen, Servé W. M.; Wilson, Ian A.

    2012-01-01

    TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-β-D-xylopyranoside monoacetates as substrates in a β-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3 and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 Å and 2.5 Å resolution, respectively, revealing a classic α/β-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride (PMSF) and paraoxon were determined to 2.4 Å and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which this Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction. PMID:22411095

  17. Complexed Structures of Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima Describe a Novel ATP Binding Protein Superfamily

    SciTech Connect

    Morar, Mariya; Anand, Ruchi; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E.

    2008-09-11

    Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the ATP-dependent synthesis of formylglycinamidine ribonucleotide (FGAM) from formylglycinamide ribonucleotide (FGAR) and glutamine in the fourth step of the purine biosynthetic pathway. FGAR-AT is encoded by the purL gene. Two types of PurL have been detected. The first type, found in eukaryotes and Gram-negative bacteria, consists of a single 140 kDa polypeptide chain and is designated large PurL (lgPurL). The second type, small PurL (smPurL), is found in archaea and Gram-positive bacteria and consists of an 80 kDa polypeptide chain. SmPurL requires two additional gene products, PurQ and PurS, for activity. PurL is a member of a protein superfamily that contains a novel ATP-binding domain. Structures of several members of this superfamily are available in the unliganded form. We determined five different structures of FGAR-AT from Thermotoga maritima in the presence of substrates, a substrate analogue, and a product. These complexes have allowed a detailed description of the novel ATP-binding motif. The availability of a ternary complex enabled mapping of the active site, thus identifying potential residues involved in catalysis. The complexes show a conformational change in the active site compared to the unliganded structure. Surprising discoveries, an ATP molecule in an auxiliary site of the protein and the conformational changes associated with its binding, provoke speculation about the regulatory role of the auxiliary site in formation of the PurLSQ complex as well as the evolutionary relationship of PurLs from different organisms.

  18. Modulation of superoxide dismutase (SOD) isozymes by organ development and high long-term salinity in the halophyte Cakile maritima.

    PubMed

    Houmani, Hayet; Rodríguez-Ruiz, Marta; Palma, José M; Abdelly, Chedly; Corpas, Francisco J

    2016-05-01

    Superoxide dismutase (SOD) activity catalyzes the disproportionation of superoxide radicals into hydrogen peroxide and oxygen. This enzyme is considered to be a first line of defense for controlling the production of reactive oxygen species (ROS). In this study, the number and type of SOD isozymes were identified in the principal organs (roots, stems, leaves, flowers, and seeds) of Cakile maritima. We also analyzed the way in which the activity of these SOD isozymes is modulated during development and under high long-term salinity (400 mM NaCl) stress conditions. The data indicate that this plant contains a total of ten SOD isozymes: two Mn-SODs, one Fe-SOD, and seven CuZn-SODs, with the Fe-SOD being the most prominent isozyme in the different organs analyzed. Moreover, the modulation of SOD isozymes, particularly CuZn-SODs, was only detected during development and under severe salinity stress conditions. These data suggest that, in C. maritima, the occurrence of these CuZn-SODs in roots and leaves plays an adaptive role since this CuZn-SOD isozyme might replace the diminished Fe-SOD activity under salinity stress to overcome this adverse environmental condition. PMID:26159565

  19. Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima.

    PubMed Central

    Kluskens, Leon D; van Alebeek, Gert-Jan W M; Voragen, Alphons G J; de Vos, Willem M; van der Oost, John

    2003-01-01

    The ability of the hyperthermophilic bacterium Thermotoga maritima to grow on pectin as a sole carbon source coincides with the secretion of a pectate lyase A (PelA) in the extracellular medium. The pel A gene of T. maritima was functionally expressed in Escherichia coli as the first heterologously produced thermophilic pectinase, and purified to homogeneity. Gel filtration indicated that the native form of PelA is tetrameric. Highest activity (422 units/mg, with a K(m) of 0.06 mM) was demonstrated on polygalacturonic acid (PGA), whereas pectins with an increasing degree of methylation were degraded at a decreasing rate. In the tradition of pectate lyases, PelA demonstrated full dependency on Ca(2+) for stability and activity. The enzyme is highly thermoactive and thermostable, operating optimally at 90 degrees C and pH 9.0, with a half-life for thermal inactivation of almost 2 h at 95 degrees C, and an apparent melting temperature of 102.5 degrees C. Detailed characterization of the product formation with PGA indicated that PelA has a unique eliminative exo-cleavage pattern liberating unsaturated trigalacturonate as the major product, in contrast with unsaturated digalacturonate for other exopectate lyases known. The unique exo-acting mode of action was supported by progression profiles of PelA on oligogalacturonides (degree of polymerization, 3-8) and the examination of the bond cleavage frequencies. PMID:12443532

  20. Molecular and biochemical characterization of bifunctional pyruvate decarboxylases and pyruvate ferredoxin oxidoreductases from Thermotoga maritima and Thermotoga hypogea.

    PubMed

    Eram, Mohammad S; Wong, Alton; Oduaran, Erica; Ma, Kesen

    2015-12-01

    Hyperthermophilic bacteria Thermotoga maritima and Thermotoga hypogea produce ethanol as a metabolic end product, which is resulted from acetaldehyde reduction catalysed by an alcohol dehydrogenase (ADH). However, the enzyme that is involved in the production of acetaldehyde from pyruvate is not well characterized. An oxygen sensitive and coenzyme A-dependent pyruvate decarboxylase (PDC) activity was found to be present in cell free extracts of T. maritima and T. hypogea. Both enzymes were purified and found to have pyruvate ferredoxin oxidoreductase (POR) activity, indicating their bifunctionality. Both PDC and POR activities from each of the purified enzymes were characterized in regards to their optimal assay conditions including pH dependency, oxygen sensitivity, thermal stability, temperature dependency and kinetic parameters. The close relatedness of the PORs that was shown by sequence analysis could be an indication of the presence of such bifunctionality in other hyperthermophilic bacteria. This is the first report of a bifunctional PDC/POR enzyme in hyperthermophilic bacteria. The PDC and the previously reported ADHs are most likely the key enzymes catalysing the production of ethanol from pyruvate in bacterial hyperthermophiles. PMID:26032540

  1. Expansion of genetic diversity in randomly mating founder populations of Alternaria brassicicola infecting Cakile maritima in Australia.

    PubMed

    Linde, C C; Liles, J A; Thrall, P H

    2010-03-01

    Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction between Cakile maritima and the fungal pathogen Alternaria brassicicola to explore genetic expectations associated with such situations. The host, C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. Eleven A. brassicicola populations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggest A. brassicicola reproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested that A. brassicicola has been introduced into Australia multiple times, potentially increasing the diversity and size of any A. brassicola populations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions. PMID:20097819

  2. Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia▿

    PubMed Central

    Linde, C. C.; Liles, J. A.; Thrall, P. H.

    2010-01-01

    Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction between Cakile maritima and the fungal pathogen Alternaria brassicicola to explore genetic expectations associated with such situations. The host, C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. Eleven A. brassicicola populations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggest A. brassicicola reproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested that A. brassicicola has been introduced into Australia multiple times, potentially increasing the diversity and size of any A. brassicola populations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions. PMID:20097819

  3. Comparison of parasitic hymenoptera captured in malaise traps baited with two flowering plants Lobularia maritima (Brassicales:Brassicaceae) and Spermacoce verticillate (Gentianales:Rubiaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many adult hymenopterous parasitoids feed on floral nectar, and occasionally pollen. However, flowers differ in both accessibility and attractiveness to these insects. Malaise traps, a type of “passive/interception” trap, were baited with potted flowering plants, Lobularia maritima L. (Brassicaceae)...

  4. Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia

    PubMed Central

    Ward, Lewis M.; Pace, Laura A.; Fischer, Woodward W.

    2015-01-01

    We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced member of class Ardenticatenia of the phylum Chloroflexi. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase. PMID:26586887

  5. Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the Chloroflexi Class Ardenticatenia.

    PubMed

    Hemp, James; Ward, Lewis M; Pace, Laura A; Fischer, Woodward W

    2015-01-01

    We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced member of class Ardenticatenia of the phylum Chloroflexi. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase. PMID:26586887

  6. Redox-Active Profile Characterization of Remirea maritima Extracts and Its Cytotoxic Effect in Mouse Fibroblasts (L929) and Melanoma (B16F10) Cells.

    PubMed

    Dória, Grace Anne A; Santos, Anderson R; Bittencourt, Leonardo S; Bortolin, Rafael C; Menezes, Paula P; Vasconcelos, Bruno S; Souza, Rebeca O; Fonseca, Maria José V; Santos, Alan Diego C; Saravanan, Shanmugam; Silva, Francilene A; Gelain, Daniel P; Moreira, José Cláudio F; Prata, Ana Paula N; Quintans-Júnior, Lucindo J; Araújo, Adriano A S

    2015-01-01

    Remirea maritima is a tropical plant with a reticulated root system belonging to the family Cyperaceae, also known to have biologically active secondary metabolites. However, very few data on R. maritima's biological actions are available and there are no reports regarding the redox-active profile of this plant. In this study, we examined the total phenolic content of Remirea maritima hydroalcoholic (RMHA) extracts, redox properties against different reactive species generated in vitro and their cytotoxic effect against fibroblasts (L929) and melanoma (B16F10) cells. Total reactive antioxidant potential index (TRAP) and total antioxidant reactivity (TAR) results revealed that RMHA at all concentrations tested showed significant antioxidant capacity. RMHA was also effective against hydroxyl radical formation, reduction of Fe3+ to Fe2+ and in scavenging nitric oxide (NO) radicals. In vitro, the level of lipid peroxidation was reduced by RMHA extract and the data showed significant oxidative damage protection. The RMHA cytotoxicity was evaluated by a neutral red assay in fibroblast (L929) and melanome (B16F10) cells. The obtained results showed that the RMHA (40 and 80 µg/mL, respectively) reduced 70% of the viable cells. In conclusion, this study represents the first report regarding the antioxidant and anti-proliferative potential of R. maritima against B16F10 melanoma cells. PMID:26121396

  7. Putative free radical-scavenging activity of an extract of Cineraria maritima in preventing selenite-induced cataractogenesis in Wistar rat pups

    PubMed Central

    Anitha, Thirugnanasambandhar Sivasubramanian; Muralidharan, Arumugam Ramachandran; Annadurai, Thangaraj; Jesudasan, Christdas Arul Nelson; Thomas, Philip Aloysius

    2013-01-01

    Purpose To investigate the possible free radical-scavenging activity of an extract of Cineraria maritima on selenite-induced cataractous lenses in Wistar rat pups. Methods In the present study, Wistar rat pups were divided into three experimental groups. On P10, Group I (control) rat pups received an intraperitoneal injection of 0.89% saline. Rats in groups II (selenite-challenged, untreated) and III (selenite-challenged, C. maritima treated) received a subcutaneous injection of sodium selenite (19 μmol/kg bodyweight); Group III rat pups also received an intraperitoneal injection of the extract of C. maritima (350 mg/kg bodyweight) once daily P9–14. Both eyes of each pup were examined from P16 until P30. Cytochemical localization of nitroblue tetrazolium salts and generation of superoxide, hydroxyl, and nitric oxide levels were measured. The expression of the inducible nitric oxide synthase gene was evaluated with reverse transcription-PCR. Immunoblot analysis was also performed to confirm the differential expression of the inducible nitric oxide synthase protein. Results Subcutaneous injection of sodium selenite led to severe oxidative damage in the lenticular tissues, shown by increased formation of formazan crystals, elevated generation of superoxide, hydroxyl, and nitric oxide radicals, and elevated inducible nitric oxide synthase gene and protein expression that possibly contributed to the opacification of the lens and thus cataract formation. When rat pups were treated with intraperitoneal administration of the extract of C. maritima, the generation of free radicals as well as the messenger ribonucleic acid and protein expression of inducible nitric oxide synthase were maintained at near normal levels. Conclusions The data generated by this study suggest that an ethanolic extract of C. maritima possibly prevents cataractogenesis in a rat model by minimizing free radical generation. PMID:24357923

  8. Thermotoga maritima IscU. Structural characterization and dynamics of a new class of metallochaperone.

    PubMed

    Bertini, Ivano; Cowan, J A; Del Bianco, Cristina; Luchinat, Claudio; Mansy, Sheref S

    2003-08-22

    Members of the IscU family of proteins are among the most conserved of all protein groups, extending across all three kingdoms of life. IscU serves as a scaffold for the assembly of intermediate iron-sulfur cluster centers and further mediates delivery to apo protein targets. Several proteins that mediate delivery of single metal ions to apo targets (termed metallochaperones) have recently been characterized structurally. Each displays a ferredoxin-like betaalphabetabetaalphabeta motif as a structural core. Assembly and delivery of a polynuclear iron-sulfur cluster is, however, a more complex pathway and presumably would demand a distinctive protein mediator. Here, we demonstrate Thermotoga maritima IscU (Tm IscU) to display unique structural and motional characteristics that distinguish it from other members of this class of proteins. In particular, IscU adopts a mobile, physiologically relevant, molten globule-like state that is vastly different from the previously identified ferredoxin-like fold that has thus far been characterized for other metallochaperones. The secondary structural content of Tm IscU is consistent with previous circular dichroism measurements on apo and holo protein, consisting of six alpha-helices and three beta-strands, the latter forming an anti-parallel beta-sheet. Extensive dynamics studies are consistent with a protein that has reasonably well defined secondary structural elements, but with a tertiary structure that is fluxional among widely different conformational arrangements. Analogous conformational flexibility does not exist in other structurally characterized metallochaperones; however, such a dynamic molecule may account for the lack of long-range NOEs, and allow both for the flexibility that is necessary for the multiple roles of Fe-S cluster assembly, and recognition and delivery of that cluster to a target protein. Additionally, the fluxionality of IscU is unique in that the protein appears to be more compact (based on 1H/2H exchange, R1, R2, and NOE data) but yet more fluid (lack of long-range NOEs) than typical molten globule proteins. PMID:12909018

  9. X-ray crystal structure of CutA from thermotoga maritima at 1.4 {Angstrom} resolution.

    SciTech Connect

    Savchenko, A.; Skarina, T.; Evdokimova, E.; Watson, J. D.; Laskowski, R.; Arrowsmith, C. H.; Edwards, A. M.; Joachimiak, A.; Zhang, R.; Univ. Health Network; Univ. of Toronto; Birkbeck Coll.

    2004-01-01

    The structure of the CutA protein from Thermotoga maritima (tmCutA) was determined at 1.4 {angstrom} resolution using the Se-Met multiwavelength anomalous diffraction (MAD) technique. This protein (TIGR annotation - TM1056, DNA bases 1,069,580--1,069,885) is conserved in numerous bacteria, archaea and eucarya, including plants and mammals (COG1324). The CutA Escherichia coli homolog - CutAl (35% ID) is involved in divalent cation homeostasis, while the mammalian homolog - mCutA (40% ID) was found to be associated with cell surface acetylcholinesterase. However, the biological function of the CutA proteins is yet to be determined.

  10. Effect of dimerization on the stability and catalytic activity of dihydrofolate reductase from the hyperthermophile Thermotoga maritima.

    PubMed

    Loveridge, E Joel; Rodriguez, Robert J; Swanwick, Richard S; Allemann, Rudolf K

    2009-06-30

    In contrast to all other chromosomally encoded dihydrofolate reductases characterized so far, dihydrofolate reductase (DHFR) from the hyperthermophile Thermotoga maritima forms a highly stable dimer. The dimer interface involves residues whose mobility is important for catalysis in monomeric DHFRs. Here, we report the generation of a variant of DHFR from T. maritima, TmDHFR-V11D, in which a single amino acid replacement was sufficient to favor the monomeric form of the enzyme in the presence of the nondenaturing zwitterionic detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate. The free energy of stabilization of monomeric TmDHFR-V11D was 15 kJ mol(-1) lower than that of the wild-type dimer, while the melting temperature of monomeric TmDHFR-V11D was comparable to that of monomeric DHFR from the thermophile Bacillus stearothermophilus, supporting the hypothesis that oligomerization is required to achieve the thermal stabilities necessary for activity at temperatures optimal for growth of hyperthermophiles. Both the steady-state turnover numbers and rates of hydride transfer were reduced in TmDHFR-V11D. However, a similar reduction of the rate constants was observed in a different variant, TmDHFR-V126E, which remained as a dimer under all experimental conditions used here. Monomeric TmDHFR-V11D had a similar rate of hydride transfer to the dimeric form, but a reduced steady-state turnover rate. Intersubunit motions therefore appear to be less important than correlated motions within individual subunits for TmDHFR-catalyzed hydride transfer, but are critical to the overall progression of the catalytic cycle. Hence, the reduced catalytic activity of TmDHFR relative to the monomeric Escherichia coli enzyme is not caused by rigidity resulting from dimerization, but is a subtle consequence of the sequence and structure of its subunits, which appear to have evolved to allow thermostability at the expense of catalysis. PMID:19453185

  11. Drought and cadmium may be as effective as salinity in conferring subsequent salt stress tolerance in Cakile maritima.

    PubMed

    Ellouzi, Hasna; Ben Hamed, Karim; Asensi-Fabado, Maria Amparo; Müller, Maren; Abdelly, Chedly; Munné-Bosch, Sergi

    2013-05-01

    Plants are often exposed to a combination of stresses, which can occur simultaneously or at different times throughout their life. In this study, the effects of salinity, drought and cadmium pre-treatments were evaluated on the subsequent response of Cakile maritima, a halophytic species, to various levels of salinity (from 100 to 800 mM NaCl) after a recovery time of 2 weeks. Studies were performed in two sets of experiments in a glasshouse under short and long photoperiod (November and July, respectively). In both experiments and in contrast to control plants (not exposed to any previous stress), plants previously exposed to drought, salt or cadmium stress showed lower levels of hydrogen peroxide and malondialdehyde, an indicator of lipid peroxidation, upon salt treatment, particularly at high NaCl concentrations. Oxidative stress alleviation was not only observed at 800 mM NaCl under short photoperiod, but also at 600 and 800 mM NaCl under long photoperiod in terms of reduced salt-induced increases in hydrogen peroxide and malondialdehyde levels in plants previously exposed to drought, salt or cadmium stress. Previous exposure of plants to all stresses additionally caused decreased levels of jasmonic acid, which might be associated with a lower oxidative stress, differences being observed again at 800 mM NaCl only under short photoperiod and at 600 and 800 mM NaCl under long photoperiod. In conclusion, a relatively long-term stress memory was found in C. maritima pre-exposed to salinity, drought or cadmium, which resulted in a lower oxidative stress when subsequently exposed to salinity. The positive effects of drought and cadmium were of similar magnitude to those provided by salt pre-exposure, which indicated an effective cross-tolerance response in this species. PMID:23381736

  12. Phenological development stages variation versus mercury tolerance, accumulation, and allocation in salt marsh macrophytes Triglochin maritima and Scirpus maritimus prevalent in Ria de Aveiro coastal lagoon (Portugal).

    PubMed

    Anjum, Naser A; Ahmad, Iqbal; Válega, Mónica; Figueira, Etelvina; Duarte, Armando C; Pereira, Eduarda

    2013-06-01

    Efficient and sustainable management of rapidly mounting environmental issues has been the focus of current intensive research. The present study aimed to investigate the impact of plant phenological development stage variation on mercury (Hg) tolerance, accumulation, and allocation in two salt marsh macrophytes Triglochin maritima and Scirpus maritimus prevalent in historically Hg-contaminated Ria de Aveiro coastal lagoon (Portugal). Both plant samples and the sediments vegetated by monospecific stands of T. maritima and S. maritimus were collected from reference (R) and sites with moderate (M) and high (H) Hg contamination in Laranjo bay within Ria de Aveiro lagoon. Hg tolerance, uptake, and allocation in T. maritima and S. maritimus, physico-chemical traits (pH, redox potential, and organic matter content) and Hg concentrations in sediments vegetated by these species were impacted differentially by phenological development stages variation irrespective of the Hg contamination level. In T. maritima, Hg concentration increased with increase in Hg contamination gradient where root displayed significantly higher Hg followed by rhizome and leaf maximally at H. However, in S. maritimus, the highest Hg concentration was perceptible in rhizome followed by root maximally at M. Between the two studied plant species, S. maritimus displayed higher Hg tolerance index (depicted by higher plant dry mass allocated to reproductive stage) and higher available Hg at M (during all growth stages) and H (during senescent stage) when compared to T. maritimus. Both plant species proved to be Hg excluder (low root/rhizome-leaf Hg translocation). Additionally, T. maritima also acted as Hg stabilizer while, S. maritimus as Hg accumulator. It can be inferred from the study that (a) the plant phenological development stage variations significantly influenced plant Hg sensitivity by impacting sediment chemistry, plant growth (in terms of plant dry mass), Hg accumulation, and its subsequent allocation capacity, contingent to Hg contamination gradient; (b) S. maritimus accumulated higher Hg but restricted its translocation to above-ground part using exclusion process at both M and H due to its accelerated growth during Hg-tolerant reproductive/metabolically active phenological development stage greater than its counterpart T. maritima; and (c) the studied salt marsh plants although hailed from the same C3 and monocot group did not necessarily display similar phenotypic plasticity and behavior towards Hg-contaminated scenario during their life cycle. PMID:23184133

  13. Overproduction, purification, crystallization and preliminary X-ray analysis of the peroxiredoxin domain of a larger natural hybrid protein from Thermotoga maritima

    SciTech Connect

    Barbey, Carole; Rouhier, Nicolas; Haouz, Ahmed; Navaza, Alda; Jacquot, Jean-Pierre

    2008-01-01

    Crystals of the peroxiredoxin domain of a larger natural hybrid protein from T. maritima were obtained which diffracted to 2.9 Å resolution on a synchrotron source. Thermotoga maritima contains a natural hybrid protein constituted of two moieties: a peroxiredoxin domain at the N-terminus and a nitroreductase domain at the C-terminus. The peroxiredoxin (Prx) domain has been overproduced and purified from Escherichia coli cells. The recombinant Prx domain, which is homologous to bacterial Prx BCP and plant Prx Q, folds properly into a stable protein that possesses biological activity. The recombinant protein was crystallized and synchrotron data were collected to 2.9 Å resolution. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 176.67, c = 141.20 Å.

  14. Periplasmic Binding Proteins in Thermophiles: Characterization and Potential Application of an Arginine-Binding Protein from Thermotoga maritima: A Brief Thermo-Story

    PubMed Central

    Ausili, Alessio; Staiano, Maria; Dattelbaum, Jonathan; Varriale, Antonio; Capo, Alessandro; D'Auria, Sabato

    2013-01-01

    Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. Due to its features, this protein could be taken into account as a potential candidate for the design of a biosensor for arginine. It is important to investigate the stability of proteins when they are used for biotechnological applications. In this article, we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga maritima with a particular eye on its potential biotechnological applications. PMID:25371336

  15. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima.

    PubMed

    Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

    2015-01-01

    Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5'-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

  16. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

    PubMed Central

    Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

    2015-01-01

    Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

  17. Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes

    PubMed Central

    Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

    2014-01-01

    Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity. PMID:24963380

  18. Diversity and Ecological Characterization of Sporulating Higher Filamentous Marine Fungi Associated with Spartina maritima (Curtis) Fernald in Two Portuguese Salt Marshes.

    PubMed

    Calado, Maria da Luz; Carvalho, Luís; Pang, Ka-Lai; Barata, Margarida

    2015-10-01

    Fungal communities associated with early stages of decomposition of Spartina maritima (Curtis) Fernald were assessed in two geographically distinct salt marshes in Portugal by direct observation of fungal sporulating structures. Twenty-three fungal taxa were identified from 390 plant samples, 11 of which were common to both study sites. Natantispora retorquens, Byssothecium obiones, Phaeosphaeria spartinicola, Phoma sp. 1 and Stagonospora sp. were the most frequent fungal taxa in the studied communities. The fungal species Anthostomella spissitecta, Camarosporium roumeguerii, Coniothyrium obiones, Decorospora gaudefroyi, Halosarpheia trullifera, Leptosphaeria marina and Stagonospora haliclysta were recorded for the first time on S. maritima plants; with the exception of C. roumeguerii and L. marina, all of these species were also new records for Portugal. The differences between species composition of the communities associated with S. maritima were attributed to differences in abiotic conditions of the salt marshes. Although the fungal taxa were distributed differently along the host plants, common species to both fungal communities were found on the same relative position, e.g. B. obiones, Lulworthia sp. and N. retorquens occurred on the basal plant portions, Buergenerula spartinae, Dictyosporium pelagicum and Phoma sp. 1 on the middle plant portions and P. spartinicola and Stagonospora sp. on the top plant portions. The distinct vertical distribution patterns reflected species-specific salinity requirements and flooding tolerance, but specially substrate preferences. The most frequent fungi in both communities also exhibited wider distribution ranges and produced a higher number of fruiting structures, suggesting a more active key role in the decay process of S. maritima. PMID:25851444

  19. Prevention of selenite-induced cataractogenesis by an ethanolic extract of Cineraria maritima: an experimental evaluation of the traditional eye medication.

    PubMed

    Anitha, Thirugnanasambandhar Sivasubramanian; Annadurai, Thangaraj; Thomas, Philip A; Geraldine, Pitchairaj

    2011-10-01

    In the present study, the antioxidant potential of an ethanolic extract of Cineraria maritima and its efficacy in preventing selenite-induced cataractogenesis were assessed in vitro and in vivo. In the in vitro phase of the study, lenses dissected out from the eyes of Wistar rats were incubated for 24 h at 37 °C in Dulbecco's modified Eagle medium (DMEM) alone (group I), in DMEM containing 100 μM of selenite only (group II), or in DMEM containing 100 μM of selenite and 300 μg/ml C. maritima extract added at the same time (group III). Gross morphological examination of the lenses revealed dense opacification in group II, minimal opacification in group III, and no opacification in group I lenses. The mean activities of the antioxidant enzymes catalase, glutathione peroxidase, and superoxide dismutase were significantly lower in group II than in group I or group III lenses, while malondialdehyde concentration was significantly higher in group II lenses than in group I and group III lenses. In the in vivo phase of the study, dense opacification of lenses was noted in all rat pups (100%) that had received a single subcutaneous injection of sodium selenite alone (19 μM/kg body weight) on postpartum day 10, whereas cataract formation occurred in only 33.3% of rat pups that had received selenite as well as an intraperitoneal injection of the extract of C. maritima (350 mg/kg body weight) for five consecutive days. These observations suggest that the ethanolic extract of C. maritima may prevent experimental selenite-induced cataractogenesis. PMID:20949376

  20. Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein

    PubMed Central

    Tian, Yaji; Cuneo, Matthew J.; Changela, Anita; Höcker, Birte; Beese, Lorena S.; Hellinga, Homme W.

    2007-01-01

    We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Å resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 ± 1°C and 144 ± 2°C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C•Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1–30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature. PMID:17766373

  1. Nutritional and biological qualities of the ripened beans of Canavalia maritima from the coastal sand dunes of India.

    PubMed

    Bhagya, B; Sridhar, K R; Raviraja, N S; Young, C-C; Arun, A B

    2009-01-01

    Raw and pressure-cooked ripened beans of Canavalia maritima were assessed for nutritional quality. The beans possess high protein, carbohydrate, fiber and energy contents. Potassium, magnesium, zinc and manganese of the raw and cooked beans meet NRC/NAS recommended pattern for infants. The essential amino acids (threonine, valine, isoleucine, leucine, tyrosine/phenylalanine and lysine) in raw and cooked ripened beans fulfill the FAO/WHO/UNU recommended pattern for adults. Oleic acid in raw beans and linolenic acid in cooked beans were highest and linoleic and arachidonic acids were confined to raw beans. Cooking lowered the total phenolics, while tannins were negligible and devoid of orthodihydric phenols and trypsin inhibitors. Hemagglutinating activity decreased up to 50% in cooked beans. Rats fed with a pressure-cooked bean diet showed significant elevation of all growth and nitrogen balance parameters (P<0.05) than the rats which received the raw bean diet. The low protein quality of beans warrants appropriate thermal processing to eliminate antinutritional factors. PMID:19200923

  2. Histone acetylation influences the transcriptional activation of POX in Beta vulgaris L. and Beta maritima L. under salt stress.

    PubMed

    Yolcu, Seher; Ozdemir, Filiz; Güler, Aybüke; Bor, Melike

    2016-03-01

    Acetylation of histone proteins is a type of chromatin modification which facilitates the activation of genes. Recent studies brought up the importance of this reversible and rapid process for the regulation of gene expression especially in plant defense against a variety of environmental stresses. Deciphering the exact mechanisms of chromatin modifications under abiotic stress conditions is important for improving crop plants' performance and yield. In a previous study we compared the salt stress responses of Beta vulgaris (sugar beet) and Beta maritima (wild beet). In accordance with those results we suggested that chromatin remodeling can be an active process in the regulation of genes related to salt stress tolerance of these plants. Therefore we performed ChIP assay in control and salt stressed (250 and 500 mM NaCl) plants and compared the enrichment of acetylation in the associated chromatin sites. We found that the transcriptional activation of one peroxidase (POX) encoding gene was associated with the elevated levels of acetylation in H3K9 and H3K27 sites. The acetylation patterns were remarkably different between two species in which the highest acetylation levels were found at H3K9 and H3K27 in wild beet and sugar beet respectively. PMID:26773543

  3. Structure-Based Design of Robust Glucose Biosensors using a Thermotoga maritima Periplasmic Glucose-Binding Protein

    SciTech Connect

    Tian,Y.; Cunco, M.; Changela, A.; Hocker, B.; Beese, L.; Hellinga, H.

    2007-01-01

    We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstroms resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 {+-} 1 C and 144 {+-} 2 C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.

  4. Structural Dissection of the Active Site of Thermotoga maritima β-Galactosidase Identifies Key Residues for Transglycosylating Activity.

    PubMed

    Talens-Perales, David; Polaina, Julio; Marín-Navarro, Julia

    2016-04-13

    Glycoside hydrolases, specifically β-galactosidases, can be used to synthesize galacto-oligosaccharides (GOS) due to the transglycosylating (secondary) activity of these enzymes. Site-directed mutagenesis of a thermoresistant β-galactosidase from Thermotoga maritima has been carried out to study the structural basis of transgalactosylation and to obtain enzymatic variants with better performance for GOS biosynthesis. Rational design of mutations was based on homologous sequence analysis and structural modeling. Analysis of mutant enzymes indicated that residue W959, or an alternative aromatic residue at this position, is critical for the synthesis of β-3'-galactosyl-lactose, the major GOS obtained with the wild-type enzyme. Mutants W959A and W959C, but not W959F, showed an 80% reduced synthesis of this GOS. Other substitutions, N574S, N574A, and F571L, increased the synthesis of β-3'-galactosyl-lactose about 40%. Double mutants F571L/N574S and F571L/N574A showed an increase of about 2-fold. PMID:26998654

  5. Transcriptomic profiling of the salt stress response in excised leaves of the halophyte Beta vulgaris ssp. maritima.

    PubMed

    Skorupa, Monika; Gołębiewski, Marcin; Domagalski, Krzysztof; Kurnik, Katarzyna; Abu Nahia, Karim; Złoch, Michał; Tretyn, Andrzej; Tyburski, Jarosław

    2016-02-01

    Beta vulgaris ssp. maritima is a halophytic relative of cultivated beets. In the present work a transcriptome response to acute salt stress imposed to excised leaves of sea beet was investigated. Salt treatments consisted of adding NaCl directly to the transpiration stream by immersing the petioles of excised leaves into the salt solutions. Sequencing libraries were generated from leaves subjected to either moderate or strong salt stress. Control libraries were constructed from untreated leaves. Sequencing was performed using the Illumina MiSeq platform. We obtained 32970 unigenes by assembling the pooled reads from all the libraries with Trinity software. Screening the nr database returned 18 362 sequences with functional annotation. Using the reference transcriptome we identified 1 246 genes that were differentially expressed after 48h of NaCl stress. Genes related to several cellular functions such as membrane transport, osmoprotection, molecular chaperoning, redox metabolism or protein synthesis were differentially expressed in response to salt stress. The response of sea beet leaves to salt treatments was marked out by transcriptomic up-regulation of genes related to photosynthetic carbon fixation, ribosome biogenesis, cell wall-building and cell wall expansion. Furthermore, several novel and undescribed transcripts were responsive to salinity in leaves of sea beet. PMID:26795151

  6. Proteomic and physiological responses of the halophyte Cakile maritima to moderate salinity at the germinative and vegetative stages.

    PubMed

    Debez, Ahmed; Braun, Hans-Peter; Pich, Andreas; Taamalli, Wael; Koyro, Hans-Werner; Abdelly, Chedly; Huchzermeyer, Bernhard

    2012-10-22

    Responses of the halophyte Cakile maritima to moderate salinity were addressed at germination and vegetative stages by bringing together proteomics and eco-physiological approaches. 75 mM NaCl-salinity delayed significantly the germination process and decreased slightly the seed germination percentage compared to salt-free conditions. Monitoring the proteome profile between 0 h and 120 h after seed sowing revealed a delay in the degradation of seed storage proteins when germination took place under salinity, which may explain the slower germination rate observed. Of the sixty-seven proteins identified by mass spectrometry, several proteins involved in glycolysis, amino acid metabolism, photosynthesis, and protein folding showed significantly increased abundance during germination. This pattern was less pronounced under salinity. At the vegetative stage, 100mM NaCl-salinity stimulated significantly the plant growth, which was sustained by enhanced leaf expansion, water content, and photosynthetic activity. Comparative proteome analyses of leaf tissue revealed 44 proteins with different abundance changes, most of which being involved in energy metabolism. A specific set of proteins predominantly involved in photosynthesis and respiration showed significantly higher abundance in salt-treated plants. Altogether, combining proteomics with eco-physiological tools provides valuable information, which contributes to improve our understanding in the salt-response of this halophyte during its life cycle. PMID:22940175

  7. The Structural Basis of Alpha-Glucan Recognition by a Family 41 Carbohydrate-Binding Module from Therotoga Maritima

    SciTech Connect

    van Bueren,A.; Boraston, A.

    2006-01-01

    Starch recognition by carbohydrate-binding modules (CBMs) is important for the activity of starch-degrading enzymes. The N-terminal family 41 CBM, TmCBM41 (from pullulanase PulA secreted by Thermotoga maritima) was shown to have {alpha}-glucan binding activity with specificity for {alpha}-1, 4-glucans but was able to tolerate the {alpha}-1, 6-linkages found roughly every three or four glucose units in pullulan. Using X-ray crystallography, the structures were solved for TmCBM41 in an uncomplexed form and in complex with maltotetraose and 63-{alpha}-d-glucosyl-maltotriose (GM3). Ligand binding was facilitated by stacking interactions between the {alpha}-faces of the glucose residues and two tryptophan side-chains in the two main subsites of the carbohydrate-binding site. Overall, this mode of starch binding is quite well conserved by other starch-binding modules. The structure in complex with GM3 revealed a third binding subsite with the flexibility to accommodate an {alpha}-1, 4- or an {alpha}-1, 6-linked glucose.

  8. Ligands of Thermophilic ABC Transporters Encoded in a Newly Sequenced Genomic Region of Thermotoga maritima MSB8 Screened by Differential Scanning Fluorimetry ▿ †

    PubMed Central

    Boucher, Nathalie; Noll, Kenneth M.

    2011-01-01

    The chromosome of Thermotoga maritima strain MSB8 was found to have an 8,870-bp region that is not present in its published sequence. The isolate that was sequenced by The Institute for Genomic Research (TIGR) in 1999 is apparently a laboratory variant of the isolate deposited at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSM 3109) in 1986. This newly sequenced region from the DSMZ culture was located between TM1848 (cbp, cellobiose phosphorylase) and TM1847 (the 3′ end of a truncated ROK regulator). The new region contained seven genes: a beta glucosidase gene (bglA), three trehalose ABC transporter genes (treEFG), three xylose ABC transporter genes (xylE2F2K2), and the 5′ end of a gene encoding the ROK regulator TM1847. We present a new differential scanning fluorimetry method using a low pH that was necessary to screen potential ligands of these exceptionally thermostable periplasmic substrate-binding proteins. This method showed that trehalose, sucrose, and glucose stabilized TreE, and their binding was confirmed by measuring changes in intrinsic fluorescence upon ligand binding. Binding constants of 0.024 μM, 0.300 μM, and 56.78 μM at 60°C, respectively, were measured. XylE2 ligands were similarly determined and xylose, glucose, and fucose bound with Kd (dissociation constant) values of 0.042 μM, 0.059 μM, and 1.436 μM, respectively. Since there is no discernible phenotypic difference between the TIGR isolate and the DSMZ isolate despite the variance in their genomes, we propose that they be called genomovars: T. maritima MSB8 genomovar TIGR and T. maritima MSB8 genomovar DSM 3109, respectively. PMID:21764944

  9. Phenotypic Changes in Transgenic Tobacco Plants Overexpressing Vacuole-Targeted Thermotoga maritima BglB Related to Elevated Levels of Liberated Hormones

    PubMed Central

    Nguyen, Quynh Anh; Lee, Dae-Seok; Jung, Jakyun; Bae, Hyeun-Jong

    2015-01-01

    The hyperthermostable β-glucosidase BglB of Thermotoga maritima was modified by adding a short C-terminal tetrapeptide (AFVY, which transports phaseolin to the vacuole, to its C-terminal sequence). The modified β-glucosidase BglB was transformed into tobacco (Nicotiana tabacum L.) plants. We observed a range of significant phenotypic changes in the transgenic plants compared to the wild-type (WT) plants. The transgenic plants had faster stem growth, earlier flowering, enhanced root systems development, an increased biomass biosynthesis rate, and higher salt stress tolerance in young plants compared to WT. In addition, programed cell death was enhanced in mature plants. Furthermore, the C-terminal AFVY tetrapeptide efficiently sorted T. maritima BglB into the vacuole, which was maintained in an active form and could perform its glycoside hydrolysis function on hormone conjugates, leading to elevated hormone [abscisic acid (ABA), indole 3-acetic acid (IAA), and cytokinin] levels that likely contributed to the phenotypic changes in the transgenic plants. The elevation of cytokinin led to upregulation of the transcription factor WUSCHELL, a homeodomain factor that regulates the development, division, and reproduction of stem cells in the shoot apical meristems. Elevation of IAA led to enhanced root development, and the elevation of ABA contributed to enhanced tolerance to salt stress and programed cell death. These results suggest that overexpressing vacuole-targeted T. maritima BglB may have several advantages for molecular farming technology to improve multiple targets, including enhanced production of the β-glucosidase BglB, increased biomass, and shortened developmental stages, that could play pivotal roles in bioenergy and biofuel production. PMID:26618153

  10. Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima.

    PubMed Central

    Kletzin, A; Adams, M W

    1996-01-01

    Previous studies have shown that the hyperthermophilic archaeon Pyrococcus furiosus contains four distinct cytoplasmic 2-ketoacid oxidoreductases (ORs) which differ in their substrate specificities, while the hyperthermophilic bacterium Thermotoga maritima contains only one, pyruvate ferredoxin oxidoreductase (POR). These enzymes catalyze the synthesis of the acyl (or aryl) coenzyme A derivative in a thiamine PPi-dependent oxidative decarboxylation reaction with reduction of ferredoxin. We report here on the molecular analysis of the POR (por) and 2-ketoisovalerate ferredoxin oxidoreductase (vor) genes from P. furiosus and of the POR gene from T. maritima, all of which comprise four different subunits. The operon organization for P. furiosus POR and VOR was porG-vorDAB-porDAB, wherein the gamma subunit is shared by the two enzymes. The operon organization for T. maritima POR was porGDAB. The three enzymes were 46 to 53% identical at the amino acid level. Their delta subunits each contained two ferredoxin-type [4Fe-4S] cluster binding motifs (CXXCXXCXXXCP), while their beta subunits each contained four conserved cysteines in addition to a thiamine PPi-binding domain. Amino-terminal sequence comparisons show that POR, VOR, indolepyruvate OR, and 2-ketoglutarate OR of P. furiosus all belong to a phylogenetically homologous OR family. Moreover, the single-subunit pyruvate ORs from mesophilic and moderately thermophilic bacteria and from an amitochondriate eucaryote each contain four domains which are phylogenetically homologous to the four subunits of the hyperthermophilic ORs (27% sequence identity). Three of these subunits are also homologous to the dimeric POR from a mesophilic archaeon, Halobacterium halobium (21% identity). A model is proposed to account for the observed phenotypes based on genomic rearrangements of four ancestral OR subunits. PMID:8550425

  11. Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana

    PubMed Central

    2010-01-01

    Background In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods. Results We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino acid residues with a calculated molecular mass of 16.30 and 16.58 kDa, respectively. The similarity between amino acid sequences of these proteins is very high: 90% identity and 95% similarity. Surprisingly, both TmaSSB and TneSSB possess a quite low sequence similarity to Escherichia coli SSB (36 and 35% identity, 55 and 56% similarity, respectively). They are functional as homotetramers containing one single-stranded DNA binding domain (OB-fold) in each monomer. Agarose mobility assays indicated that the ssDNA-binding site for both proteins is salt independent, and fluorescence spectroscopy resulted in a size of 68 ± 2 nucleotides. The half-lives of TmaSSB and TneSSB were 10 h and 12 h at 100°C, respectively. When analysed by differential scanning microcalorimetry (DSC) the melting temperature (Tm) was 109.3°C and 112.5°C for TmaSSB and TneSSB, respectively. Conclusion The results showed that TmaSSB and TneSSB are the most thermostable SSB proteins identified to date, offering an attractive alternative to TaqSSB and TthSSB in molecular biology applications, especially with using high temperature e. g. polymerase chain reaction (PCR). PMID:20950419

  12. Improved Activity of a Thermophilic Cellulase, Cel5A, from Thermotoga maritima on Ionic Liquid Pretreated Switchgrass

    PubMed Central

    Chen, Zhiwei; Pereira, Jose H.; Liu, Hanbin; Tran, Huu M.; Hsu, Nathan S. Y.; Dibble, Dean; Singh, Seema; Adams, Paul D.; Sapra, Rajat; Hadi, Masood Z.; Simmons, Blake A.; Sale, Kenneth L.

    2013-01-01

    Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and ultimately fuels from lignocellulosic biomass. Much of the high cost of enzymes is due to the low catalytic efficiency and stability of lignocellulolytic enzymes, especially cellulases, under conditions that include high temperatures and the presence of residual pretreatment chemicals, such as acids, organic solvents, bases, or ionic liquids. Improving the efficiency of the saccharification process on ionic liquid pretreated biomass will facilitate reduced enzyme loading and cost. Thermophilic cellulases have been shown to be stable and active in ionic liquids but their activity is typically at lower levels. Cel5A_Tma, a thermophilic endoglucanase from Thermotoga maritima, is highly active on cellulosic substrates and is stable in ionic liquid environments. Here, our motivation was to engineer mutants of Cel5A_Tma with higher activity on 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) pretreated biomass. We developed a robotic platform to screen a random mutagenesis library of Cel5A_Tma. Twelve mutants with 25–42% improvement in specific activity on carboxymethyl cellulose and up to 30% improvement on ionic-liquid pretreated switchgrass were successfully isolated and characterized from a library of twenty thousand variants. Interestingly, most of the mutations in the improved variants are located distally to the active site on the protein surface and are not directly involved with substrate binding. PMID:24244549

  13. Complexed Structures of Formylglycinamide Ribonucleotide Amidotransferase from Thermotoga maritima Describe a Novel ATP-binding Protein Superfamily†,‡

    PubMed Central

    Morar, Mariya; Anand, Ruchi; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E.

    2008-01-01

    Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the ATP-dependent synthesis of formylglycinamidine ribonucleotide (FGAM) from formylglycinamide ribonucleotide (FGAR) and glutamine in the fourth step of the purine biosynthetic pathway. FGAR-AT is encoded by the purL gene. Two types of PurL have been detected. The first type, found in eukaryotes and Gram-negative bacteria, consists of a single 140 kDa polypeptide chain and is designated large PurL (lgPurL). The second type, small PurL (smPurL), is found in archaea and Gram-positive bacteria and consists of an 80 kDa polypeptide chain. Small PurL requires two additional gene products, PurQ and PurS, for activity. PurL is a member of a protein superfamily that contains a novel ATP-binding domain. Structures of several members of this superfamily are available in the apo form. We determined five different structures of FGAR-AT from Thermotoga maritima in the presence of substrates, a substrate analog, and a product. These complexes have allowed a detailed description of the novel ATP-binding motif. Availability of a ternary complex enabled mapping of the active site thus identifying potential residues involved in catalysis. The complexes show a conformational change in the active site compared to the unliganded structure. A surprising discovery, an ATP molecule in an auxiliary site of the protein and the conformational changes associated with its binding, provoke speculations about the regulatory role of the auxiliary site in PurLSQ complex formation as well as the evolutionary relationship of PurL's from different organisms. PMID:17154526

  14. Crystal Structure of Butyrate Kinase 2 from Thermotoga maritima, a Member of the ASKHA Superfamily of Phosphotransferases

    SciTech Connect

    Diao, Jiasheng; Hasson, Miriam S.

    2009-04-01

    The enzymatic transfer of phosphoryl groups is central to the control of many cellular processes. One of the phosphoryl transfer mechanisms, that of acetate kinase, is not completely understood. Besides better understanding of the mechanism of acetate kinase, knowledge of the structure of butyrate kinase 2 (Buk2) will aid in the interpretation of active-site structure and provide information on the structural basis of substrate specificity. The gene buk2 from Thermotoga maritima encodes a member of the ASKHA (acetate and sugar kinases/heat shock cognate/actin) superfamily of phosphotransferases. The encoded protein Buk2 catalyzes the phosphorylation of butyrate and isobutyrate. We have determined the 2.5-{angstrom} crystal structure of Buk2 complexed with ({beta},{gamma}-methylene) adenosine 5'-triphosphate. Buk2 folds like an open-shelled clam, with each of the two domains representing one of the two shells. In the open active-site cleft between the N- and C-terminal domains, the active-site residues consist of two histidines, two arginines, and a cluster of hydrophobic residues. The ATP binding region of Buk2 in the C-terminal domain consists of abundant glycines for nucleotide binding, and the ATP binding motif is similar to those of other members of the ASKHA superfamily. The enzyme exists as an octamer, in which four disulfide bonds form between intermolecular cysteines. Sequence alignment and structure superposition identify the simplicity of the monomeric Buk2 structure, a probable substrate binding site, the key residues in catalyzing phosphoryl transfer, and the substrate specificity differences among Buk2, acetate, and propionate kinases. The possible enzyme mechanisms are discussed.

  15. Directed evolution of the alpha-L-fucosidase from Thermotoga maritima into an alpha-L-transfucosidase.

    PubMed

    Osanjo, George; Dion, Michel; Drone, Jullien; Solleux, Claude; Tran, Vinh; Rabiller, Claude; Tellier, Charles

    2007-01-30

    The alpha-L-fucosidase from Thermotoga maritima (Tm alpha fuc) was converted into alpha-L-transfucosidase variants by directed evolution. The wild-type enzyme catalyzes oligosaccharide synthesis by transfer of a fucosyl residue from a pNP-fucoside donor to pNP-fucoside (self-condensation) with alpha-(1-->3) regioselectivity or pNP-galactoside (transglycosylation) with alpha-(1-->2) regioselectivity at low yields (7%). The wild-type enzyme was submitted to one cycle of mutagenesis, followed by rational recombination of the selected mutations, which allowed identification of variants with improved transferase activity. The transferase and hydrolytic kinetics of all the mutants were assessed by NMR methods and capillary electrophoresis. It was shown that the best mutant exhibited a dramatic 32-fold increase in the transferase/hydrolytic kinetic ratio, while keeping 60% of the overall wild-type enzyme activity. Accordingly, the maximum yield of a specific transglycosylation product [pNP-Gal-alpha-(1-->2)-Fuc] reached more than 60% compared to 7% with WT enzyme at equimolar and low concentrations of donor and acceptor (10 mM). Such an improvement was obtained with only three mutations (T264A, Y267F, L322P), which were all located in the second amino acid shell of the fucosidase active site. Molecular modeling suggested that some of these mutations (T264A, Y267F) cause a reorientation of the amino acids that are in direct contact with the substrates, resulting in a better docking energy. Such mutants with high transglycosidase activity may constitute novel enzymatic tools for the synthesis of fucooligosaccharides. PMID:17240986

  16. Site-Directed Mutagenesis of a Hyperthermophilic Endoglucanase Cel12B from Thermotoga maritima Based on Rational Design

    PubMed Central

    Zhang, Jinfeng; Shi, Hao; Xu, Linyu; Zhu, Xiaoyan; Li, Xiangqian

    2015-01-01

    To meet the demand for the application of high activity and thermostable cellulases in the production of new-generation bioethanol from nongrain-cellulose sources, a hyperthermostable β-1,4-endoglucase Cel12B from Thermotoga maritima was selected for further modification by gene site-directed mutagenesis method in the present study, based on homology modeling and rational design. As a result, two recombinant enzymes showed significant improvement in enzyme activity by 77% and 87%, respectively, higher than the parental enzyme TmCel12B. Furthermore, the two mutants could retain 80% and 90.5% of their initial activity after incubation at 80°C for 8 h, while only 45% for 5 h to TmCel12B. The Km and Vmax of the two recombinant enzymes were 1.97±0.05 mM, 4.23±0.15 μmol·mg-1·min-1 of TmCel12B-E225H-K207G-D37V, and 2.97±0.12 mM, 3.15±0.21 μmol·mg-1·min-1 of TmCel12B-E225H-K207G, respectively, when using CMC-Na as the substrate. The roles of the mutation sites were also analyzed and evaluated in terms of electron density, hydrophobicity of the modeled protein structures. The recombinant enzymes may be used in the hydrolysis of cellulose at higher temperature in the future. It was concluded that the gene mutagenesis approach of a certain active residues may effectively improve the performance of cellulases for the industrial applications and contribute to the study the thermostable mechanism of thermophilic enzymes. PMID:26218520

  17. Relationship between the photosynthetic activity and the performance of Cakile maritima after long-term salt treatment.

    PubMed

    Debez, Ahmed; Koyro, Hans-Werner; Grignon, Claude; Abdelly, Chedly; Huchzermeyer, Bernhard

    2008-06-01

    Cakile maritima is a halophyte with potential for ecological, economical and medicinal uses. We address here the impact of salinity on its growth, photosynthesis and seed quality. Whole plant growth rate and shoot development were stimulated at moderate salinity (100-200 mM NaCl) and inhibited at higher salt concentrations. Although diminished in the presence of salt, potassium and calcium uptake per unit of root biomass was maintained at relatively high value, while nutrient-use efficiency (NUE) was improved in salt-treated plants. Chl and carotenoid concentrations decreased at extreme salinities, but anthocyanin concentration continuously grew with salinity. Net photosynthetic rate (A), stomatal conductance, maximum quantum efficiency of PSII and quantum yield were stimulated in the 100-200 mM NaCl range. Higher salinity adversely affected gas exchange and changed PSII functional characteristics, resulting in a reduction of A per leaf area unit. This phenomenon was associated with increased non-photochemical quenching. Harvest index, silique number and seeds per fruit valve were maximal at 100 mM NaCl. Despite the decreasing salt accumulation gradient from the vegetative to the reproductive organs, high salinities were detrimental for the seed viability and increased the proportion of empty siliques. Overall, the salt-induced changes in the plant photosynthetic activity resulted into analogous responses at the vegetative and reproductive stages. The enhancement of NUE, the absence of pigment degradation, the reduction of water loss and the concomitant PSII protection from photodamage through thermal dissipation of excess excitation significantly accounted for Cakile survival capacity at high salinity. PMID:18346075

  18. Proline 235 plays a key role in the regulation of the oligomeric states of Thermotoga maritima Arginine Binding Protein.

    PubMed

    Smaldone, Giovanni; Vigorita, Marilisa; Ruggiero, Alessia; Balasco, Nicole; Dattelbaum, Jonathan D; D'Auria, Sabato; Del Vecchio, Pompea; Graziano, Giuseppe; Vitagliano, Luigi

    2016-07-01

    The Arginine Binding Protein isolated from Thermotoga maritima (TmArgBP) is a protein endowed with several peculiar properties. We have previously shown that TmArgBP dimerization is a consequence of the swapping of the C-terminal helix. Here we explored the structural determinants of TmArgBP domain swapping and oligomerization. In particular, we report a mutational analysis of the residue Pro235, which is located in the hinge region of the swapping dimer. This residue was either replaced with a Gly-Lys dipeptide (TmArgBP(P235GK)) or a Gly residue (TmArgBP(P235G)). Different forms of these mutants were generated and extensively characterized using biophysical techniques. For both TmArgBP(P235GK) and TmArgBP(P235G) mutants, the occurrence of multiple oligomerization states (monomers, dimers and trimers) was detected. The formation of well-folded monomeric forms for these mutants indicates that the dimerization through C-terminal domain swapping observed in wild-type TmArgBP is driven by conformational restraints imposed by the presence of Pro235 in the hinge region. Molecular dynamics studies corroborate this observation by showing that Gly235 assumes conformational states forbidden for Pro residues in the TmArgBP(P235G) monomer. Unexpectedly, the trimeric forms present: (a) peculiar circular dichroism spectra, (b) a great susceptibility to heating, and (c) the ability to bind the Thioflavin T dye. The present findings clearly demonstrate that single-point mutations have an important impact on the TmArgBP oligomerization process. In a wider context, they also indicate that proteins endowed with an intrinsic propensity to swap have an easy access to states with altered structural and, possibly, functional properties. PMID:27087545

  19. Anti-hyperalgesic and Anti-inflammatory Activity of Alternanthera Maritima Extract and 2″-O-α-L-rhamnopyranosylvitexin in Mice.

    PubMed

    de Santana Aquino, Diana Figuereido; Piccinelli, Ana Claudia; Soares, Fabíola Lacerda Pires; Arena, Arielle Cristina; Salvador, Marcos José; Kassuya, Candida Aparecida Leite

    2015-12-01

    Alternanthera maritima are used in Brazilian popular medicine for the treatment of inflammatory and infectious diseases. Species of Alternanthera have demonstrated biological activities in previous scientific studies. The aim of this study was to determine whether the ethanol extract of the aerial parts of A. maritima (EEAM) and the isolated compound 2″-O-α-L-rhamnopyranosyl-vitexin inhibit mechanical hyperalgesia and parameters of inflammation in mice. The oral administration of EEAM significantly inhibited carrageenan (Cg)-induced paw edema and reduced leukocyte migration into the pleural cavity. 2″-O-α-L-rhamnopyranosylvitexin significantly inhibited paw edema and reduced both leukocyte migration and the leakage of protein into the pleural cavity. Both EEAM and 2″-O-α-L-rhamnopyranosylvitexin significantly prevented the Cg-induced hyperalgesia. Local administration of 2″-O-α-L-rhamnopyranosylvitexin significantly prevented the Cg- and tumor necrosis factor (TNF)-induced hyperalgesia. In conclusion, this study demonstrated that EEAM is an anti-inflammatory and anti-hyperalgesic agent, and the results suggested that 2″-O-α-L-rhamnopyranosylvitexin is responsible for the effects of EEAM and the mechanism involves the TNF pathway. PMID:26045342

  20. Crystallization and preliminary X-ray crystallographic characterization of TrmFO, a folate-dependent tRNA methyltransferase from Thermotoga maritima

    SciTech Connect

    Cicmil, Nenad

    2008-03-01

    T. maritima TrmFO was overexpressed, purified and crystallized. A diffraction data set was collected to a resolution of 2.6 Å. TrmFO, previously classified as GID, is a methyltransferase that catalyzes the formation of 5-methyluridine or ribothymidine (T) at position 54 in tRNA in some Gram-positive bacteria. To date, TrmFO is the only characterized tRNA methyltransferase that does not use S-adenosylmethionine as the methyl-group donor. Instead, the donor of the methyl group is N{sup 5},N{sup 10}-methylenetetrahydrofolate. The crystallization and preliminary X-ray crystallographic studies of TrmFO are reported here. The recombinant protein, cloned from Thermotoga maritima genomic DNA, was overproduced in Esherichia coli and crystallized in 25%(v/v) PEG 4000, 100 mM NaCl and sodium citrate buffer pH 5.0 at 291 K using the hanging-drop vapor-diffusion method. The plate-shaped crystals diffracted to 2.6 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 79.94, b = 92.46, c = 127.20 Å.

  1. Historical biogeography in a linear system: genetic variation of sea rocket (Cakile maritima) and sea holly (Eryngium maritimum) along European coasts.

    PubMed

    Clausing, G; Vickers, K; Kadereit, J W

    2000-11-01

    The exclusively coastal Cakile maritima and Eryngium maritimum represent a linear biogeographical system. Genetic variation among 25 individuals of C. maritima and 16 individuals of E. maritimum, from the coasts of Europe, North Africa and the Canary Islands, was analysed using random amplified polymorphic DNAs (RAPDs) and intersimple sequence repeats (ISSRs). Genetic distances (Dice) were calculated and used to investigate the correlation between genetic and geographical distances, to construct Neighbour Joining (NJ) trees, and to compare mean genetic distances between areas within and across species. Genetic distances and geographical distances measured along the coast are well correlated in Cakile and Eryngium. This implies that dispersal in both species is largely along the coast. The NJ analyses resulted in the recognition of Atlantic and Mediterranean clusters in both Cakile and Eryngium. The genetic distance between these two clusters is much larger in Eryngium (0. 285) than in Cakile (0.037). Mean genetic distances are substantially higher in the Mediterranean than in the Atlantic clusters in both species, and higher in Cakile than in Eryngium particularly in the Atlantic cluster. It is argued that all similarities and differences between the two species can be explained with the presumed distribution of the two species in the Würm glacial as reconstructed from their extant temperature requirements, the distribution of ice cover, permafrost, and sea surface temperatures in that period, and indirect fossil evidence. PMID:11091318

  2. Understanding the population genetic structure of coastal species (Cakile maritima): seed dispersal and the role of sea currents in determining population structure.

    PubMed

    Gandour, Mhemmed; Hessini, Kamel; Abdelly, Chedly

    2008-04-01

    The nature and extent of long-distance seed dispersal are currently poorly understood, largely due to the inherent difficulty in detecting such a phenomenon. Genetic methods provide one of the few general approaches that offer the potential to accurately address this issue. Phenotypic and allozymic approaches were applied to characterize inter-population seed dispersal of the sea rocket (Cakile maritima, Brassicaceae), a glabrous and succulent annual herb. Genetic variation was assessed on 360 individuals sampled from nine populations. Genetic diversity across populations was high, 37% of which was represented by Qst and 16% by Fst. When genetic distances were used to construct the UPGMA dendrogram, populations were clustered into three groups at the 90% similarity level. The pattern of clustering can be explained by examining the direction of sea currents around Tunisian coasts. We have shown in this study that C. maritima seeds can survive up to 4 months immersion in sea water and up to 1 year of floating in sea water; therefore, seed dispersal between populations is possible both in terms of seed survival and current patterns. PMID:18426620

  3. Regulation of Endo-Acting Glycosyl Hydrolases in the Hyperthermophilic Bacterium Thermotoga maritima Grown on Glucan- and Mannan-Based Polysaccharides

    PubMed Central

    Chhabra, Swapnil R.; Shockley, Keith R.; Ward, Donald E.; Kelly, Robert M.

    2002-01-01

    The genome sequence of the hyperthermophilic bacterium Thermotoga maritima encodes a number of glycosyl hydrolases. Many of these enzymes have been shown in vitro to degrade specific glycosides that presumably serve as carbon and energy sources for the organism. However, because of the broad substrate specificity of many glycosyl hydrolases, it is difficult to determine the physiological substrate preferences for specific enzymes from biochemical information. In this study, T. maritima was grown on a range of polysaccharides, including barley β-glucan, carboxymethyl cellulose, carob galactomannan, konjac glucomannan, and potato starch. In all cases, significant growth was observed, and cell densities reached 109 cells/ml. Northern blot analyses revealed different substrate-dependent expression patterns for genes encoding the various endo-acting β-glycosidases; these patterns ranged from strong expression to no expression under the conditions tested. For example, cel74 (TM0305), a gene encoding a putative β-specific endoglucananse, was strongly expressed on all substrates tested, including starch, while no evidence of expression was observed on any substrate for lam16 (TM0024), xyl10A (TM0061), xyl10B (TM0070), and cel12A (TM1524), which are genes that encode a laminarinase, two xylanases, and an endoglucanase, respectively. The cel12B (TM1525) gene, which encodes an endoglucanase, was expressed only on carboxymethyl cellulose. An extracellular mannanase encoded by man5 (TM1227) was expressed on carob galactomannan and konjac glucomannan and to a lesser extent on carboxymethyl cellulose. An unexpected result was the finding that the cel5A (TM1751) and cel5B (TM1752) genes, which encode putative intracellular, β-specific endoglucanases, were induced only when T. maritima was grown on konjac glucomannan. To investigate the biochemical basis of this finding, the recombinant forms of Man5 (Mr, 76,900) and Cel5A (Mr, 37,400) were expressed in Escherichia coli and characterized. Man5, a T. maritima extracellular enzyme, had a melting temperature of 99°C and an optimun temperature of 90°C, compared to 90 and 80°C, respectively, for the intracellular enzyme Cel5A. While Man5 hydrolyzed both galactomannan and glucomannan, no activity was detected on glucans or xylans. Cel5A, however, not only hydrolyzed barley β-glucan, carboxymethyl cellulose, xyloglucan, and lichenin but also had activity comparable to that of Man5 on galactomannan and higher activity than Man5 on glucomannan. The biochemical characteristics of Cel5A, the fact that Cel5A was induced only when T. maritima was grown on glucomannan, and the intracellular localization of Cel5A suggest that the physiological role of this enzyme includes hydrolysis of glucomannan oligosaccharides that are transported following initial hydrolysis by extracellular glycosidases, such as Man5. PMID:11823189

  4. Crystallization and preliminary crystallographic studies of PotA, a membrane-associated ATPase of the spermidine-preferential uptake system in Thermotoga maritima.

    PubMed

    Sugiyama, Shigeru; Kashiwagi, Keiko; Kakinouchi, Keisuke; Tomitori, Hideyuki; Kanai, Ken; Murata, Michio; Adachi, Hiroaki; Matsumura, Hiroyoshi; Takano, Kazufumi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Igarashi, Kazuei

    2014-06-01

    A membrane-associated ATPase, PotA, is a component of the spermidine-preferential uptake system in prokaryotes that plays an important role in normal cell growth by regulating the cellular polyamine concentration. No three-dimensional structures of membrane-associated ATPases in polyamine-uptake systems have been determined to date. Here, the crystallization and preliminary X-ray diffraction analysis of PotA from Thermotoga maritima are reported. Diffraction data were collected and processed to 2.7 Å resolution from both native and selenomethionine-labelled crystals. Preliminary crystallographic analysis revealed that the crystals belonged to the hexagonal space group P3₁12 (or P3₂12), with unit-cell parameters a=b=88.9, c=221.2 Å, α=90, β=90, γ=120°, indicating that a dimer was present in the asymmetric unit. PMID:24915082

  5. Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima.

    PubMed

    Ethayathulla, Abdul S; Bessho, Yoshitaka; Shinkai, Akeo; Padmanabhan, Balasundaram; Singh, Tej P; Kaur, Punit; Yokoyama, Shigeyuki

    2008-06-01

    Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6(4)22, with unit-cell parameters a = b = 148.49, c = 106.96 A, gamma = 120.0 degrees . Assuming the presence of two molecules in the asymmetric unit, the calculated V(M) is 2.84 A(3) Da(-1), which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3 A resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan. PMID:18540059

  6. Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn{sup 2+}-binding FCD domains

    SciTech Connect

    Zheng, Meiying; Cooper, David R.; Grossoehme, Nickolas E.; Yu, Minmin; Hung, Li-Wei; Cieslik, Marcin; Derewenda, Urszula; Lesley, Scott A.; Wilson, Ian A.; Giedroc, David P.; Derewenda, Zygmunt S.

    2009-04-01

    Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-α-helical regulatory domains classified into two related Pfam families: FadR-C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni{sup 2+} ions but that it is able to bind Zn{sup 2+} with K{sub d} < 70 nM. It is concluded that Zn{sup 2+} is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.

  7. Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface.

    PubMed

    Lebbink, J H; Knapp, S; van der Oost, J; Rice, D; Ladenstein, R; de Vos, W M

    1999-06-01

    The role of an 18-residue ion-pair network, that is present in the glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus, in conferring stability to other, less stable homologous enzymes, has been studied by introducing four new charged amino acid residues into the subunit interface of glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima. These two GDHs are 55 % identical in amino acid sequence, differ greatly in thermo-activity and stability and derive from microbes with different phylogenetic positions. Amino acid substitutions were introduced as single mutations as well as in several combinations. Elucidation of the crystal structure of the quadruple mutant S128R/T158E/N117R/S160E T. maritima glutamate dehydrogenase showed that all anticipated ion-pairs are formed and that a 16-residue ion-pair network is present. Enlargement of existing networks by single amino acid substitutions unexpectedly resulted in a decrease in resistance towards thermal inactivation and thermal denaturation. However, combination of destabilizing single mutations in most cases restored stability, indicating the need for balanced charges at subunit interfaces and high cooperativity between the different members of the network. Combination of the three destabilizing mutations in triple mutant S128R/T158E/N117R resulted in an enzyme with a 30 minutes longer half-life of inactivation at 85 degrees C, a 3 degrees C higher temperature optimum for catalysis, and a 0.5 degrees C higher apparent melting temperature than that of wild-type glutamate dehydrogenase. These findings confirm the hypothesis that large ion-pair networks do indeed stabilize enzymes from hyperthermophilic organisms. PMID:10366510

  8. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

    PubMed Central

    Ferreira de Carvalho, J; Poulain, J; Da Silva, C; Wincker, P; Michon-Coudouel, S; Dheilly, A; Naquin, D; Boutte, J; Salmon, A; Ainouche, M

    2013-01-01

    Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38?478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16?753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNA-seq and further gene expression evolution analyses in natural populations. PMID:23149455

  9. TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin binding protein involved in response of the cell to oxidative conditions

    PubMed Central

    Dermoun, Zorah; Foulon, Amélie; Miller, Mitchell D.; Harrington, Daniel J.; Deacon, Ashley M.; Sebban-Kreuzer, Corinne; Roche, Philippe; Lafitte, Daniel; Bornet, Olivier; Wilson, Ian A.; Dolla, Alain

    2010-01-01

    Using the COG database, a comparative genome analysis from anaerobic and aerobic microorganisms, was performed with the aim of identifying proteins specific to the anaerobic way of life. Thirty-three COGs were identified, five of which corresponded to proteins of unknown function. We focused our study on TM0486, from Thermotoga maritima, that belongs to one of these latter COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 Å resolution. The structure adopts a βαββαβ ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand NMR and calorimetric experiments revealed that TM0486 specifically bound thiamin with a Kd of 1.58 µM, but not hydroxymethyl pyrimidine (HMP), that was implicated previously as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have already been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes for an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions. PMID:20471400

  10. Fungal decontamination and enhancement of shelf life of edible split beans of wild legume Canavalia maritima by the electron beam irradiation

    NASA Astrophysics Data System (ADS)

    Supriya, P.; Sridhar, K. R.; Ganesh, S.

    2014-03-01

    Ripened split beans of the coastal sand dune wild legume Canavalia maritima serve as one of the traditional nutritional sources of the coastal dwellers in Southwest coast of India. Nine fungi were isolated from the unirradiated dry beans by plating on the potato dextrose agar medium. Toxigenic fungus Aspergillus niger showed the highest incidence (33-50%) followed by Aspergillus flavus (14-20%) and Penicillium chrysogenum (7-13%). Unirradiated dry beans and irradiated dry beans with electron beam doses 2.5, 5, 10 and 15 kGy were monitored for occurrence of fungal species and their incidence during 0, 3 and 6 months storage period under laboratory conditions. Irradiation resulted in dose-dependent decrease in fungal species (5-7, 4-6, 3-6 and 0 on irradiation at 0, 2.5, 5 and 10 or 15 kGy, respectively) as well as incidence (80-99, 19-46, 13-21 and 0%, respectively). Although aflatoxins (B1 and B2) were found below detectable level (<2 ng/g) in 0, 3 and 6 months stored unirradiated and irradiated beans (2.5 and 5 kGy), they were not present in beans irradiated with 10 and 15 kGy. In spite of occurrence of toxigenic fungus Aspergillus ochraceus in unirradiated and irradiated beans (2.5 and 5 kGy) stored for 3 and 6 months, the beans were devoid of ochratoxin-A. Electron beam irradiation dose 10 kGy could be recommended for fungal decontamination and improvement of shelf life of C. maritima ripened dry split beans.

  11. Iron-sulfur cluster biosynthesis: biochemical characterization of the conformational dynamics of Thermotoga maritima IscU and the relevance for cellular cluster assembly.

    PubMed

    Mansy, Sheref S; Wu, Shu-pao; Cowan, J A

    2004-03-12

    Important for the understanding of the functional properties of the iron-sulfur scaffold IscU is knowledge of the structure and dynamics of this protein class. Structural characterization of Thermotoga maritima IscU by CD (Mansy, S. S., Wu, G., Surerus, K. K., and Cowan, J. A. (2002) J. Biol. Chem. 277, 21397-21404) and high resolution NMR (Bertini, I., Cowan, J. A., Del Bianco, C., Luchinat, C., and Mansy, S. S. (2003) J. Mol. Biol. 331, 907-924) yielded data indicating a high degree of secondary structure. However, the latter also revealed IscU to exist in a dynamic equilibrium between two or more distinct conformations, possibly existing in a molten globule state. Herein, we further characterize the molten globule characteristics of T. maritima IscU by near-ultraviolet circular dichroism, 1-anilino-8-naphthalenesulfonic acid binding, free energy of unfolding, hydrodynamic radius measurements, and limited tryptic digestion. The data suggest unusual dynamic behavior that is not fully consistent with typical protein states such as fully folded, fully unfolded, or molten globule. For instance, the existence of a stable tertiary fold is supported by near-UV CD spectra and hydrodynamic radius measurements, whereas other data are less clearly interpretable and may be viewed as consistent with either a molten globule or fully folded state. However, all of the data are consistent with our previous hypothesis of a protein sampling multiple discrete tertiary conformations in which these structural transitions occur on a "slow" time scale. To describe such proteins, we introduce the term multiple discrete conformers. PMID:14688265

  12. Structural Analysis of Semi-specific Oligosaccharide Recognition by a Cellulose-binding Protein of Thermotoga maritima Reveals Adaptations for Functional Diversification of the Oligopeptide Periplasmic Binding Protein Fold

    SciTech Connect

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.

    2010-05-25

    Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of {beta}(1 {yields} 4)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures.

  13. Isolation, identification and expression analysis of salt-induced genes in Suaeda maritima, a natural halophyte, using PCR-based suppression subtractive hybridization

    PubMed Central

    Sahu, Binod B; Shaw, Birendra P

    2009-01-01

    Background Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. Thus, there is a need of continued effort to understand the salt tolerance mechanism using suitable biotechnological techniques and test plants (species) to enable development of salt tolerant cultivars of interest. Therefore, the present study was undertaken to generate information on salt stress responsive genes in a natural halophyte, Suaeda maritima, using PCR-based suppression subtractive hybridization (PCR-SSH) technique. Results Forward and reverse SSH cDNA libraries were constructed after exposing the young plants to 425 mM NaCl for 24 h. From the forward SSH cDNA library, 429 high quality ESTs were obtained. BLASTX search and TIGR assembler programme revealed overexpression of 167 unigenes comprising 89 singletons and 78 contigs with ESTs redundancy of 81.8%. Among the unigenes, 32.5% were found to be of special interest, indicating novel function of these genes with regard to salt tolerance. Literature search for the known unigenes revealed that only 17 of them were salt-inducible. A comparative analysis of the existing SSH cDNA libraries for NaCl stress in plants showed that only a few overexpressing unigenes were common in them. Moreover, the present study also showed increased expression of phosphoethanolamine N-methyltransferase gene, indicating the possible accumulation of a much studied osmoticum, glycinebetaine, in halophyte under salt stress. Functional categorization of the proteins as per the Munich database in general revealed that salt tolerance could be largely determined by the proteins involved in transcription, signal transduction, protein activity regulation and cell differentiation and organogenesis. Conclusion The study provided a clear indication of possible vital role of glycinebetaine in the salt tolerance process in S. maritima. However, the salt-induced expression of a large number of genes involved in a wide range of cellular functions was indicative of highly complex nature of the process as such. Most of the salt inducible genes, nonetheless, appeared to be species-specific. In light of the observations made, it is reasonable to emphasize that a comparative analysis of ESTs from SSH cDNA libraries generated systematically for a few halophytes with varying salt exposure time may clearly identify the key salt tolerance determinant genes to a minimum number, highly desirable for any genetic manipulation adventure. PMID:19497134

  14. Inexpensive one-step purification of polypeptides expressed in Escherichia coli as fusions with the family 9 carbohydrate-binding module of xylanase 10A from T. maritima.

    PubMed

    Kavoosi, Mojgan; Meijer, Julia; Kwan, Emily; Creagh, A Louise; Kilburn, Douglas G; Haynes, Charles A

    2004-07-25

    A novel inexpensive affinity purification technology is described based on recombinant expression in Escherichia coli of the polypeptide or protein target fused through its N-terminus to TmXyn10ACBM9-2 (CBM9), the C-terminal family 9 carbohydrate-binding module of xylanase 10A from Thermotoga maritima. Measured association constants (K(a)) for adsorption of CBM9 to insoluble allomorphs of cellulose are between 2 x 10(5) and 8 x 10(6) M(-1). CBM9 also binds a range of soluble sugars, including glucose. As a result, a 1M glucose solution is effective in eluting CBM9 and CBM9-tagged fusion proteins from a very inexpensive commercially-available cellulose-based capture column. A processing site is encoded at the C-terminus of the tag to facilitate its rapid and quantitative removal by Factor X(a) to recover the desired target protein sequence following affinity purification. Fusion of the CBM9 affinity tag to the N-terminus of green fluorescent protein (GFP) from the jellyfish, Aquorin victoria, is shown to yield >200 mgl(-1) of expressed soluble fusion protein that can be affinity separated from clarified cell lysate to a purity of >95% at a yield of 86%. PMID:15177165

  15. Production of xylobiose from the autohydrolysis explosion liquor of corncob using Thermotoga maritima xylanase B (XynB) immobilized on nickel-chelated Eupergit C.

    PubMed

    Tan, S S; Li, D Y; Jiang, Z Q; Zhu, Y P; Shi, B; Li, L T

    2008-01-01

    In this study, a thermostable recombinant xylanase B (XynB) from Thermotoga maritima MSB8 was immobilized on nickel-chelated Eupergit C 250L. This immobilized XynB was then used to hydrolyze the autohydrolysis explosion liquor of corncob (AELC) in a packed-bed enzyme reactor for continuous production of xylooligosaccharides, especially xylobiose. When tested in batch hydrolysis of AELC, the immobilized XynB still retained its relative activity of 92.5% after 10 cycles of hydrolysis at 90 degrees C. The immobilized XynB retained 83.6% of its initial hydrolysis activity even after 168 h of hydrolysis reaction at 90 degrees C and demonstrated a half-life time of 577.6 h (24 days) for continuous hydrolysis. HPLC showed that xylobiose (49.8%) and xylose (22.6%) were the main hydrolysis products yielded during continuous hydrolysis. Xylobiose was adsorbed on an activated charcoal column and eluted with a linear gradient of 15% (v/v) ethanol to yield xylobiose with 84.7% of recovery. Also, the purity of xylobiose was up to 97.2% as determined by HPLC. Therefore, the immobilized XynB was suitable for the efficient production of xylobiose from AELC. This is the first report on the immobilization of xylanase for xylobiose production. PMID:17258452

  16. Subcellular concentrations of sugar alcohols and sugars in relation to phloem translocation in Plantago major, Plantago maritima, Prunus persica, and Apium graveolens

    PubMed Central

    Nadwodnik, Jan

    2008-01-01

    Sugar and sugar alcohol concentrations were analyzed in subcellular compartments of mesophyll cells, in the apoplast, and in the phloem sap of leaves of Plantago major (common plantain), Plantago maritima (sea plantain), Prunus persica (peach) and Apium graveolens (celery). In addition to sucrose, common plantain, sea plantain, and peach also translocated substantial amounts of sorbitol, whereas celery translocated mannitol as well. Sucrose was always present in vacuole and cytosol of mesophyll cells, whereas sorbitol and mannitol were found in vacuole, stroma, and cytosol in all cases except for sea plantain. The concentration of sorbitol, mannitol and sucrose in phloem sap was 2- to 40-fold higher than that in the cytosol of mesophyll cells. Apoplastic carbohydrate concentrations in all species tested were in the low millimolar range versus high millimolar concentrations in symplastic compartments. Therefore, the concentration ratios between the apoplast and the phloem were very strong, ranging between 20- to 100-fold for sorbitol and mannitol, and between 200- and 2000-fold for sucrose. The woody species, peach, showed the smallest concentration ratios between the cytosol of mesophyll cells and the phloem as well as between the apoplast and the phloem, suggesting a mixture of apoplastic and symplastic phloem loading, in contrast to the herbal plant species (common plantain, sea plantain, celery) which likely exhibit an active loading mode for sorbitol and mannitol as well as sucrose from the apoplast into the phloem. PMID:18188589

  17. Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.

    PubMed

    Damián-Almazo, Juanita Yazmin; Moreno, Alina; López-Munguía, Agustin; Soberón, Xavier; González-Muñoz, Fernando; Saab-Rincón, Gloria

    2008-08-01

    AmyA, an alpha-amylase from the hyperthermophilic bacterium Thermotoga maritima, is able to hydrolyze internal alpha-1,4-glycosidic bonds in various alpha-glucans at 85 degrees C as the optimal temperature. Like other glycoside hydrolases, AmyA also catalyzes transglycosylation reactions, particularly when oligosaccharides are used as substrates. It was found that when methanol or butanol was used as the nucleophile instead of water, AmyA was able to catalyze alcoholysis reactions. This capability has been evaluated in the past for some alpha-amylases, with the finding that only the saccharifying fungal amylases from Aspergillus niger and from Aspergillus oryzae present measurable alcoholysis activity (R. I. Santamaria, G. Del Rio, G. Saab, M. E. Rodriguez, X. Soberon, and A. Lopez, FEBS Lett. 452:346-350, 1999). In the present work, we found that AmyA generates larger quantities of alkyl glycosides than any amylase reported so far. In order to increase the alcoholytic activity observed in AmyA, several residues were identified and mutated based on previous analogous positions in amylases, defining the polarity and geometry of the active site. Replacement of residue His222 by glutamine generated an increase in the alkyl glucoside yield as a consequence of a higher alcoholysis/hydrolysis ratio. The same change in specificity was observed for the mutants H222E and H222D, but instability of these mutants toward alcohols decreased the yield of alkyl glucoside. PMID:18552192

  18. Constitutive high-level expression of a codon-optimized β-fructosidase gene from the hyperthermophile Thermotoga maritima in Pichia pastoris.

    PubMed

    Menéndez, Carmen; Martínez, Duniesky; Trujillo, Luis E; Mazola, Yuliet; González, Ernesto; Pérez, Enrique R; Hernández, Lázaro

    2013-02-01

    Enzymes for use in the sugar industry are preferred to be thermotolerant. In this study, a synthetic codon-optimized gene encoding a highly thermostable β-fructosidase (BfrA, EC 3.2.1.26) from the bacterium Thermotoga maritima was expressed in the yeast Pichia pastoris. The gradual increase of the transgene dosage from one to four copies under the control of the constitutive glyceraldehyde 3-phosphate dehydrogenase promoter had an additive effect on BfrA yield without causing cell toxicity. Maximal values of cell biomass (115 g/l, dry weight) and overall invertase activity (241 U/ml) were reached at 72 h in fed-batch fermentations using cane sugar as the main carbon source for growth. Secretion driven by the Saccharomyces cerevisiae α-factor signal peptide resulted in periplasmic retention (44 %) and extracellular release (56 %) of BfrA. The presence of N-linked oligosaccharides did not influence the optimal activity, thermal stability, kinetic properties, substrate specificity, and exo-type action mode of the yeast-secreted BfrA in comparison to the native unglycosylated enzyme. Complete inversion of cane sugar at initial concentration of 60 % (w/v) was achieved by periplasmic BfrA in undisrupted cells reacting at pH 5.5 and 70 °C, with average productivity of 4.4 g of substrate hydrolyzed per grams of biomass (wet weight) per hour. The high yield of fully active glycosylated BfrA here attained by recombinant P. pastoris in a low-cost fermentation process appears to be attractive for the large-scale production of this thermostable enzyme useful for the manufacture of inverted sugar syrup. PMID:22821437

  19. Crystal structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains

    SciTech Connect

    Zheng, Meiying; Cooper, David; Grossoehmerb, Nickolas; Yu, Minmin; Hung, Li-Wei; Cieslik, Murcin; Derewendaro, Urszula; Lesley, Scott; Wilson, Ian; Giedrocb, David; Derewenda, Zygmunt

    2009-06-06

    The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged helix (WH) DNA-binding domains and diverse C-terminal, regulatory domains, which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all a-helical regulatory domains classified into two related Pfam families: FadR{_}C and FCD. Only two crystal structures of the FadR family members, i.e. the E. coli FadR protein and the LldR from C. glutamicum, have been described to date in literature. Here we describe the crystal structure of TM0439, a GntR regulator with an FCD domain, found in the Thermotoga maritima genome. The FCD domain is similar to that of the LldR regulator, and contains a buried metal binding site. Using atomic absorption spectroscopy and Trp fluorescence, we show that the recombinant protein contains bound Ni{sup 2+} ions, but it is able to bind Zn{sup 2+} with K{sub D} < 70 nM . We conclude that Zn{sup 2+} is the likely physiological metal, where it may perform either or both structural and regulatory roles. Finally, we compare the TM0439 structure to two other FadR family structures recently deposited by Structural Genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.

  20. Contrasting effects of ecosystem engineering by the cordgrass Spartina maritima and the sandprawn Callianassa kraussi in a marine-dominated lagoon

    NASA Astrophysics Data System (ADS)

    Pillay, D.; Branch, G. M.; Dawson, J.; Henry, D.

    2011-01-01

    Ecosystem engineering by plants and animals significantly influences community structure and the physico-chemical characteristics of marine habitats. In this paper we document the contrasting effects of ecosystem engineering by the cordgrass Spartina maritima and the burrowing sandprawn Callianassa kraussi on physico-chemical characteristics, microflora, macrofaunal community structure and morphological attributes in the high shore intertidal sandflats of Langebaan Lagoon, a marine-dominated system on the west coast of South Africa. Comparisons were made at six sites in the lagoon within Spartina and Callianassa beds, and in a "bare zone" of sandflat between these two habitats that lacks both sandprawns and cordgrass. Sediments in Spartina habitats were consolidated by the root-shoot systems of the cordgrass, leading to low sediment penetrability, while sediments in beds of C. kraussi were more penetrable, primarily due to the destabilising effects of sandprawn bioturbation. Sediments in the "bare zone" had intermediate to low values of penetrability. Sediment organic content was lowest in bare zones and greatest in Spartina beds, while sediment chl- a levels were greatest on bare sand, but were progressively reduced in the Spartina and Callianassa beds. These differences among habitats induced by ecosystem engineering in turn affected the macrofauna. Community structure was different between all three habitats sampled, with species richness being surprisingly greater in Callianassa beds than either the bare zone or Spartina beds. In general, the binding of surface sediments by the root systems of Spartina favoured rigid-bodied, surface-dwelling and tube-building species, while the destabilising effect of bioturbation by C. kraussi favoured burrowing species. The contrasting effects of these ecosystem engineers suggest that they play important roles in increasing habitat heterogeneity. Importantly, the role of bioturbation by C. kraussi in enhancing macrofaunal richness was unexpected. By loosening sediments, reducing anoxia and enhancing organic content, C. kraussi may engineer these high shore habitats to ameliorate environmental stresses or increase food availability.

  1. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima-ancestor of all beet crops-and modern sugar beets.

    PubMed

    Zachow, Christin; Müller, Henry; Tilcher, Ralf; Berg, Gabriele

    2014-01-01

    The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8%) than for sugar beet (≤57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes. PMID:25206350

  2. Structural and biochemical characterization of the β-N-acetylglucosaminidase from Thermotoga maritima: toward rationalization of mechanistic knowledge in the GH73 family.

    PubMed

    Lipski, Alexandra; Hervé, Mireille; Lombard, Vincent; Nurizzo, Didier; Mengin-Lecreulx, Dominique; Bourne, Yves; Vincent, Florence

    2015-03-01

    Members of the GH73 glycosidase family cleave the β-1,4-glycosidic bond between the N-acetylglucosaminyl (GlcNAc) and N-acetylmuramyl (MurNAc) moieties in bacterial peptidoglycan. A catalytic mechanism has been proposed for members FlgJ, Auto, AcmA and Atl(WM) and the structural analysis of FlgJ and Auto revealed a conserved α/β fold reminiscent of the distantly related GH23 lysozyme. Comparison of the active site residues reveals variability in the nature of the catalytic general base suggesting two distinct catalytic mechanisms: an inverting mechanism involving two distant glutamate residues and a substrate-assisted mechanism involving anchimeric assistance by the C2-acetamido group of the GlcNAc moiety. Herein, we present the biochemical characterization and crystal structure of TM0633 from the hyperthermophilic bacterium Thermotoga maritima. TM0633 adopts the α/β fold of the family and displays β-N-acetylglucosaminidase activity on intact peptidoglycan sacculi. Site-directed mutagenesis identifies Glu34, Glu65 and Tyr118 as important residues for catalysis. A thorough bioinformatic analysis of the GH73 sequences identified five phylogenetic clusters. TM0633, FlgJ and Auto belong to a group of three clusters that conserve two carboxylate residues involved in a classical inverting acid-base mechanism. Members of the other two clusters lack a conserved catalytic general base supporting a substrate-assisted mechanism. Molecular modeling of representative members from each cluster suggests that variability in length of the β-hairpin region above the active site confers ligand-binding specificity and modulates the catalytic mechanisms within the GH73 family. PMID:25344445

  3. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima.

    PubMed

    Ruggiero, Alessia; Dattelbaum, Jonathan D; Staiano, Maria; Berisio, Rita; D'Auria, Sabato; Vitagliano, Luigi

    2014-01-01

    The arginine binding protein from Thermatoga maritima (TmArgBP), a substrate binding protein (SBP) involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule. The availability of an accurate 3D model represents a powerful tool for the design of new TmArgBP suited for biotechnological applications. PMID:24832102

  4. Post-translational Modification of Ribosomal Proteins: Structural and Functional Characterization of RimO from Thermotoga maritima, a Radical S-adenosylmethionine methylthiotransferase

    SciTech Connect

    Arragain, S.; Latour, J; Forouhar, F; Neely, H; Montelione, G; Hunt, J; Mulliez, E; Fontecave, M; Atta, M; et al.

    2010-01-01

    Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 {angstrom} crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

  5. Post-translational Modification of Ribosomal Proteins - Structural and Functional Characterization of RimO from Thermotoga Maritima, A Radiacal S-Adenosylmethionine Methylthiotransferase

    SciTech Connect

    Arragain, S.; Garcia-Serres, R; Blondin, G; Douki, T; Clemancey, M; Latour, J; Forouhar, F; Neely, H; Montelione, G; et. al.

    2010-01-01

    Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 {angstrom} crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.

  6. Exploring Phylogeographic Congruence in a Continental Island System

    PubMed Central

    Goldberg, Julia; Trewick, Steven A.

    2011-01-01

    A prediction in phylogeographic studies is that patterns of lineage diversity and timing will be similar within the same landscape under the assumption that these lineages have responded to past environmental changes in comparable ways. Eight invertebrate taxa from four different orders were included in this study of mainland New Zealand and Chatham Islands lineages to explore outcomes of island colonization. These comprised two orthopteran genera, one an endemic forest-dwelling genus of cave weta (Rhaphidophoridae, Talitropsis) and the other a grasshopper (Acrididae, Phaulacridum) that inhabits open grassland; four genera of Coleoptera including carabid beetles (Mecodema), stag beetles (Geodorcus), weevils (Hadramphus) and clickbeetles (Amychus); the widespread earwig genus Anisolabis (Dermaptera) that is common on beaches in New Zealand and the Chatham Islands, and an endemic and widespread cockroach genus Celatoblatta (Blattodea). Mitochondrial DNA data were used to reconstruct phylogeographic hypotheses to compare among these taxa. Strikingly, despite a maximum age of the Chathams of ∼4 million years there is no concordance among these taxa, in the extent of genetic divergence and partitioning between Chatham and Mainland populations. Some Chatham lineages are represented by insular endemics and others by haplotypes shared with mainland populations. These diverse patterns suggest that combinations of intrinsic (taxon ecology) and extrinsic (extinction and dispersal) factors can result in apparently very different biogeographic outcomes. PMID:26467734

  7. Genetic structure and gene flow in Beta vulgaris subspecies maritima along the Atlantic coast of France

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Locating and quantifying genetic variation within crop wild relatives is an ongoing activity of gene banks tasked with ex situ conservation. Without detailed information about the population genetics of a species geography often serves as a reasonable proxy for differentiation. With this in mind, ...

  8. Cytotoxicity of the Sesquiterpene Lactones Neoambrosin and Damsin from Ambrosia maritima Against Multidrug-Resistant Cancer Cells

    PubMed Central

    Saeed, Mohamed; Jacob, Stefan; Sandjo, Louis P.; Sugimoto, Yoshikazu; Khalid, Hassan E.; Opatz, Till; Thines, Eckhard; Efferth, Thomas

    2015-01-01

    Multidrug resistance is a prevailing phenomenon leading to chemotherapy treatment failure in cancer patients. In the current study two known cytotoxic pseudoguaianolide sesquiterpene lactones; neoambrosin (1) and damsin (2) that circumvent MDR were identified. The two cytotoxic compounds were isolated using column chromatography, characterized using 1D and 2D NMR, MS, and compared with literature values. The isolated compounds were investigated for their cytotoxic potential using resazurin assays and thereafter confirmed with immunoblotting and in silico studies. MDR cells overexpressing ABC transporters (P-glycoprotein, BCRP, ABCB5) did not confer cross-resistance toward (1) and (2), indicating that these compounds are not appropriate substrates for any of the three ABC transporters analyzed. Resistance mechanisms investigated also included; the loss of the functions of the TP53 and the mutated EGFR. The HCT116 p53-/- cells were sensitive to 1 but resistant to 2. It was interesting to note that resistant cells transfected with oncogenic ΔEGFR exhibited hypersensitivity CS toward (1) and (2) (degrees of resistances were 0.18 and 0.15 for (1) and (2), respectively). Immunoblotting and in silico analyses revealed that 1 and 2 silenced c-Src kinase activity. It was hypothesized that inhibition of c-Src kinase activity may explain CS in EGFR-transfected cells. In conclusion, the significant cytotoxicity of 1 and 2 against different drug-resistant tumor cell lines indicate that they may be promising candidates to treat refractory tumors. PMID:26617519

  9. Local and global influences on population declines of coastal waders: Purple Sandpiper Calidris maritima numbers in the Moray Firth, Scotland

    NASA Astrophysics Data System (ADS)

    Summers, Ron W.; Foster, Simon; Swann, Bob; Etheridge, Brian

    2012-05-01

    Declines in numbers by several wader species in Britain have been linked to climate change, but the mechanism for the declines has rarely been explored. Britain lies at the northern end of the East Atlantic Flyway, and supports 1.3 million out of the Flyway's 8.5 million coastal waders (Charadrii) in winter and the Purple Sandpiper is one of the species whose numbers have declined. Here, we examine the dynamics of the decline as observed in the Moray Firth, northeast Scotland, investigating whether the decline was due to poorer apparent survival (return rate) or poorer recruitment of young birds. The maximum number in the Moray Firth declined from 860 in 1987/88 to 236 in 2006/07, with some increase during winters 2007/08 and 2008/09. At the three main high-tide roosts (Balintore, Lossiemouth and Buckie) the maximum combined number declined from 574 to 90. Changes in survival and recruitment (percentage of first-year birds) were examined at these roosts from captured samples, which were ringed and recaptured. There were no significant changes between winters in survival rates, nor were there differences between the survival rates of age groups (first-year and adult) or bill size groups, which represented birds of different sex and breeding origin. Annual survival estimates for the three roosts ranged from 72 to 77%. The percentage of first-year birds varied among roosts and years; the lowest values were during the late 1980s/early 1990s and early 2000s. A free-running population model incorporating varying percentages of first-year birds and constant mortality for each roost provided a plausible explanation for the decline. Although modelled numbers followed the observed pattern, a discrepancy in one year was carried forward in subsequent years, so that the fit with the observed numbers was parallel rather than similar. However, it seems that the decline in numbers was largely due to poorer recruitment. We discuss whether breeding success had declined, whether the population had responded to changes in the local sewage treatment systems, which could affect invertebrate food for Purple Sandpipers, or whether fewer birds chose to winter in Scotland. The Moray Firth population is derived from Norway and possibly Canada, and there is evidence that the Norwegian population was disproportionately affected. The reason for poor recruitment requires further study, and other wader species require examination to test if poor recruitment is a common feature of decline in numbers.

  10. The feasibility and efficacy of early-season releases of a generalist predator (Forficula auricularia L.) to control populations of the RAA (Dysaphis plantaginea Passerini) in Southeastern France.

    PubMed

    Dib, H; Jamont, M; Sauphanor, B; Capowiez, Y

    2016-04-01

    Augmentative biological control is not commonly used in commercial orchards. We used an exclusion system to evaluate the potential of early-season releases of the European earwig (Forficula auricularia L., Dermaptera: Forficulidae) for control of the rosy apple aphid (Dysaphis plantaginea Passerini, Hemiptera: Aphididae) in the spring of 2009 in two pesticide-free apple orchards. In order to conduct this experiment we successfully reared earwigs with a high survival rate of nymphs (more than 96%) which may have commercial application. There were three treatments in the study: (i) a 'release treatment' where we confined the released earwigs in the canopy by using a barrier system; (ii) an 'exclusion treatment' where we blocked free access of earwigs into the canopy using the same barrier system; and (iii) a 'control treatment' that represented the natural situation. Contrary to expectations, earwig releases did not reduce D. plantaginea populations. In general, the abundance of natural enemies and their groups did not differ significantly among treatments, except for earwigs. We observed that the exclusion systems we used successfully kept both earwigs and ants away from tree canopies; total numbers on trees in the 'exclusion treatment' were significantly lower than on the other two treatments. Due to the complexity and difficulty of evaluating augmentative releases of natural enemies in open orchard conditions, we conclude that new technical approaches to control site conditions are needed when conducting such studies. PMID:26780826

  11. An anterior medial cell population with an apical-organ-like transcriptional profile that pioneers the central nervous system in the centipede Strigamia maritima.

    PubMed

    Hunnekuhl, Vera S; Akam, Michael

    2014-12-01

    The apical plate of primary marine larvae is characterized by a common set of transcription factors comprising six3, rx, hbn, nk2.1 and FoxQ2. It harbours the apical organ, a neural and ciliary structure with neurosecretory properties. Recent studies in lophotrochozoans have found that apical organ cells form the anterior tip of the developing central nervous system. We identify an anterior medial tissue in the embryonic centipede head that shares the transcriptional profile of the apical plate of marine larvae, including nested domains of FoxQ2 and six3 expression. This domain gives rise to an anterior medial population of neural precursors distinct from those arising within the segmental neuroectoderm. These medial cells do not express achaete scute homologue in proneural clusters, but express collier, a marker for post mitotic cells committed to a neural fate, while they are still situated in the surface ectodermal layer. They then sink under the surface to form a compact cell cluster. Once internalized these cells extend axons that pioneer the primary axonal scaffold of the central nervous system. The same cells express phc2, a neural specific prohormone convertase, which suggests that they form an early active neurosecretory centre. Some also express markers of hypothalamic neurons, including otp, vtn and vax1. These medial neurosecretory cells of the centipede are distinct from those of the pars intercerebralis, the anterior neurosecretory part of the insect brain. The pars intercerebralis derives from vsx positive placodal-like invagination sites. In the centipede, vsx expressing invaginating ectoderm is situated bilaterally adjacent to the medial pioneer cell population. Hence the pars intercerebralis is present in both insect and centipede brains, whereas no prominent anterior medial cluster of pioneer neurons is present in insects. These observations suggest that the arthropod brain retained ancestrally an anterior medial population of neurosecretory cells homologous to those of the apical plate in other invertebrate phyla, but that this cell population has been lost or greatly reduced in insects. PMID:25263198

  12. Vegetation dynamics and plant species interactions under grazed and ungrazed conditions in a western European salt marsh

    NASA Astrophysics Data System (ADS)

    Tessier, Marc; Vivier, Jean-Paul; Ouin, Annie; Gloaguen, Jean-Claude; Lefeuvre, Jean-Claude

    2003-05-01

    Experiments in exclosures were conducted on a salt marsh in a macrotidal system in western France. The aim of this study was threefold: (1) to compare vegetation dynamics over a period of 8 years in grazed and ungrazed conditions (2) to investigate the response of annual species to grazing duration during seedling establishment (3) to test the effect of an increase in soil nitrogen availability after cessation of grazing on interactions between Suaeda maritima and Puccinellia maritima. In grazed conditions, during all the survey, vegetation was dominated by a short P. maritima sward with the annual Salicornia europaea in the lower and middle marshes. However, after cessation of grazing in 1994, a homogeneous matrix of the forb Halimione portulacoides, quickly replaced P. maritima in the well drained lower marsh. At the middle marsh level, fine sediment and poor drainage maintained P. maritima while the annual S. maritima which tolerates taller and denser vegetation replaced S. europaea. Elymus pungens cover was limited till 2000 but its rising in 2001 let expect its dominance in the future. While P. maritima abundance remained high, spring abundance of annual species such as S. europaea and S. maritima globally decreased with sheep grazing duration on the salt marsh between February and June. Experiments with monocultures of P. maritima and S. maritima demonstrated that nitrogen was a limiting factor on the salt marsh. In a mixed community, a moderate application of nitrogen (15 g N m -2 year -1 as NH 4-NO 3) promoted growth of P. maritima and limited the biomass of S. maritima, but growth of the latter was enhanced by a high application of nitrogen (30 g N m -2 year -1). An increase in the abundance of annuals such as S. maritima on the salt marsh is discussed.

  13. Epilogue to Special Issue on Developmental Robotics: Can Experiments with Machines Inform Theory in Infant Development?

    ERIC Educational Resources Information Center

    Prince, Christopher G.

    2008-01-01

    Developmental robotics has forwarded a range of models of development and behaviours. With the variety of systems that have been created, and with some of these approximating prominent human behaviours (e.g. joint attention, word learning, imitation), one may argue that developmental robotics has started to go past robotic models of earwigs

  14. Host-parasite relationship between colonial terns and bacteria is modified by a mutualism with a plant with antibacterial defenses.

    PubMed

    Møller, Anders Pape; Flensted-Jensen, Einar; Mardal, Willy; Soler, J J

    2013-09-01

    Predator-prey and host-parasite interactions and mutualisms are common and may have profound effects on ecosystems. Here we analyze the parasitic and mutualistic associations between three groups of organisms: the plant Artemisia maritima, bacteria, and a colonial seabird (the sandwich tern Sterna sandvicensis) that breeds in dense colonies covered in feces produced by both adults and chicks. A disproportionately large fraction of colonies of the sandwich tern in Denmark were located in patches covered by A. maritima. This association was specific for the densely colonial sandwich tern, but was not present for four other sympatric species of terns that breed in much less dense colonies. A. maritima reduced the abundance of pathogenic Staphylococcus on chicken eggshells in a field experiment. Recruitment by sandwich terns breeding in patches of A. maritima was 18 % higher than for sandwich terns breeding in the absence of A. maritima. A. maritima benefitted from the association with sandwich terns due to the supply of nutrients from feces and uneaten food lost by young. These findings are consistent with sandwich terns exploiting the association with A. maritima and its antimicrobial properties to improve their reproductive success, while sandwich terns and A. maritima are involved in a mutualistic interaction. PMID:23404068

  15. An Insight into the Interaction Mode Between CheB and Chemoreceptor from Two Crystal Structures of CheB Methylesterase Catalytic Domain

    SciTech Connect

    K Cho; B Crane; S Park

    2011-12-31

    We have determined 2.2 {angstrom} resolution crystal structure of Thermotoga maritima CheB methylesterase domain to provide insight into the interaction mode between CheB and chemoreceptors. T. maritima CheB methylesterase domain has identical topology of a modified doubly-wound {alpha}/{beta} fold that was observed from the previously reported Salmonella typhimurium counterpart, but the analysis of the electrostatic potential surface near the catalytic triad indicated considerable charge distribution difference. As the CheB demethylation consensus sites of the chemoreceptors, the CheB substrate, are not uniquely conserved between T. maritima and S. typhimurium, such surfaces with differing electrostatic properties may reflect CheB regions that mediate protein-protein interaction. Via the computational docking of the two T. maritima and S. typhimurium CheB structures to the respective T. maritima and Escherichia coli chemoreceptors, we propose a CheB:chemoreceptor interaction mode.

  16. Which insect species numerically respond to allochthonous inputs?

    PubMed

    Sugiura, Shinji; Ikeda, Hiroshi

    2013-08-01

    Herons (Ardeidae) frequently breed in inland forests and provide organic material in the form of carcasses of prey (that they drop) and chicks (that die) to the forest floor. Such allochthonous inputs of organic materials are known to increase arthropod populations in forests. However, the exact species that show numerical responses to allochthonous inputs in heron breeding colonies remains unclear. Very few studies have clarified which factors determine numerical responses in individual species. We used pitfall and baited traps to compare the densities of arthropods between forest patches in heron breeding colonies (five sites) and areas outside of colonies (five sites) in central Japan. The density of all arthropods was not significantly different between colonies and non-colony areas. However, significant differences between colonies and non-colony areas were found in four arthropod groups. Earwigs (Dermaptera: Anisolabididae), hister beetles (Coleoptera: Histeridae), and carrion beetles (Coleoptera: Silphidae) were more abundant in colonies, while ants (Hymenoptera: Formicidae) were less abundant in colonies. We detected numerical responses to heron breeding in two earwig, one histerid, five silphid, and one ant species. Chick and prey carcasses from herons may have directly led to increases in consumer populations such as earwigs, histerids, and silphids in colonies, while microenvironmental changes caused by heron breeding may have reduced ant abundance. In the Silphidae, five species showed numerical responses to allochthonous inputs, and the other two species did not. Numerical responses in individual species may have been determined by life history traits such as reproductive behaviour. PMID:23780624

  17. Which insect species numerically respond to allochthonous inputs?

    NASA Astrophysics Data System (ADS)

    Sugiura, Shinji; Ikeda, Hiroshi

    2013-08-01

    Herons (Ardeidae) frequently breed in inland forests and provide organic material in the form of carcasses of prey (that they drop) and chicks (that die) to the forest floor. Such allochthonous inputs of organic materials are known to increase arthropod populations in forests. However, the exact species that show numerical responses to allochthonous inputs in heron breeding colonies remains unclear. Very few studies have clarified which factors determine numerical responses in individual species. We used pitfall and baited traps to compare the densities of arthropods between forest patches in heron breeding colonies (five sites) and areas outside of colonies (five sites) in central Japan. The density of all arthropods was not significantly different between colonies and non-colony areas. However, significant differences between colonies and non-colony areas were found in four arthropod groups. Earwigs (Dermaptera: Anisolabididae), hister beetles (Coleoptera: Histeridae), and carrion beetles (Coleoptera: Silphidae) were more abundant in colonies, while ants (Hymenoptera: Formicidae) were less abundant in colonies. We detected numerical responses to heron breeding in two earwig, one histerid, five silphid, and one ant species. Chick and prey carcasses from herons may have directly led to increases in consumer populations such as earwigs, histerids, and silphids in colonies, while microenvironmental changes caused by heron breeding may have reduced ant abundance. In the Silphidae, five species showed numerical responses to allochthonous inputs, and the other two species did not. Numerical responses in individual species may have been determined by life history traits such as reproductive behaviour.

  18. Agronomy of strip intercropping broccoli with alyssum for biological control of aphids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Organic broccoli growers in California typically control aphids by intercropping broccoli with strips of alyssum (Lobularia maritima (L.) Desv.) which attracts hoverflies (Diptera: Syrphidae) that are important predators of aphids. A three year study with transplanted organic broccoli in Salinas, ...

  19. A floral-derived compound attractive to the tephritid fruit fly parasitoid Diachasmimorpha longicaudata (Hymenoptera: Braconidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many adult hymenopteran parasitoids, even host-feeding species, consume the nectar of flowering plants. Previous field studies had identified plants attractive (Lobularia maritima L.) and unattractive (Spermacoce verticillata L) to certain opiine braconids (Hymenoptera). Under laboratory conditions,...

  20. Cues of Maternal Condition Influence Offspring Selfishness

    PubMed Central

    Wong, Janine W. Y.; Lucas, Christophe; Kölliker, Mathias

    2014-01-01

    The evolution of parent-offspring communication was mostly studied from the perspective of parents responding to begging signals conveying information about offspring condition. Parents should respond to begging because of the differential fitness returns obtained from their investment in offspring that differ in condition. For analogous reasons, offspring should adjust their behavior to cues/signals of parental condition: parents that differ in condition pay differential costs of care and, hence, should provide different amounts of food. In this study, we experimentally tested in the European earwig (Forficula auricularia) if cues of maternal condition affect offspring behavior in terms of sibling cannibalism. We experimentally manipulated female condition by providing them with different amounts of food, kept nymph condition constant, allowed for nymph exposure to chemical maternal cues over extended time, quantified nymph survival (deaths being due to cannibalism) and extracted and analyzed the females’ cuticular hydrocarbons (CHC). Nymph survival was significantly affected by chemical cues of maternal condition, and this effect depended on the timing of breeding. Cues of poor maternal condition enhanced nymph survival in early broods, but reduced nymph survival in late broods, and vice versa for cues of good condition. Furthermore, female condition affected the quantitative composition of their CHC profile which in turn predicted nymph survival patterns. Thus, earwig offspring are sensitive to chemical cues of maternal condition and nymphs from early and late broods show opposite reactions to the same chemical cues. Together with former evidence on maternal sensitivities to condition-dependent nymph chemical cues, our study shows context-dependent reciprocal information exchange about condition between earwig mothers and their offspring, potentially mediated by cuticular hydrocarbons. PMID:24498046

  1. Piper kelleyi, a hotspot of ecological interactions and a new species from Ecuador and Peru

    PubMed Central

    Tepe, Eric. J.; Rodríguez-Castañeda, Genoveva; Glassmire, Andrea E.; Dyer, Lee A.

    2014-01-01

    Abstract We describe Piper kelleyi sp. nov., a new species from the eastern Andes of Ecuador and Peru, named in honor of Dr. Walter Almond Kelley. Piper kelleyi is a member of the Macrostachys clade of the genus Piper and supports a rich community of generalist and specialist herbivores, their predators and parasitoids, as well as commensalistic earwigs, and mutualistic ants. This new species was recognized as part of an ecological study of phytochemically mediated relationships between plants, herbivores, predators, and parasitoids. Compared to over 100 other Piper species surveyed, Piper kelleyi supports the largest community of specialist herbivores and parasitoids observed to date. PMID:24596490

  2. Sugar Transport and Metabolism in Thermotoga

    SciTech Connect

    Noll, Kenneth M.; Romano, Antonio H.

    2003-02-11

    The work conducted under this grant demonstrated that the hyperthermophilic bacterium Thermotoga neapolitana carries out glucose and lactose transport in a sodium-dependent manner and that energization of anaerobic cells is required to observe transport. We also demonstrated that Thermotoga maritima carries out maltose and glucose transport using periplasmic sugar binding proteins. We began defining patterns of expression of genes encoding sugar transport and catabolic functions in both T. maritima and T. neapolitana. We began a collaborative effort to identify all the genes regulated at the transcriptional level in response to sugars substrates. These funds also allowed us to begin an examination of the functions of several periplasmic substrate binding proteins encoded in the genome of T. maritima.

  3. Genome Sequence of Thermotoga sp Strain RQ2, a Hyperthermophilic Bacterium Isolated from a Geothermally Heated Region of the Seafloor near Ribeira Quente, the Azores

    SciTech Connect

    Swithers, Kristen S; DiPippo, Jonathan L; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Woyke, Tanja; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Mikhailova, Natalia; Lykidis, A; Land, Miriam L; Stetter, Karl O; Nelson, Karen E; Gogarten, Peter; Noll, Kenneth M

    2011-01-01

    Thermotoga sp. strain RQ2 is probably a strain of Thermotoga maritima. Its complete genome sequence allows for an examination of the extent and consequences of gene flow within Thermotoga species and strains. Thermotoga sp. RQ2 differs from T. maritima in its genes involved in myo-inositol metabolism. Its genome also encodes an apparent fructose phosphotransferase system (PTS) sugar transporter. This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales.

  4. Paternal signature in kin recognition cues of a social insect: concealed in juveniles, revealed in adults

    PubMed Central

    Wong, Janine W. Y.; Meunier, Joël; Lucas, Christophe; Kölliker, Mathias

    2014-01-01

    Kin recognition is a key mechanism to direct social behaviours towards related individuals or avoid inbreeding depression. In insects, recognition is generally mediated by cuticular hydrocarbon (CHC) compounds, which are partly inherited from parents. However, in social insects, potential nepotistic conflicts between group members from different patrilines are predicted to select against the expression of patriline-specific signatures in CHC profiles. Whereas this key prediction in the evolution of insect signalling received empirical support in eusocial insects, it remains unclear whether it can be generalized beyond eusociality to less-derived forms of social life. Here, we addressed this issue by manipulating the number of fathers siring clutches tended by females of the European earwig, Forficula auricularia, analysing the CHC profiles of the resulting juvenile and adult offspring, and using discriminant analysis to estimate the information content of CHC with respect to the maternal and paternal origin of individuals. As predicted, if paternally inherited cues are concealed during family life, increases in mating number had no effect on information content of CHC profiles among earwig juveniles, but significantly decreased the one among adult offspring. We suggest that age-dependent expression of patriline-specific cues evolved to limit the risks of nepotism as family-living juveniles and favour sibling-mating avoidance as group-living adults. These results highlight the role of parental care and social life in the evolution of chemical communication and recognition cues. PMID:25165768

  5. Rhizoctonia Crown and Root Rot Resistance of Beta Plant Introductions from the USDA, Agricultural Research Service's National Plant Germplasm System, 2010

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty wild beet (Beta vulgaris subsp. maritima (L.) Arcang) plant introduction (PI) accessions from the Beta collection of the USDA-ARS National Plant Germplasm System were screened for resistance to Rhizoctonia root and crown rot, at the USDA-ARS Fort Collins, CO Research Farm. The Rhizoctonia sc...

  6. Beet curly top resistance of USDA-ARS National Plant Germplasm System plant introductions, 2010

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twenty-six wild beet (Beta vulgaris subsp. maritima (L.) Arcang) accessions from the Beta collection of the USDA-ARS National Plant Germplasm System were screened for resistance to Beet severe curly top virus (BSCTV) and other closely related Curtovirus species in 2010. The curly top evaluation was...

  7. Genome evolution: groping in the soil interstices.

    PubMed

    Minelli, Alessandro

    2015-03-01

    Centipedes are a very old lineage of terrestrial animals. The first completely sequenced myriapod genome reveals that the blind centipede Strigamia maritima has no gene for light-sensory proteins, lacks the canonical circadian clock and possesses unusual features related to chemosensory perception. PMID:25734267

  8. Evaluation of genetic diversity and root traits of sea beet accessions of the Adriatic Sea coast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty nine sea beet [Beta vulgaris L. subsp. maritima (L.) Arcang.] accessions of the Adriatic coast were screened genetically and for their adaptive morpho-functional root traits in order to identify new sources of abiotic resistances for sugar beet breeding programs. Genetic diversity was evaluat...

  9. Molecular and Morpho-Physiological Characterization of Sea, Ruderal and Cultivated Beets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta vulgaris genetic resources are essential for broadening genetic base of sugar beet and developing cultivars adapted to adverse environmental conditions. Wild beets (sea beets, B. vulgaris spp. maritima and their naturalized introgressions with cultivated beets known as ruderal beets) harbor su...

  10. Chromatographic fingerprint analysis of Pycnogenol® dietary supplements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    French maritime bark (Pinus maritima) has been widely used as an herbal remedy for various degenerative diseases. A standardized bark extract is available that complies with its USP monograph and is derived from Pinus pinaster, Ait. (Pycnogenol®, Horphag Research Ltd., UK). The method specified in...

  11. A CLEAVED AMPLIFIED POLYMORPHIC SEQUENCE (CAPS) MARKER ASSOCIATED WITH ROOT-KNOT NEMATODE IN SUGAR BEET (BETA VULGARIS L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance to root-knot nematode (Meloidogyne spp.) was introgressed into sugarbeet (Beta vulgaris L.) from wild beet [B. vulgaris ssp. maritima (L.) Arcang] and was demonstrated to be dominant and simply inherited. Since resistance conferred by this gene was effective against six different species...

  12. Registration of EL54 and EL55 sugarbeet germplasms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    EL54 (PI 654357) is a sugarbeet germplasm derived from wild beet (Beta vulgaris ssp. maritima) accession WB879 (PI 540625), released in the interest of broadening the genetic base of sugar beet. The parent accession WB879, collected in 1989 from Port-de-Houet, France. EL54 has shown excellent Aphan...

  13. Release of EL54 Sugarbeet Germplasm Derived from WB879 Wild Germplasm With Resistance to Aphanomyces and Excellent Stand Establishment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    EL54 (PI 654357) is a sugarbeet germplasm derived from wild beet (Beta vulgaris ssp. maritima) accession WB879 (PI 540625). EL54 is being released in the interest of broadening the genetic base of sugar beet. The parent accession WB879, collected in 1989 from Port-de-Houet, France (3 m elevation), w...

  14. A tale of two spartinas: Climatic, photobiological and isotopic insights on the fitness of non-indigenous versus native species

    NASA Astrophysics Data System (ADS)

    Duarte, B.; Baeta, A.; Rousseau-Gueutin, M.; Ainouche, M.; Marques, J. C.; Caçador, I.

    2015-12-01

    Salt marshes are facing a new threat: the invasion by non-indigenous species (NIS), Although its introduction time is not established yet, in 1999 Spartina versicolor was already identified as a NIS in the Mediterranean marshes, significantly spreading its area of colonization. Using the Mediterranean native Spartina maritima as a reference, the present research studied the ecophysiological fitness of this NIS in its new environment, as a tool to understand its potential invasiveness. It was found that Spartina versicolor had a stable photobiological pattern, with only minor fluctuations during an annual cycle, and lower efficiencies comparated to S. maritima. The NIS seems to be rather insensitive to the observed abiotic factors fluctuations (salinity and pH of the sediment), and thus contrasts with the native S. maritima, known to be salinity dependent with higher productivity values in higher salinity environments. Most of the differences observed between the photobiology of these species could be explained by their nitrogen nutrition (here evaluated by the δ15N stable isotope) and directly related with the Mediterranean climate. Enhanced by a higher N availability during winter, the primary production of S. maritima which lead to dilution of the foliar δ15N concentration in the newly formed biomass, similarly to what is observed along a rainfall gradient. On the other hand, S. versicolor showed an increased δ15N in its tissues along the annual rainfall gradient, probably due to a δ15N concentration effect during low biomass production periods (winter and autumn). Together with the photobiological traits, these isotopic data point out to a climatic misfit of S. versicolor to the Mediterranean climate compared to the native S. maritima. This appears to be the major constrain shaping the ecophysiological fitness of this NIS, its primary production and consequently, its spreading rate along the Mediterranean marshes.

  15. Woolly apple aphid Eriosoma lanigerum Hausmann ecology and its relationship with climatic variables and natural enemies in Mediterranean areas.

    PubMed

    Lordan, Jaume; Alegre, Sim; Gatius, Ferran; Sarasa, M Jos; Alins, Georgina

    2015-02-01

    A multilateral approach that includes both biotic and climatic data was developed to detect the main variables that affect the ecology and population dynamics of woolly apple aphid Eriosoma lanigerum (Hausmann). Crawlers migrated up and down the trunk mainly from spring to autumn and horizontal migration through the canopy was observed from May to August. Winter temperatures did not kill the canopy colonies, and both canopy and root colonies are the source of reinfestations in Mediterranean areas. Thus, control measures should simultaneously address roots and canopy. European earwigs Forficula auricularia (Linnaeus) were found to reduce the survival of overwintering canopy colonies up to June, and this can allow their later control by the parasitoid Aphelinus mali (Haldeman) from summer to fall. Preliminary models to predict canopy infestations were developed. PMID:25335497

  16. Embryos of the Viviparous Dermapteran, Arixenia esau Develop Sequentially in Two Compartments: Terminal Ovarian Follicles and the Uterus

    PubMed Central

    Tworzydlo, Waclaw; Kisiel, Elzbieta; Bilinski, Szczepan M.

    2013-01-01

    Three main reproductive strategies have been described among insects: most common oviparity, ovoviviparity and viviparity. In the latter strategy, the embryonic development takes place within the body of the mother which provides gas exchange and nutrients for embryos. Here we present the results of histological and EM analyses of the female reproductive system of the viviparous earwig, Arixenia esau, focusing on all the modifications related to the viviparity. We show that in the studied species the embryonic development consists of two “physiological phases” that take place in two clearly disparate compartments, i.e. the terminal ovarian follicle and the uterus. In both compartments the embryos are associated with synthetically active epithelial cells. We suggest that these cells are involved in the nourishment of the embryo. Our results indicate that viviparity in arixeniids is more complex than previously considered. We propose the new term “pseudoplacento-uterotrophic viviparity” for this unique two-phase reproductive strategy. PMID:23667700

  17. Structure of ovaries and oogenesis in dermapterans. II. The nurse cells, nuage aggregates and sponge bodies.

    PubMed

    Tworzyd?o, Wac?aw; Kisiel, Elzbieta

    2010-01-01

    In three studied dermapteran species, Doru lineare, Opisthocosmia silvestris and Forficula auricularia, ovarian follicles are composed of two cells only, the oocyte and a single nurse cell. The nuclei of the nurse cells are large, ameboid and contain highly active nucleoli. RER elements, ribosomes, mitochondria and electron-dense aggregations of nuage material are present in the cytoplasm. Immunolocalization analysis revealed that in earwigs the nuage does not contain snRNAs. In one of the studied species, Doru lineare, apart from "canonical" nuage aggregations, characteristic RER/nuage complexes were found. These structures are morphologically similar to the sponge bodies present in the cytoplasm of the Drosophila germline cells. We suggest that RER/nuage complexes in Doru, as sponge bodies in Drosophila, are implicated in mRNA translocation. PMID:20420198

  18. Effect of habitat quality on diet flexibility in Barbary macaques.

    PubMed

    Ménard, Nelly; Motsch, Peggy; Delahaye, Alexia; Saintvanne, Alice; Le Flohic, Guillaume; Dupé, Sandrine; Vallet, Dominique; Qarro, Mohamed; Tattou, Mohamed Ibn; Pierre, Jean-Sébastien

    2014-07-01

    Barbary macaques live in extreme temperate environments characterized by strongly seasonal resource availability. They are mainly terrestrial while foraging, harvesting food from the herbaceous layer. These monkeys are threatened mainly because of anthropogenic habitat degradation. We studied the adaptive capacities of wild groups of Barbary macaques that lived in different cedar forests undergoing varying extents of grazing pressure from domestic livestock. In all three sites, diet varied seasonally. Heavy grazing led to a significant decrease in herbaceous production and species richness. As a consequence, the monkeys' diet in this poor habitat showed a decreased plant species richness. Moreover, it incorporated fewer above-ground herbaceous resources, and a greater proportion of subterranean resources (especially hypogeous fungi and subterranean invertebrates such as earthworms, eggs and adults of earwigs, and ant's larvae) than the diet of monkeys inhabiting ungrazed forest. Cedar bark, cedar strobiles, earthworms, and earwigs were part of the monkeys' diet only in grazed forest. Monkeys in heavily grazed forest compensated for a lack of herbaceous foods by eating subterranean foods preferentially to tree and shrub products. The foods they consumed take longer to harvest and process than the seeds or leaves consumed by Barbary macaques in less heavily grazed forest habitats. Our results suggest that monkeys do differ in their diets according to the degree of habitat change induced by human activities. They also highlight the dietary flexibility of Barbary macaques as a key element that allows them to cope with degraded habitats. We later compare the dietary adjustments of Barbary macaques facing environmental change to dietary strategies of other macaques and temperate-zone primates. PMID:24573596

  19. Polysaccharide degradation and synthesis by extremely thermophilic anaerobes.

    PubMed

    Vanfossen, Amy L; Lewis, Derrick L; Nichols, Jason D; Kelly, Robert M

    2008-03-01

    Extremely thermophilic fermentative anaerobes (growth T(opt) > or = 70 degrees C) have the capacity to use a variety of carbohydrates as carbon and energy sources. As such, a wide variety of glycoside hydrolases and transferases have been identified in these microorganisms. The genomes of three model extreme thermophiles-an archaeon Pyrococcus furiosus (T(opt) = 98 degrees C), and two bacteria, Thermotoga maritima (T(opt) = 80 degrees C) and Caldicellulosiruptor saccharolyticus (T(opt) = 70 degrees C)-encode numerous carbohydrate-active enzymes, many of which have been characterized biochemically in their native or recombinant forms. In addition to their voracious appetite for polysaccharide degradation, polysaccharide production has also been noted for extremely thermophilic fermentative anaerobes; T. maritima generates exopolysaccharides that aid in biofilm formation, a process that appears to be driven by intraspecies and interspecies interactions. PMID:18378602

  20. [The floristic diversity of the psammophyte vegetation in the region of Tlemcen (north-west Algeria)].

    PubMed

    Stambouli-Meziane, Hassiba; Bouazza, M; Thinon, Michel

    2009-08-01

    This study is devoted to the analysis of the psammophyte of the coastal and semi-continental dunes in Tlemcen. Interesting results have been obtained, in particular, on the biological and ecological aspects of the psammophyte. The interpretation from Factoriel analysis of correspondences enabled us to identify the different phytosociological classes (Cakiletea maritimae, Ammophiletea, Quercetea ilicis, Therobrachypodietea and Stellarietea mediae). Some of these classes (Cakiletea maritimae and Ammophiletea) inhabit, exceedingly well, the embryonic dunes. Some species (Therobrachypodietea) colonize the quickset dunes. Lastly, some others (Quercetea ilicis) settle in the more mature and stable dunes. By using the phytosociological and phytodynamical data, we have been able to understand the vegetation and its diversity. PMID:19632654

  1. Characterization of ribonuclease P RNAs from thermophilic bacteria.

    PubMed Central

    Brown, J W; Haas, E S; Pace, N R

    1993-01-01

    The catalytic RNA component of bacterial RNase P is responsible for the removal of 5' leader sequences from precursor tRNAs. As part of an on-going phylogenetic comparative characterization of bacterial RNase P, the genes encoding RNase P RNA from the thermophiles Thermotoga maritima, Thermotoga neapolitana, Thermus aquaticus, and a mesophilic relative of the latter, Deinococcus radiodurans, have been cloned and sequenced. RNAs transcribed from these genes in vitro are catalytically active in the absence of other components. Active holoenzymes have been reconstituted from the T.aquaticus and T.maritima RNAs and the protein component of RNase P from Escherichia coli. The RNase P RNAs of T.aquaticus and T.martima, synthesized in vitro, were characterized biochemically and shown to be inherently resistant to thermal disruption. Several features of these RNAs suggest mechanisms contributing to thermostability. The new sequences provide correlations that refine the secondary structure model of bacterial RNase P RNA. Images PMID:7680125

  2. Large methyl halide emissions from south Texas salt marshes

    NASA Astrophysics Data System (ADS)

    Rhew, R. C.; Whelan, M. E.; Min, D.-H.

    2014-11-01

    Coastal salt marshes are natural sources of methyl chloride (CH3Cl) and methyl bromide (CH3Br) to the atmosphere, but measured emission rates vary widely by geography. Here we report large methyl halide fluxes from subtropical salt marshes of south Texas. Sites with the halophytic plant, Batis maritima, emitted methyl halides at rates that are orders of magnitude greater than sites containing other vascular plants or macroalgae. B. maritima emissions were generally highest at midday; however, diurnal variability was more pronounced for CH3Br than CH3Cl, and surprisingly high nighttime CH3Cl fluxes were observed in July. Seasonal and intra-site variability were large, even taking into account biomass differences. Overall, these subtropical salt marsh sites show much higher emission rates than temperate salt marshes at similar times of the year, supporting the contention that low-latitude salt marshes are significant sources of CH3Cl and CH3Br.

  3. A variable-temperature direct electrochemical study of metalloproteins from hyperthermophilic microorganisms involves in hydrogen production from pyruvate

    SciTech Connect

    Smith, E.T.; Blamey, J.; Zhou, Z.Z.; Adams, M.W.W.

    1995-05-30

    The hyperthomophilic bacterium Thermotoga maritima and the hyperthermolic archaeon Pyrococcus furiosus grow optimally at 80{degrees} and 100{degrees}C, respectively, by the fermentation of carbohydrates to organic acids, CO{sub 2}, and H{sub 2}. Pyruvate is a major source of reductant for H{sub 2} production during fermentation, and pyruvate ferredoxin oxidoreductase (POR), a 4Fe-type ferredoxin, and hydrogenase have been previously purified from both species. P. furiosus utilizes copper-iron-containing POR and a nickel-iron-containing hydrogenase, whereas the POR of T. maritima lacks copper and its hydrogenase lacks nickel. For all four enzymes and for the two ferredoxins, we have determined their reproduction potentials (E{degrees}` and, where possible, thermodynamic parameters associated with electron transfer {Delta}S{degrees} and {Delta}H{degrees}), using differential pulse voltammetry at temperatures ranging from 25 to 95{degrees}C. 55 refs., 7 fig., 2 tabs.

  4. Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

    PubMed Central

    Han, Gye Won; Yang, Xiang-Lei; McMullan, Daniel; Chong, Yeeting E.; Krishna, S. Sri; Rife, Christopher L.; Weekes, Dana; Brittain, Scott M.; Abdubek, Polat; Ambing, Eileen; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Caruthers, Jonathan; Chiu, Hsiu-Ju; Clayton, Thomas; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Slawomir K.; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; van den Bedem, Henry; White, Aprilfawn; Wolf, Guenter; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc-André; Schimmel, Paul; Wilson, Ian A.

    2010-01-01

    A novel aminoacyl-tRNA synthetase that contains an iron–sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron–sulfur [4Fe–­4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an l-­tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe–4S] cluster-binding motif (C-x 22-C-x 6-C-x 2-C). It is speculated that the iron–sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon. PMID:20944229

  5. [Does sea-grass biomass control the density of peracarids (Crustacea: Peracarida) in tropical lagoons?].

    PubMed

    Winfield, Ignacio; Chzaro-Olvera, Sergio; Alvarez, Fernando

    2007-03-01

    We analyzed the time-space variation of the peracarid crustaceans that inhabit seagrasses of the Alvarado Lagoon System, Veracruz, Gulf of Mexico. The organisms were collected from 108 samples in six sites with Ruppia maritima beds (December 1992 to November 1994). The assemblage was composed of 11 species. Eight species of Amphipoda (Hourstonius laguna, Cerapus benthophilus, Apocorophium louisianum, Grandidierella bonnieroides, Leptocheirus rhizophorae, Gammarus mucronatus, Melita longisetosa and Haustorius sp.), one of Isopoda (Cassidinidea ovalis) and two of Tanaidacea (Discapseudes holthuisi and Leptochelia savignyi) were identified. Taxocoenosis, density and biomass of peracarids showed seasonal pulses related to R. maritima biomass, salinity variation, epicontinental affluent and inlets. The species C. ovalis, G. mucronatus, A. louisianum and D. holthuisi were dominant. PMID:18457113

  6. An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in the Hyperthermophilic Bacterium Thermotoga maritima†

    PubMed Central

    Conners, Shannon B.; Montero, Clemente I.; Comfort, Donald A.; Shockley, Keith R.; Johnson, Matthew R.; Chhabra, Swapnil R.; Kelly, Robert M.

    2005-01-01

    Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, β-xylan, and β-glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable. PMID:16237010

  7. Photochemical and biophysical feedbacks of C₃ and C₄ Mediterranean halophytes to atmospheric CO₂ enrichment confirmed by their stable isotope signatures.

    PubMed

    Duarte, B; Santos, D; Silva, H; Marques, J C; Caçador, I

    2014-07-01

    According the latest predictions, an increase of about two times in atmospheric CO2 concentrations, is expected to occur by the end of this century. In order to understand the effects of this atmospheric composition changes on two abundant Mediterranean halophytes (Halimione portulacoides and Spartina maritima), mesocosmos trials were performed simulating two atmospheric CO2 environments (380 ppm and 760 ppm of CO2 respectively). The two chosen halophyte species present different metabolic characteristics: H. portulacoides, is a C3 specie while S. maritima is a C4 species. Distinct feedbacks were obtained for each of the studied species. Stable Isotope discrimination showed that both species showed an enhancement of the Rubisco carboxylation capacity and photosynthetic efficiency mostly due to an increase in intracellular [CO2]. In H. portulacoides CO2 fertilization induced an enhancement of ETR and a decrease in non-photochemical quenching and in dissipated energy fluxes. On the other hand the C4 grass S. maritima, already at full capacity, showed no photosynthetic enhancement. In fact this highly productive grass presented lower photosynthetic efficiencies accompanied by increases in dissipated energy fluxes mostly due to reductions in energy flux associated with the transport of reducing power throughout the quinone pool. The accumulation of reducing power led to oxidative stress, and thus the photosynthetic ability of this grass was greatly reduced. Both these feedbacks to realistic future CO2 concentrations are important consideration for in future primary productivity models, indicating a possible reduced abundance of the pioneer S. maritima and an increased biomass spreading of the sediment stabilizer H. portulacoides, inevitably affecting the morphology and function of the salt marshes imposed by these atmospheric changes, both in terms of ecosystem functioning and loss of biodiversity. PMID:24713121

  8. Thermostable cellulases, and mutants thereof, capable of hydrolyzing cellulose in ionic liquid

    DOEpatents

    Sapra, Rajat; Datta, Supratim; Chen, Zhiwei; Holmes, Bradley M.; Simmons, Blake A.; Blanch, Harvey W.

    2016-04-26

    The present invention provides for a composition comprising an ionic liquid and a thermostable cellulose, and a method of hydrolyzing a cellulose, comprising: (a) providing a composition comprising a solution comprising an ionic liquid and a cellulose, and (b) introducing a thermostable cellulase to the solution, such that the cellulose is hydrolyzed by the cellulase. The present invention also provides for a Thermatoga maritima thermostable cellulase mutant with increased cellulase activity.

  9. Screening of common Plantago species in Hungary for bioactive molecules and antioxidant activity.

    PubMed

    Gonda, S; Tóth, L; Parizsa, P; Nyitrai, M; Vasas, G

    2010-01-01

    Five species of Plantago genus, namely P. lanceolata, P. major, P. media, P. altissima and P. maritima were screened for iridoid content (CE-MEKC), total caffeoyl phenylethanoid glycoside (CPG) content and antioxidant activity (CUPRAC assay). The five species could be distinguished by TLC pattern analysis in a single run in a system commonly used for quality management of P. lanceolata leaves, as shown by cluster analysis of major bands; with the exception, that P. altissima and P. lanceolata did not show enough pattern difference to be fully separated. P. maritima was shown to have the highest antioxidant capacity (0.42 μmol ascorbic acid equivalent (AAE)/g DW), and the highest level of CPGs (4.29%). P. altissima was shown to be chemically indistinguishable from P. lanceolata with repsect to iridoid content (aucubin 0.55 ± 0.04%, 0.68 ± 0.23%, catalpol 0.66 ± 0.13% and 0.89 ± 0.22%, respectively), CPG content (2.40 ± 0.38% and 2.54 ± 0.56%, respectively) and antioxidant capacity (0.2206 ± 0.0290 and 0.2428 ± 0.0191 μmol AAEAC/g DW). The presented data show the potency of medicinal use of Hungarian wild populations of the studied five species, especially in the case of P. maritima, and that P. altissima can be a potential replacement of P. lanceolata in herbal mixtures. PMID:21565762

  10. Improved protein identification using automated high mass measurement accuracy MALDI FT-ICR MS peptide mass fingerprinting

    NASA Astrophysics Data System (ADS)

    Horn, David M.; Peters, Eric C.; Klock, Heath; Meyers, Andrew; Brock, Ansgar

    2004-11-01

    A comparison between automated peptide mass fingerprinting systems using MALDI-TOF and MALDI FT-ICR MS is presented using 86 overexpressed proteins from Thermotoga maritima. The high mass measurement accuracy of FT-ICR MS greatly reduces the probability of an incorrect assignment of a protein in peptide mass fingerprinting by significantly decreasing the score and peptide sequence coverage of the highest ranked random protein match from the database. This improved mass accuracy led to the identification of all 86 proteins with the FT-ICR data versus 84 proteins using the TOF data against the T. maritima database. The beneficial effect of mass accuracy becomes much more evident with the addition of variable modifications and an increase in the size of the database used in the search. A search of the same data against the T. maritima database with the addition of a variable modification resulted in 77 identifications using MALDI-TOF and 84 identifications using MALDI FT-ICR MS. When searching the NCBInr database, the FT-ICR based system identified 82 of 86 proteins while the TOF based system could only identify 73. The MALDI FT-ICR based system has the further advantage of producing fewer unassigned masses in each peptide mass fingerprint, resulting in greatly reduced sequence coverage and score for the highest ranked random match and improving confidence in the correctly assigned top scoring protein. Finally, the use of rms error as a measure for instrumental mass accuracy is discussed.

  11. Productivity and nutrient cycling in salt marshes: Contribution to ecosystem health

    NASA Astrophysics Data System (ADS)

    Sousa, Ana I.; Lillebø, Ana I.; Pardal, Miguel A.; Caçador, Isabel

    2010-05-01

    This study aimed to assess the contribution of different salt marsh halophytes ( Spartina maritima, Scirpus maritimus, Halimione portulacoides, Sarcocornia fruticosa, and Sarcocornia perennis) to nutrient cycling and sequestration in warm-temperate salt marshes. Carbon, nitrogen and phosphorus concentration in plant organs and rhizosediment, as well as plant biomass were monitored every two months during one year. Results show that the C retained in the rhizosediment does not seem to be species or site specific. However, some halophytes seem to have a higher contribution to retain C from external sources, namely S. perennis and S. maritima. Regarding N, halophytes colonizing the upper and middle marsh areas had the highest NBPP (net belowground primary production) as well as the retention of N in the rhizosediment. Yet, excluding S. maritimus, all halophytes seem to contribute to the retention of N from external sources. The P retained in the rhizosediment does not seem to be species or site specific. Still, only S. maritima colonizing the lower marsh areas, which also had comparatively lower NBPP, seem to have a higher contribution to retain P from external sources. Additionally, it seems that there is no relation between plants sequestration capacity for nutrients and plant photosynthetic pathway. This work shows that nutrient cycling and accumulation processes by salt marsh halophytes contribute to reduce eutrophication (N and P retention) and also to reduce atmospheric CO 2 (C retention), highlighting salt marsh ecosystems services and the crucial role of halophytes in maintaining ecosystem functions and health.

  12. Structural insights into a key carotenogenesis related enzyme phytoene synthase of P. falciparum: a novel drug target for malaria.

    PubMed

    Agarwal, Shalini; Sharma, Vijeta; Phulera, Swastik; Abdin, M Z; Ayana, R; Singh, Shailja

    2015-12-01

    Carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. Phytoene synthase (PSY), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. PSYs have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. In an effort to characterize PSY in apicomplexans especially the malaria parasite Plasmodium falciparum (P. falciparum), a detailed bioinformatics analysis is undertaken. We have analysed the Phylogenetic relationship of PSY also referred to as octaprenyl pyrophosphate synthase (OPPS) in P. falciparum with other taxonomic groups. Further, we in silico characterized the secondary and tertiary structures of P. falciparum PSY/OPPS and compared the tertiary structures with crystal structure of Thermotoga maritima (T. maritima) OPPS. Our results evidenced the resemblance of P. falciparum PSY with the active site of T. maritima OPPS. Interestingly, the comparative structural analysis revealed an unconserved unique loop in P. falciparum OPPS/PSY. Such structural insights might contribute novel accessory functions to the protein thus, offering potential drug targets. PMID:26702306

  13. Salt marsh vegetation as a carbonyl sulfide (COS) source to the atmosphere

    NASA Astrophysics Data System (ADS)

    Whelan, Mary E.; Min, Dong-Ha; Rhew, Robert C.

    2013-07-01

    Carbonyl sulfide (COS) is the most abundant and longest-lived reduced sulfur compound in the atmosphere; changes in its atmospheric concentration could significantly affect global climate and the biogeochemical sulfur cycle. The largest sink of COS in the troposphere is its destruction in plant leaves by the enzymes involved in photosynthesis. In this study, net fluxes of COS were measured from a coastal salt marsh on a subtropical barrier island on the Texas shore of the Gulf of Mexico. We find net emissions from sites with the common salt marsh plant Batis maritima compared to the net uptake from vegetated plots of most previously investigated biomes. The magnitude of the COS production from vegetated plots in this study was twice the emissions of soil-only salt marsh plots. This is the first time that emissions of COS have been found to be significantly enhanced by the presence of vegetation compared to soil alone. COS fluxes exceeded +110 pmol m-2 s-1 for non-inundated plots during daytime hours and were correlated with soil temperature at the depth of 5 cm. Tidal flooding inhibited soil COS exchange; however, we found continued net emissions from emergent B. maritima. This study suggests that emissions of COS resulted from interactions with the plants themselves, which would mean that B. maritima can mediate the production of atmospheric COS.

  14. Accumulation, distribution and cellular partitioning of mercury in several halophytes of a contaminated salt marsh.

    PubMed

    Castro, Rita; Pereira, Sofia; Lima, Ana; Corticeiro, Sofia; Válega, Mónica; Pereira, Eduarda; Duarte, Armando; Figueira, Etelvina

    2009-09-01

    This work evaluates the role of a plant community in mercury (Hg) stabilization and mobility in a contaminated Portuguese salt marsh. With this aim, the distribution of Hg in below and aboveground tissues, as well as the metal partitioning between cellular fractions (soluble and insoluble) in four different species (Triglochin maritima L., Juncus maritimus Lam, Sarcocornia perennis (Miller) A.J. Scott, and Halimione portulacoides (L.) Aellen) was assessed. Mercury accumulation, translocation and compartmentation between organs and cellular fractions were related to the plant species. Results showed that the degree of Hg absorption and retention was influenced both by environmental parameters and metal translocation/partitioning strategies. Different plant species presented different allocation patterns, with marked differences between monocots (T. maritima and J. maritimus) and dicots (S. perennis, H. portulacoides). Overall, the two monocots, in particular T. maritima showed higher Hg retention in the belowground organs whereas the dicots, particularly S. perennis presented a more pronounced translocation to the aboveground tissues. Considering cellular Hg partitioning, all species showed a higher Hg binding to cell walls and membranes rather than in the soluble fractions. This strategy can be related to the high degree of tolerance observed in the studied species. These results indicate that the composition of salt marsh plant communities can be very important in dictating the Hg mobility within the marsh ecosystem and in the rest of the aquatic system as well as providing important insights to future phytoremediation approaches in Hg contaminated salt marshes. PMID:19595432

  15. Liposome-mediated DNA uptake and transient expression in Thermotoga.

    PubMed

    Yu, J S; Vargas, M; Mityas, C; Noll, K M

    2001-02-01

    We report here the successful application of a PCR-based method to detect genetic transformation of Thermotoga neapolitana and Thermotoga maritima. Plasmid vectors were constructed using pRQ7, an 846-bp plasmid found in Thermotoga species strain RQ7, which replicates by a rolling circle mechanism. The vector pJY1 was constructed by placing a gene encoding a thermostable chloramphenicol acetyltransferase from Stacphylococcus aureus under the control of the tac promoter and joining this with pRQ7 in a pBluescript vector. A second vector, pJY2, was similarly constructed using a gene encoding a kanamycin nucleotidyltransferase previously engineered for thermostability. Genetic transformation of T. neapolitana and T. maritima spheroplasts was achieved using cationic liposomes. The transforming DNA was detected in cells grown in liquid cultures using polymerase chain reaction amplification of the cat or kan genes. T. neapolitana could maintain pJY1 for at least 25 generations in liquid medium containing chloramphenicol. The pJY2 vector conferred kanamycin resistance to T. maritima cells grown in liquid culture. Isolation of stable transformants on solid media after 2-3 days of incubation at 77 degrees C was not possible with either vector, probably because of the instability of both vectors and antibiotics under these conditions. However, this transformation procedure provides, for the first time, a method to introduce DNA into this hyperthermophilic bacterium for potential applications such as targeted gene disruption analyses. PMID:11302503

  16. Selection of a halophytic plant for assessing the phytotoxicity of dredged seaport sediment stored on land.

    PubMed

    Bedell, J-P; Ferro, Y; Bazin, C; Perrodin, Y

    2014-01-01

    The filling of dry quarries in coastal areas with sediments dredged in seaports represents a potentially interesting method of recycling of these materials. However, this recycling requires the prior carrying out of an Environmental Risk Assessment of the scenario concerned. For this, the question arose as to the type of plants capable of developing on the surface of such a deposit and the method to implement for assessing the possible phytotoxicity of dredged sediments. To answer this question, we chose to work with halophytic plants to be free from the salt-related effect and to assess only the effect related to the toxic compounds present. Based on the objectives set, these works led to the use of common plants of the French coast, with direct seeding, and with pollution-sensitive plants. Three species of angiosperms, Armeria maritima, Anthemis maritima and Plantago coronopus, were finally tested. As a result of this work, Armeria maritima was retained as the most suitable plant for testing the possible phytotoxic effect of dredged marine sediments stored on land. The results obtained with this plant are as follows: germination of 40 % of the seeds in 31 days, produced biomass of 493 mg FW in 6 months and a capacity to bioaccumulate metal pollutants in roots with 350 and 720 mg/kg DW for Zn and Cu, respectively. PMID:23955497

  17. Effects of migratory geese on plant communities of an Alaskan salt marsh

    USGS Publications Warehouse

    Zacheis, A.; Hupp, J.W.; Ruess, R.W.

    2001-01-01

    1. We studied the effects of lesser snow geese (Anser caerulescens caerulescens) and Canada geese (Branta canadensis) on two salt marsh plant communities in Cook Inlet, Alaska, a stopover area used during spring migration. From 1995 to 1997 we compared plant species composition and biomass on plots where geese were excluded from feeding with paired plots where foraging could occur. 2. Foraging intensity was low (650-1930 goose-days km-2) compared to other goose-grazing systems. 3. Canada geese fed mainly on above-ground shoots of Triglochin maritimum, Puccinellia spp. and Carex ramenskii, whereas the majority of the snow goose diet consisted of below-ground tissues of Plantago maritima and Triglochin maritimum. 4. Plant communities responded differently to goose herbivory. In the sedge meadow community, where feeding was primarily on above-ground shoots, there was no effect of grazing on the dominant species Carex ramenskii and Triglochin maritimum. In the herb meadow community, where snow geese fed on Plantago maritima roots and other below-ground tissues, there was a difference in the relative abundance of plant species between treatments. Biomass of Plantago maritima and Potentilla egedii was lower on grazed plots compared with exclosed, whereas biomass of Carex ramenskii was greater on grazed plots. There was no effect of herbivory on total standing crop biomass in either community. The variable effect of herbivory on Carex ramenskii between communities suggests that plant neighbours and competitive interactions are important factors in a species' response to herbivory. In addition, the type of herbivory (above- or below-ground) was important in determining plant community response to herbivory. 5. Litter accumulation was reduced in grazed areas compared with exclosed in both communities. Trampling of the previous year's litter into the soil surface by geese incorporated more litter into soils in grazed areas. 6. This study illustrates that even light herbivore pressure can alter plant communities and affect forage availability.

  18. Genes for the Major Structural Components of Thermotogales Species' Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    SciTech Connect

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman R.; Wu, Si; Brewer, Heather M.; Gogarten, J. Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-06-29

    The unifying structural characteristic of members of the bacterial order Thermotogales is an unusual cell envelope that includes a loose-fitting sheath around each cell, often called a toga. Only two toga-associated structural proteins have been identified in Thermotoga maritima: the anchor protein OmpA1 (previously termed Ompα) and the porin OmpB (previously termed Ompβ). The gene encoding OmpA (ompA1) was assigned in the genome sequence to TM0477, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. Here we identify the ompB gene as TM0476, determined by LC/MS/MS analysis of the native OmpB protein purified from T. maritima cells. The purified OmpB had β-sheet secondary structure as determined by circular dichroism. Analysis of the sequence of ompB product shows it has porin characteristics including a carboxy terminus anchoring motif and a porin-specific amino acid composition. Orthologs of ompB were found in the genomes of some, but not all, Thermotogales. Those without orthologs have putative analogs. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one to three OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1(TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  19. The influence of prolonged mouth closure on selected components of the hyperbenthos in the littoral zone of the temporarily open/closed Kasouga Estuary, South Africa

    NASA Astrophysics Data System (ADS)

    Froneman, P. W.; Henninger, T. O.

    2009-07-01

    The influence of prolonged mouth closure on the population dynamics of the caridian shrimp, Palaemon peringueyi and the estuarine isopod, Exosphaeroma hylocoetes, in the littoral zone of temporarily open/closed Kasouga Estuary located on the south-eastern coastline of southern Africa was assessed monthly over the period October 2007 to September 2008. Prolonged mouth closure of the estuary contributed to hypersaline conditions (psu > 35) prevailing throughout the estuary for the last four months of the study. The high salinities coincided with a decrease in the areal extent (up to 80%) of the submerged macrophytes, mainly Ruppia maritima, within the littoral zone of the estuary. Total abundance and biomass values of the shrimp and isopod over the period of investigation ranged from 0 to 14.6 ind m -2, from 0 to 13.3 mg dwt m -2, from 12 to 1540 ind m -2 and from 0.1 to 2.16 mg dwt m -2, respectively. Maximum values of both the shrimp and isopod were recorded in the upper reaches of the estuary in close association with R. maritima. Over the course of the investigation, both the abundance and biomass values of the shrimp decreased significantly ( P < 0.05 in both cases) which could be related to reduced habitat availability, R. maritima, that acts as a refuge against fish predation. Additionally, the decrease in abundance and biomass values could be attributed to reduced recruitment opportunities for the shrimp and the cessation of reproduction in the estuarine isopod. The establishment of a link to the marine environment following an overtopping event in September 2008 contributed to a decrease in salinity within the system although no recruitment of either the isopod or shrimp was recorded.

  20. Prokaryotes in salt marsh sediments of Ria de Aveiro: Effects of halophyte vegetation on abundance and diversity

    NASA Astrophysics Data System (ADS)

    Oliveira, Vanessa; Santos, Ana L.; Aguiar, Claúdia; Santos, Luisa; Salvador, Ângelo C.; Gomes, Newton C. M.; Silva, Helena; Rocha, Sílvia M.; Almeida, Adelaide; Cunha, Ângela

    2012-09-01

    The aim of this study was to investigate the influence of monospecific colonization of sediment stands by Spartina maritima or Halimione portulacoides on benthic prokaryote assemblages in a salt marsh located in Ria de Aveiro (Portugal). The distribution of Bacteria, Archaea and sulfate-reducing bacteria (SRB) in sediments with monospecific plant stands and in unvegetated sediments was characterized by Fluorescence In Situ Hybridization (FISH). Total prokaryote abundance (0.4 × 109-1.7 × 109 cells gdw-1) was highest in sediments from the surface layer. The domain Bacteria comprised approximately 40% of total prokaryote communities with the highest percentages occurring in the surface layer. Archaeal cells corresponded to an average of 25% of total prokaryote population, with higher abundance in the vegetation banks, and displaying homogeneous vertical distribution. The relative abundance of SRB represented approximately 3% of total 4', 6-diamidino-2-phenylindole dihydrochloride (DAPI) stained cells at unvegetated sediment and H. portulacoides stand and 7% at S. maritima stand. Headspace solid-phase microextraction (HS-SPME) combined with Comprehensive Two-Dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry (GC × GC-ToFMS) was used to analyse the volatile and semi-volatile fraction of root exudates. A total of 171 compounds were identified and Principal Component Analysis showed a clear separation between the chemical composition (volatile and semi-volatile organic compounds) of the exudates of the two plants. The patterns of vertical distribution and differences in the proportion of SRB and Archaea in the prokaryote communities developing in sediments colonized by Spartina maritima or Halimione portulacoides suggest the existence of plant-specific interactions between halophyte vegetation and estuarine sediment bacteria in Ria de Aveiro salt marshes, exerted via sediment lithology and root-derived exudates.

  1. Structure of Csm2 elucidates the relationship between small subunits of CRISPR-Cas effector complexes.

    PubMed

    Venclovas, Česlovas

    2016-05-01

    Type I and type III CRISPR-Cas effector complexes share similar architecture and have homologous key subunits. However, the relationship between the so-called small subunits of these complexes remains a contentious issue. Here, it is shown that the recently solved structure of Thermotoga maritima Csm2 represents a dimer with the extensive structure swapping between monomers. Unswapping the structure generates a compact globular monomer which shares similar structure and surface properties with Cmr5, the small subunit of a related Cmr complex. Detailed analysis of available structures of small subunits reveals that they all have a common fold suggesting their common origin. PMID:27091242

  2. Opening a can of centipedes: new insights into mechanisms of body segmentation.

    PubMed

    Valentin, Guillaume; Oates, Andrew C

    2013-01-01

    The search for a common developmental genetic mechanism of body segmentation appears to become more difficult, and more interesting, as new segmented organisms are added to the roster. Recent work in this journal by Brena and Akam on segmentation of the geophilomorph centipede Strigamia maritima, an arthropod distantly related to the standard insect models, contains developmental and evolutionary surprises that highlight the importance of a wider sampling of phyla.See research article: http://www.biomedcentral.com/1741-7007/11/112. PMID:24289333

  3. Antimicrobial activity of fatty acid methyl esters of some members of Chenopodiaceae.

    PubMed

    Chandrasekaran, Manivachagam; Kannathasan, Krishnan; Venkatesalu, Venugopalan

    2008-01-01

    Fatty acid methyl ester (FAME) extracts of four halophytic plants, viz. Arthrocnemum indicum, Salicornia brachiata, Suaeda maritima and Suaeda monoica belonging to the family Chenopodiaceae, were prepared and their composition was analyzed by GC-MS. The FAME extracts were also screened for antibacterial and antifungal activities. The GC-MS analysis revealed the presence of more saturated fatty acids than unsaturated fatty acids. Among the fatty acids analyzed, the relative percentage of lauric acid was high in S. brachiata (61.85%). The FAME extract of S. brachiata showed the highest antibacterial and antifungal activities among the extracts tested. The other three extracts showed potent antibacterial and moderate anticandidal activities. PMID:18669016

  4. Remote sensing of biomass of salt marsh vegetation in France

    NASA Technical Reports Server (NTRS)

    Gross, M. F.; Klemas, V.; Levasseur, J. E.

    1988-01-01

    Spectral data (gathered using a hand-held radiometer) and harvest data were collected from four salt marsh vegetation types in Brittany, France, to develop equations predicting live aerial biomass from spectral measurements. Remote sensing estimates of biomass of the general salt marsh community (GSM) and of Spartina alterniflora can be obtained throughout the growing season if separate biomass prediction equations are formulated for different species mixtures (for the GSM) and for different canopy types (for S. alterniflora). Results suggest that remote sensing will not be useful for predicting Halimione portulacoides biomass, but can be used to estimate Puccinellia maritima biomass early in the growing season.

  5. Screening seeds of Scottish plants for antibacterial activity.

    PubMed

    Kumarasamy, Yashodharan; Cox, Philip John; Jaspars, Marcel; Nahar, Lutfun; Sarker, Satyajit Dey

    2002-11-01

    Based on ethnopharmacological and taxonomic information, seeds of 21 Scottish plant species from 14 different families were obtained from authentic seed suppliers. Their n-hexane, dichloromethane and methanol extracts were assessed for antibacterial activity against 11 pathogenic bacterial species. Methanol extracts of 11 plant species showed significant antibacterial activity. Malva moschata and Prunus padus were active against five bacterial species, Reseda lutea against four, Centaurium erythraea and Crithmum maritimum against three, Calluna vulgaris against two, and Armeria maritima, Centaurea scabiosa, Daucus carota, Rosa canina and Stellaria holostea against one bacterial species. C. erythraea and P. padus were also active against methicillin resistant Staphylococcus aureus. PMID:12413709

  6. Insect phylogenomics: results, problems and the impact of matrix composition.

    PubMed

    Letsch, Harald O; Meusemann, Karen; Wipfler, Benjamin; Schütte, Kai; Beutel, Rolf; Misof, Bernhard

    2012-08-22

    In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered. PMID:22628473

  7. Insect phylogenomics: results, problems and the impact of matrix composition

    PubMed Central

    Letsch, Harald O.; Meusemann, Karen; Wipfler, Benjamin; Schütte, Kai; Beutel, Rolf; Misof, Bernhard

    2012-01-01

    In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data (‘EST’: short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered. PMID:22628473

  8. Maternal programming of offspring in relation to food availability in an insect (Forficula auricularia).

    PubMed

    Raveh, Shirley; Vogt, Dominik; Kölliker, Mathias

    2016-04-13

    Maternal effects can induce adjustments in offspring phenotype to the environment experienced by the mother. Of particular interest is if mothers can programme their offspring to cope best under matching environmental conditions, but the evidence for such anticipatory maternal effects (AME) is limited. In this study, we manipulated experimentally the food availability experienced by mothers and their offspring in the European earwig (Forficula auricularia). Offspring produced by females that had access to high or low food quantities were cross-fostered to foster mothers experiencing matched or mismatched environments. Offspring experiencing food availability matching the one of their mothers had an increased survival to adulthood compared with offspring experiencing mismatched conditions. Females experiencing high food laid larger clutches. This clutch-size adjustment statistically explained the matching effect when offspring experienced high food, but not when experiencing low food conditions. There were no effects of matching on offspring growth and developmental rate. Overall, our study demonstrates that AME occurs in relation to food availability enhancing offspring survival to adulthood under matching food conditions. PMID:27053749

  9. Parent–offspring conflict and the genetic trade-offs shaping parental investment

    PubMed Central

    Kölliker, Mathias; Boos, Stefan; Wong, Janine W.Y.; Röllin, Lilian; Stucki, Dimitri; Raveh, Shirley; Wu, Min; Meunier, Joël

    2015-01-01

    The genetic conflict between parents and their offspring is a cornerstone of kin selection theory and the gene-centred view of evolution, but whether it actually occurs in natural systems remains an open question. Conflict operates only if parenting is driven by genetic trade-offs between offspring performance and the parent's ability to raise additional offspring, and its expression critically depends on the shape of these trade-offs. Here we investigate the occurrence and nature of genetic conflict in an insect with maternal care, the earwig Forficula auricularia. Specifically, we test for a direct response to experimental selection on female future reproduction and correlated responses in current offspring survival, developmental rate and growth. The results demonstrate genetic trade-offs that differ in shape before and after hatching. Our study not only provides direct evidence for parent–offspring conflict but also highlights that conflict is not inevitable and critically depends on the genetic trade-offs shaping parental investment. PMID:25880586

  10. A chemical signal of offspring quality affects maternal care in a social insect

    PubMed Central

    Mas, Flore; Haynes, Kenneth F.; Kölliker, Mathias

    2009-01-01

    Begging signals of offspring are condition-dependent cues that are usually predicted to display information about the short-term need (i.e. hunger) to which parents respond by allocating more food. However, recent models and experiments have revealed that parents, depending on the species and context, may respond to signals of quality (i.e. offspring reproductive value) rather than need. Despite the critical importance of this distinction for life history and conflict resolution theory, there is still limited knowledge of alternative functions of offspring signals. In this study, we investigated the communication between offspring and caring females of the common earwig, Forficula auricularia, hypothesizing that offspring chemical cues display information about nutritional condition to which females respond in terms of maternal food provisioning. Consistent with the prediction for a signal of quality we found that mothers exposed to chemical cues from well-fed nymphs foraged significantly more and allocated food to more nymphs compared with females exposed to solvent (control) or chemical cues from poorly fed nymphs. Chemical analysis revealed significant differences in the relative quantities of specific cuticular hydrocarbon compounds between treatments. To our knowledge, this study demonstrates for the first time that an offspring chemical signal reflects nutritional quality and influences maternal care. PMID:19439438

  11. Insects did it first: a micropatterned adhesive tape for robotic applications.

    PubMed

    Gorb, Stanislav N; Sinha, Mitali; Peressadko, Andrei; Daltorio, Kathryn A; Quinn, Roger D

    2007-12-01

    Based on the structural and experimental studies of more than 300 insect species from different lineages, we have developed and characterized a bioinspired polymer material with the ability of multiple glue-free bonding and debonding. The material surface is covered with a pattern of microstructures, which resembles the geometry of tenent hairs previously described from the feet of flies, beetles, earwigs and other insects. The tape with such a microstructure pattern demonstrates at least two times higher pull-off force per unit apparent contact area compared to the flat polymer. Additionally, the tape is less sensitive to contamination by dust particles than a commercially available pressure-sensitive adhesive tape. Even if the 'insect tape' is contaminated, it can be washed with a soap solution in water, in order to completely recover its adhesive properties. We have successfully applied the tape to the 120 g wall-climbing robot Mini-Whegs. Furthermore, the tape can be used for multiple adhering of objects to glass surfaces or as a protective tape for sensitive glass surfaces of optical quality. Another area of potential applications is gripping and manipulation of objects with smooth surfaces. PMID:18037721

  12. Differential ant exclusion from canopies shows contrasting top-down effects on community structure.

    PubMed

    Mestre, Laia; Piñol, J; Barrientos, J A; Espadaler, X

    2016-01-01

    Predators have far-reaching effects on communities by triggering top-down trophic cascades that influence ecosystem functioning. Omnivory and intraguild interactions between predators give rise to reticulate food webs and may either strengthen or dampen trophic cascades depending on context. Disentangling the effects of multiple predator species is therefore crucial for predicting the influence of predators on community structure. We focused on ants as dominant generalist predators in arthropod communities and set up a differential ant exclusion from canopies to examine its effects on assemblage species composition and densities of five arthropod groups (psocopterans, aphids, spiders, heteropterans and beetles). We coupled a glue band with tubes allowing only the ant Lasius grandis to reach the canopies to isolate its effect from the rest of crawling predators (ants, earwigs) and compared it against a full exclusion and a control. L. grandis alone had widespread effects on assemblage species composition, with contrasting species-specific responses within groups, where some species affected by L. grandis presence were not further affected by the presence of the whole crawling predator assemblage, and vice versa. Overall, L. grandis caused two- to threefold decreases of generalist predators and a threefold increase of aphids. However, it lacked further top-down effects on primary consumers, which only emerged when all crawling predators were present. This differential exclusion demonstrates the distinctive and widespread intraguild effects on community structure of a single ant species that contrast with the top-down effects exerted by the whole crawling predator assemblage. PMID:26376660

  13. Diet of western Burrowing Owls wintering in southern Texas

    USGS Publications Warehouse

    Littles, C.J.; Williford, D.; Skoruppa, M.K.; Woodin, M.C.; Hickman, G.C.

    2007-01-01

    Winter diets of the western Burrowing Owl (Athene cunicularia hypugaea) are little known. We determined the diet of western Burrowing Owls wintering in southern Texas by analyzing the contents of 182 pellets collected over four winters (1999-2000, 2001-2002, 2002-2003, and 2003-2004) in three habitat types (agricultural, mainland grassland, and barrier island). Remains of a total of 7476 prey items were recovered, 98% of which were arthropods. Gryllidae (crickets) formed the largest component (50%) of the prey, followed by lepidopteran larvae (13%), beetles (8%), spiders (7%), and earwigs (6%). Although vertebrates, primarily small mammals and birds, represented only 2% of prey items by number, they represented most (71%) of the biomass. Northern pygmy mice (Baiomys taylori) and fulvous harvest mice (Reithrodontomys fulveccens) were the two most frequently consumed vertebrate species. In all habitats, arthropods, especially orthopterans, were the primary prey item by number, whereas vertebrates, primarily small mammals, were the most important by biomass. Greater consumption of arthropods by Burrowing Owls in agricultural areas may be a factor contributing to owl use of these highly altered environments. ?? 2007 The Raptor Research Foundation, Inc.

  14. Patch clamp studies on root cell vacuoles of a salt-tolerant and a salt-sensitive plantago species : regulation of channel activity by salt stress.

    PubMed

    Maathuis, F J; Prins, H B

    1990-01-01

    Plantago media L. and Plantago maritima L. differ in their strategy toward salt stress, a major difference being the uptake and distribution of ions. Patch clamp techniques were applied to root cell vacuoles to study the tonoplast channel characteristics. In both species the major channel found was a 60 to 70 picosiemens channel with a low ion selectivity. The conductance of this channel for Na(+) was the same as for K(+), P(K) (+)/P(Na) (+) = 1, whereas the cation/anion selectivity (P(K) (+)/P(c1) (-)) was about 5. Gating characteristics were voltage and calcium dependent. An additional smaller channel of 25 picosiemens was present in P. maritima. In the whole vacuole configuration, the summation of the single channel currents resulted in slowly activated inward currents (t((1/2)) = 1.2 second). Inwardly directed, ATP-dependent currents could be measured against a DeltapH gradient of 1.5 units over the tonoplast. This observation strongly indicated the physiological intactness of the used vacuoles. The open probability of the tonoplast channels dramatically decreased when plants were grown on NaCl, although single channel conductance and selectivity were not altered. PMID:16667252

  15. Plantain (Plantago L.) species as novel sources of flavonoid antioxidants.

    PubMed

    Beara, Ivana N; Lesjak, Marija M; Jovin, Emilija D; Balog, Kristina J; Anackov, Goran T; Orcić, Dejan Z; Mimica-Dukić, Neda M

    2009-10-14

    To examine the antioxidant properties of methanol extracts of selected Plantago species (P. argentea Chaix., P. holosteum Scop., P. major L., P. maritima L., and P. media L.), various assays that measure free radical scavenging ability were carried out: DPPH, hydroxyl radical, superoxide anion, and nitric oxide scavenger capacity tests, reducing power (FRAP) assay, and Fe(2+)/ascorbate induced lipid peroxidation. In all of the tests extracts showed a potent antioxidant effect compared with BHT, a well-known synthetic antioxidant, and the extract of P. major, accepted as an official remedy. Besides, in examined extracts the total phenolic amount (ranging from 38.43 to 70.97 mg of GAE/g of dw) and the total flavonoid content (5.31-13.10 mg of QE/g of dw) were determined. Furthermore, the presence and content of selected flavonoids (luteolin-7-O-glucoside, apigenin-7-O-glucoside, luteolin, apigenin, rutin, and quercetin) were studied using LC-MS/MS technique. LC-MS/MS analysis showed noticeable qualitative and quantitative differences between the species according to which the examined Plantago species could be regarded as a possible new source of natural antioxidants. In this study three of the species examined, P. maritima, P. argentea, and P. holosteum, have been analyzed for the first time. PMID:19754195

  16. Antioxidant activity of raw, cooked and Rhizopus oligosporus fermented beans of Canavalia of coastal sand dunes of Southwest India.

    PubMed

    Niveditha, Vedavyas R; Sridhar, Kandikere R

    2014-11-01

    The raw and processed (cooked and cooked + solid-state fermented with Rhizopus oligosporus) split beans of two landraces of coastal sand dune wild legumes (Canavalia cathartica and Canavalia maritima) of the southwest coast of India were examined for bioactive compounds (total phenolics, tannins and vitamin C) and antioxidant potential (total antioxidant activity, ferrous-ion chelating capacity, DPPH free radical-scavenging activity and reducing activity). One-way ANOVA revealed significant elevation of bioactive compounds as well as antioxidant activities in fermented beans compared to raw and cooked beans in both legumes (p < 0.001). The EC50 values in fermented beans of both legumes were significantly lowest compared to raw and cooked beans (p < 0.001). In principal component analysis, total phenolics along with antioxidant activities (total antioxidant, ferrous-ion chelating and free radical-scavenging activities) of fermented beans of C. cathartica, while total antioxidant and free radical-scavenging activities of fermented beans of C. maritima were clustered. The present study demonstrated that split beans of coastal sand dune Canavalia fermented by R. oligosporus endowed with high bioactive principles as well as antioxidant potential and thus serve as future nutraceutical source. PMID:26396318

  17. Accumulation and soil-to-plant transfer of radionuclides in the Nile Delta coastal black sand habitats.

    PubMed

    Hegazy, A K; Emam, M H

    2011-02-01

    The radionuclide content was estimated in the soil of three black sand habitats in the Mediterranean coast of Egypt, namely, sand mounds and coastal sand planes and dunes. In addition, a total of 14 heavy minerals found in the soils were characterized. The soil to plant transfer of uranium and thorium was tested on three black sand species, namely, Cakile maritima Scop., Senecio glaucus L. and Rumex Pictus Forssk. The transfer of thorium and uranium radionuclides from the soil to plant is complex process that is subjected to many variables; among which are the organic matter and clay content of the soil, the type of radionuclides and plant species. The study revealed a strong negative relationship between uranium and thorium uptake by S. glaucus and R. pictus and the clay and organic matter content of soil. Concentration of thorium in the soil has a negative correlation with soil-to-plant transfer factor. The study results suggest the possibility of using black sand species for phytoremediation of soils contaminated with radioactive elements. The potentiality of S. glaucus as phytoremediator of radionuclides polluted soils is greater than R. pictus which in turn outweigh C. maritima. PMID:21598782

  18. Conformational Flexibility and Peptide Interaction of the Translocation ATPase SecA

    SciTech Connect

    Zimmer, Jochen; Rapoport, Tom A.; Harvard-Med

    2010-09-21

    The SecA ATPase forms a functional complex with the protein-conducting SecY channel to translocate polypeptides across the bacterial cell membrane. SecA recognizes the translocation substrate and catalyzes its unidirectional movement through the SecY channel. The recent crystal structure of the Thermotoga maritima SecA-SecYEG complex shows the ATPase in a conformation where the nucleotide-binding domains (NBDs) have closed around a bound ADP-BeFx complex and SecA's polypeptide-binding clamp is shut. Here, we present the crystal structure of T. maritima SecA in isolation, determined in its ADP-bound form at 3.1 {angstrom} resolution. SecA alone has a drastically different conformation in which the nucleotide-binding pocket between NBD1 and NBD2 is open and the preprotein cross-linking domain has rotated away from both NBDs, thereby opening the polypeptide-binding clamp. To investigate how this clamp binds polypeptide substrates, we also determined a structure of Bacillus subtilis SecA in complex with a peptide at 2.5 {angstrom} resolution. This structure shows that the peptide augments the highly conserved {beta}-sheet at the back of the clamp. Taken together, these structures suggest a mechanism by which ATP hydrolysis can lead to polypeptide translocation.

  19. Light–dark O2 dynamics in submerged leaves of C3 and C4 halophytes under increased dissolved CO2: clues for saltmarsh response to climate change

    PubMed Central

    Duarte, B.; Santos, D.; Silva, H.; Marques, J. C.; Caçador, I.; Sleimi, N.

    2014-01-01

    Waterlogging and submergence are the major constraints to which wetland plants are subjected, with inevitable impacts on their physiology and productivity. Global warming and climate change, as driving forces of sea level rise, tend to increase such submersion periods and also modify the carbonate chemistry of the water column due to the increased concentration of CO2 in the atmosphere. In the present work, the underwater O2 fluxes in the leaves of two abundant Mediterranean halophytes were evaluated at different levels of dissolved CO2. Photosynthetic enhancement due to increased dissolved CO2 was confirmed for both Halimione portulacoides and Spartina maritima, probably due to high tissue porosity, formation of leaf gas films and reduction of the oxygenase activity of Rubisco. Enhancement of the photosynthetic rates in H. portulacoides and S. maritima was concomitant with an increase in energy trapping and transfer, mostly due to enhancement of the carboxylation reaction of Rubisco, leading to a reduction of the energy costs for carbon fixation. Transposing these findings to the ecosystem, and assuming increased dissolved CO2 concentration scenarios, the halophyte community displays a new ecosystem function, increasing the water column oxygenation and thus reinforcing their role as principal primary producers of the estuarine system. PMID:25381259

  20. Remispora spitsbergenensis sp. nov., a marine lignicolous ascomycete from Svalbard, Norway.

    PubMed

    Pang, Ka-Lai; Chiang, Michael W L; Vrijmoed, Lilian L P

    2009-01-01

    Abstract: Remispora was established for R. maritima, a fungus with globose/subglobose, lightly colored and coriaceous ascomata; deliquescing asci; ellipsoidal ascospores; and bipolar, pleomorphic ascospore appendages. Seven species currently are included in Remispora: R crispa, R. galerita, R maritima, R. minuta, R. pilleata, R. quadriremis and R stellata. Variations on ascospore appendages can be observed in Remispora. In general the appendage is exosporic in nature and comprises an amorphous, electron-transparent matrix, and a fibrous, electron-dense component. An eighth Remispora species, R. spitsbergenensis sp. nov., is described here, discovered from washed-up wood collected at the shore of Longyearbyen, Svalbard, Norway. Ascospore appendages of R. spitsbergenensis appear as fibrous strands and amorphic material under the scanning electron microscope, which are characteristic of a Remispora species. Remispora spitsbergenensis resembles R. quadriremis and R. stellata because all possess four or more ascospore appendages at one end. Remispora spitsbergenensis possesses consistently four polar appendages at each end in contrast to six in R. stellata. Also ascospore appendages of R. spitsbergenensis are ribbon-like, compared with the obclavate, curved and attenuate appendages in R. quadriremis and R. stellata. A key for the identification of the eight Remispora species is provided. PMID:19623932

  1. Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures.

    PubMed

    Muralidharan, V; Rinker, K D; Hirsh, I S; Bouwer, E J; Kelly, R M

    1997-11-01

    Interactions involving hydrogen transfer were studied in a coculture of two hyperthermophilic microorganisms: Thermotoga maritima, an anaerobic heterotroph, and Methanococcus jannaschii, a hydrogenotrophic methanogen. Cell densities of T. maritima increased 10-fold when cocultured with M. jannaschii at 85 degrees C, and the methanogen was able to grow in the absence of externally supplied H(2) and CO(2). The coculture could not be established if the two organisms were physically separated by a dialysis membrane, suggesting the importance of spatial proximity. The significance of spatial proximity was also supported by cell cytometry, where the methanogen was only found in cell sorts at or above 4.5 microm in samples of the coculture in exponential phase. An unstructured mathematical model was used to compare the influence of hydrogen transport and metabolic properties on mesophilic and hyperthermophilic cocultures. Calculations suggest the increases in methanogenesis rates with temperature result from greater interactions between the methanogenic and fermentative organisms, as evidenced by the sharp decline in H(2) concentration in the proximity of a hyperthermophilic methanogen. The experimental and modeling results presented here illustrate the need to consider the interactions within hyperthermophilic consortia when choosing isolation strategies and evaluating biotransformations at elevated temperatures. PMID:18636642

  2. The effects of soil amendments on heavy metal bioavailability in two contaminated Mediterranean soils.

    PubMed

    Walker, David J; Clemente, Rafael; Roig, Asuncion; Bernal, M Pilar

    2003-01-01

    Two heavy metal contaminated calcareous soils from the Mediterranean region of Spain were studied. One soil, from the province of Murcia, was characterised by very high total levels of Pb (1572 mg kg(-1)) and Zn (2602 mg kg(-1)), whilst the second, from Valencia, had elevated concentrations of Cu (72 mg kg(-1)) and Pb (190 mg kg(-1)). The effects of two contrasting organic amendments (fresh manure and mature compost) and the chelate ethylenediaminetetraacetic acid (EDTA) on soil fractionation of Cu, Fe, Mn, Pb and Zn, their uptake by plants and plant growth were determined. For Murcia soil, Brassica juncea (L.) Czern. was grown first, followed by radish (Raphanus sativus L.). For Valencia soil, Beta maritima L. was followed by radish. Bioavailability of metals was expressed in terms of concentrations extractable with 0.1 M CaCl2 or diethylenetriaminepentaacetic acid (DTPA). In the Murcia soil, heavy metal bioavailability was decreased more greatly by manure than by the highly-humified compost. EDTA (2 mmol kg(-1) soil) had only a limited effect on metal uptake by plants. The metal-solubilising effect of EDTA was shorter-lived in the less contaminated, more highly calcareous Valencia soil. When correlation coefficients were calculated for plant tissue and bioavailable metals, the clearest relationships were for Beta maritima and radish. PMID:12531318

  3. An ecological approach to measuring the evolutionary consequences of gene flow from crops to wild or weedy relatives1

    PubMed Central

    Campbell, Lesley G.; Lee, David; Shukla, Kruti; Waite, Thomas A.; Bartsch, Detlef

    2016-01-01

    Premise of the study: Agricultural practices routinely create opportunities for crops to hybridize with wild relatives, leading to crop gene introgression into wild genomes. Conservationists typically worry this introgression could lead to genetic homogenization of wild populations, over and above the central concern of transgene escape. Alternatively, viewing introgression as analogous to species invasion, we suggest that increased genetic diversity may likewise be an undesirable outcome. Methods: Here, we compare the sensitivity of conventional population genetic metrics with species diversity indices as indicators of the impact of gene flow on genetic diversity. We illustrate this novel approach using multilocus genotype data (12 allozyme loci) from 10 wild (Beta vulgaris subsp. maritima) and eight putative crop–wild hybrid beet populations (B. vulgaris subsp. vulgaris × B. vulgaris subsp. maritima) scattered throughout Europe. Results: Conventional population genetic metrics mostly failed to detect shifts in genetic composition of putative hybrid populations. By contrast, species diversity indices unambiguously revealed increased genetic diversity in putative hybrid populations. Discussion: We encourage other workers to explore the utility of our more sensitive approach for risk assessment prior to the release of transgenic crops, with a view toward widespread adoption of our method in studies aimed at detecting allelic invasion. PMID:27011898

  4. The role of macrophytes as a refuge and food source for the estuarine isopod Exosphaeroma hylocoetes (Barnard, 1940)

    NASA Astrophysics Data System (ADS)

    Henninger, Tony O.; Froneman, P. William; Richoux, Nicole B.; Hodgson, Alan N.

    2009-04-01

    The role of submerged macrophytes as refugia from fish predation and as possible food sources for the estuarine isopod Exosphaeroma hylocoetes ( Barnard, K.H., 1940) was investigated. Laboratory experiments tested the effectiveness of artificial vegetation, replicating submerged vegetation, in enabling isopods to elude selected fish predators Rhabdosargus holubi, Glossogobius callidus, Monodactylus falciformis and Clinus cottoides. Isopods preferentially hid in the vegetation (>90%), even in absence of fish. The predatory fish had varying success in finding isopods within the vegetation. Isopod mortality ranged from 2% ( R. holubi) to a maximum of 87% ( C. cottoides) within vegetation, depending on the fish predator present. Stable isotope and fatty acid analyses ruled out the submerged macrophyte Ruppia maritima and inundated fringing grasses as direct food sources, but highlighted the epiphytic biota (mainly diatoms) found on the submerged vegetation and sediments as more likely food sources. These findings are consistent with gut content analyses. The results suggest that the close association of E. hylocoetes with R. maritima is the result of the vegetation providing the isopod with a refuge against fish predation as well as areas of increased food availability.

  5. Seasonal Variation of the Macrozoobenthic Community Structure at Low Salinities in a Mediterranean Lagoon (Monolimni Lagoon, Northern Aegean)

    NASA Astrophysics Data System (ADS)

    Kevrekidis, Theodoros

    2004-09-01

    The macrozoobenthic community structure and dynamics at low salinities (0.3-6 psu) in a Mediterranean lagoon (Monolimni lagoon) were investigated. Samples were collected monthly from February 1998 to February 1999 at two sampling stations. Community structure was analyzed by means of uni- and multivariate methods. 21 taxa were collected; the amphipod Corophium orientale and the gastropod Ventrosia maritima dominated the assemblages. Total abundance peaked (50,000-60,000 individuals m-2) in mid or late autumn. Community structure showed an almost even seasonal periodicity; seasonal changes were mainly derived from the intense variation in abundance of most species and the non-occurrence of a few ones (e.g. Corophium insidiosum, Polydora ciliata) in spring and summer. Non- occurrence, which led to a depression of the most diversity indices, was possibly the only direct impact of the extremely low salinities (~0.3 psu) on community structure. The main structuring factors of the community in the deeper outer part of the lagoon were water temperature and depth, and in the innermost part, where a Ruppia maritima meadow occurred, were water temperature and predation pressure by crabs (Carcinus aestuarii) and gobies (Knipowitchia caucasica). A temporary decline in total abundance in summer followed an increase in abundance of these predators. (

  6. Evaluation of a Florida coastal golf complex as a local and watershed source of bioavailable contaminants.

    PubMed

    Lewis, Michael A; Quarles, Robert L; Dantin, Darrin D; Moore, James C

    2004-02-01

    Contaminant fate in coastal areas impacted by golf course runoff is not well understood. This report summarizes trace metal, pesticide and PCB residues for colonized periphyton, Ruppia maritima (widgeon grass), Callinectes sapidus Rathbun (blue crabs) and Crassostrea virginica Gemlin (Eastern oyster) collected from areas adjacent to a Florida golf course complex which receive runoff containing reclaimed municipal wastewater. Concentrations of 19 chlorinated pesticides and 18 PCB congeners were usually below detection in the biota. In contrast, 8 trace metals were commonly detected although concentrations were not usually significantly different for biota collected from reference and non-reference coastal areas. Residue concentrations in decreasing order were typically: zinc, arsenic, copper, chromium, lead, nickel, cadmium and mercury. Mean BCF values for the eight trace metals ranged between 160-57000 (periphyton), 79-11033 (R. maritima), 87-162625 (C. virginica) and 12-9800 (C. sapidus). Most trace metal residues in periphyton colonized adjacent to the golf complex, were either similar to or significantly less than those reported for periphyton colonized in nearby coastal areas impacted by urban stormwater runoff and treated municipal and industrial wastewater discharges. Consequently, the recreational complex does not appear to be a major source of bioavailable contaminants locally nor in the immediate watershed based on results for the selected biota. PMID:14972577

  7. Distribution and migration of seaside sparrows

    USGS Publications Warehouse

    Robbins, C.S.

    1983-01-01

    The majority of the nine presently recognized races of the Seaside Sparrow (Ammospiza maritima) are so similar to neighboring races that individual birds outside their known breeding range cannot be subspecifically identified with certainty. The northern race, A. m. maritima, is partially migratory, with most individuals departing in autumn from Chesapeake Bay and from all the coastal marshes that lie to the north of the mouth of this bay. No banded bird has been recaptured in winter south of its breeding locality, however, so even the major wintering ground of this subspecies cannot be defined. The other subspecies are presumed to be primarily sedentary. Median arrival and departure dates at Fairfield, Connecticut, are 18 May and 19 September. On Long Island, New York, the spring peak occurs in the third week of May, and the autumn peak in mid-October. Postbreeding wanderers of unknown origin move north and east in August and September to the coastal marshes of Maine, New Brunswick, and Nova Scotia. The remarkably few records away from tidewater are from North Carolina, eastern Pennsylvania, the lower Hudson River, and eastern Massachusetts.

  8. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

    PubMed Central

    Zhaxybayeva, Olga; Swithers, Kristen S.; Lapierre, Pascal; Fournier, Gregory P.; Bickhart, Derek M.; DeBoy, Robert T.; Nelson, Karen E.; Nesbø, Camilla L.; Doolittle, W. Ford; Gogarten, J. Peter; Noll, Kenneth M.

    2009-01-01

    Since publication of the first Thermotogales genome, Thermotoga maritima strain MSB8, single- and multi-gene analyses have disagreed on the phylogenetic position of this order of Bacteria. Here we present the genome sequences of 4 additional members of the Thermotogales (Tt. petrophila, Tt. lettingae, Thermosipho melanesiensis, and Fervidobacterium nodosum) and a comprehensive comparative analysis including the original T. maritima genome. While ribosomal protein genes strongly place Thermotogales as a sister group to Aquificales, the majority of genes with sufficient phylogenetic signal show affinities to Archaea and Firmicutes, especially Clostridia. Indeed, on the basis of the majority of genes in their genomes (including genes that are also found in Aquificales), Thermotogales should be considered members of the Firmicutes. This result highlights the conflict between the taxonomic goal of assigning every species to a unique position in an inclusive Linnaean hierarchy and the evolutionary goal of understanding phylogenesis in the presence of pervasive horizontal gene transfer (HGT) within prokaryotes. Amino acid compositions of reconstructed ancestral sequences from 423 gene families suggest an origin of this gene pool even more thermophilic than extant members of this order, followed by adaptation to lower growth temperatures within the Thermotogales. PMID:19307556

  9. Responses of Halophytes to High Salinities and Low Water Potentials 1

    PubMed Central

    Jefferies, Robert L.; Rudmik, Tony; Dillon, Eva M.

    1979-01-01

    The effects of nonsaline polyethylene glycol (PEG)-6000 and saline seawater solutions of comparable osmotic potential on the concentrations of organic solutes and inorganic ions in the tissues of halophytes (Plantago maritima L., Triglochin maritima L., Limonium vulgare Mill., Halimione portulacoides (L.) Aell) have been investigated. Studies were made to determine whether high salinities induce specific ion effects that are absent in plants grown in nonsaline solutions of comparable osmotic potential. Over-all, the responses of each species to the two different treatments (seawater or PEG) are similar; the accumulation of organic solutes (compatible osmotica) in tissues is primarily correlated with a decrease in the osmotic potential of culture solutions. Depending on the species, sorbitol, proline, reducing sugars, quaternary ammonium compounds, and α-amino nitrogen accumulate in tissues as the water potential of the tissues falls. Within a species there are differences in the concentrations of inorganic ions and organic solutes between roots and shoots of plants grown at high salinities or at high concentrations of PEG. PMID:16661119

  10. Organism traits determine the strength of scale-dependent bio-geomorphic feedbacks: A flume study on three intertidal plant species

    NASA Astrophysics Data System (ADS)

    Bouma, T. J.; Temmerman, S.; van Duren, L. A.; Martini, E.; Vandenbruwaene, W.; Callaghan, D. P.; Balke, T.; Biermans, G.; Klaassen, P. C.; van Steeg, P.; Dekker, F.; van de Koppel, J.; de Vries, M. B.; Herman, P. M. J.

    2013-01-01

    There is a growing recognition of the important role of scale-dependent feedback for biogeomorphological landscape formation, where organisms locally improve survival and growth but at the same time negatively affect organisms at larger distance. However, little is known on how scale-dependent bio-geomorphic feedback is influenced by organism traits in combination with abiotic forcing. This was studied by measuring in a flume, the flow patterns around patches of three contrasting marsh species (Spartina anglica, Puccinellia maritima and Salicornia procumbens), using the flow acceleration around vegetation patches and deceleration within vegetation patches as quantitative proxy for the negative and positive feedback to the vegetation performance. The importance of external forcing was assessed by comparing three realistic current velocities: 0.1, 0.2 and 0.3 m s- 1. Our results showed that the dense clonal growth of stiff Spartina anglica shoots caused strongest flow deviations, irrespective of the applied current velocity. In contrast, the more sparsely growing, shorter stiff shoots of Salicornia procumbens induced much less flow deviation, allowing more water to pass through and over the vegetation canopy. The dense but highly flexible shoots of Puccinellia maritima caused strong flow deviations at low velocities, which diminished at higher velocities due to bending of the vegetation. Overall, these hydrodynamic results demonstrate that plant species traits interact with environmental conditions in creating scale-dependent feedbacks explaining why the effects of vegetation on landscape formation in saltmarshes are species specific.

  11. A taste for exotic food: Neotropical land planarians feeding on an invasive flatworm

    PubMed Central

    Boll, Piter K.; Rossi, Ilana; Amaral, Silvana V.

    2015-01-01

    Invasive species establish successfully in new habitats especially due to their ability to include new species in their diet and due to the freedom from natural enemies. However, native species may also adapt to the use of new elements in their ecosystem. The planarian Endeavouria septemlineata, first recorded in Hawaii, was later found in Brazil. Recently, we found it in human-disturbed areas in southern Brazil and here we investigate its interactions with other invertebrates both in the field and in the laboratory. We observed the species in the field during collecting activities and hence maintained some specimens alive in small terraria in the laboratory, where we offered different invertebrate species as potential prey and also put them in contact with native land planarians in order to examine their interaction. Both in the field and in the laboratory, E. septemlineata showed a gregarious behavior and was found feeding on woodlice, millipedes, earwigs and gastropods. In the laboratory, specimens often did not attack live prey, but immediately approached dead specimens, indicating a scavenging behavior. In an experiment using the slug Deroceras laeve and the woodlouse Atlantoscia floridana, there was a higher consumption of dead specimens of woodlice and slugs compared to live specimens, as well as a higher consumption of dead woodlice over dead slugs. Four native land planarians of the genus Obama and one of the genus Paraba attacked and consumed E. septemlineata, which, after the beginning of the attack, tried to escape by tumbling or using autotomy. As a scavenger, E. septemlineata would have no impact on the populations of species used as food, but could possibly exclude native scavengers by competition. On the other hand, its consumption by native land planarians may control its spread and thus reduce its impact on the ecosystem. PMID:26500817

  12. A taste for exotic food: Neotropical land planarians feeding on an invasive flatworm.

    PubMed

    Boll, Piter K; Rossi, Ilana; Amaral, Silvana V; Leal-Zanchet, Ana

    2015-01-01

    Invasive species establish successfully in new habitats especially due to their ability to include new species in their diet and due to the freedom from natural enemies. However, native species may also adapt to the use of new elements in their ecosystem. The planarian Endeavouria septemlineata, first recorded in Hawaii, was later found in Brazil. Recently, we found it in human-disturbed areas in southern Brazil and here we investigate its interactions with other invertebrates both in the field and in the laboratory. We observed the species in the field during collecting activities and hence maintained some specimens alive in small terraria in the laboratory, where we offered different invertebrate species as potential prey and also put them in contact with native land planarians in order to examine their interaction. Both in the field and in the laboratory, E. septemlineata showed a gregarious behavior and was found feeding on woodlice, millipedes, earwigs and gastropods. In the laboratory, specimens often did not attack live prey, but immediately approached dead specimens, indicating a scavenging behavior. In an experiment using the slug Deroceras laeve and the woodlouse Atlantoscia floridana, there was a higher consumption of dead specimens of woodlice and slugs compared to live specimens, as well as a higher consumption of dead woodlice over dead slugs. Four native land planarians of the genus Obama and one of the genus Paraba attacked and consumed E. septemlineata, which, after the beginning of the attack, tried to escape by tumbling or using autotomy. As a scavenger, E. septemlineata would have no impact on the populations of species used as food, but could possibly exclude native scavengers by competition. On the other hand, its consumption by native land planarians may control its spread and thus reduce its impact on the ecosystem. PMID:26500817

  13. Parental antagonism and parent–offspring co-adaptation interact to shape family life

    PubMed Central

    Meunier, Joël; Kölliker, Mathias

    2012-01-01

    The family is an arena for conflicts between offspring, mothers and fathers that need resolving to promote the evolution of parental care and the maintenance of family life. Co-adaptation is known to contribute to the resolution of parent–offspring conflict over parental care by selecting for combinations of offspring demand and parental supply that match to maximize the fitness of family members. However, multiple paternity and differences in the level of care provided by mothers and fathers can generate antagonistic selection on offspring demand (mediated, for example, by genomic imprinting) and possibly hamper co-adaptation. While parent–offspring co-adaptation and parental antagonism are commonly considered two major processes in the evolution of family life, their co-occurrence and the evolutionary consequences of their joint action are poorly understood. Here, we demonstrate the simultaneous and entangled effects of these two processes on outcomes of family interactions, using a series of breeding experiments in the European earwig, Forficula auricularia, an insect species with uniparental female care. As predicted from parental antagonism, we show that paternally inherited effects expressed in offspring influence both maternal care and maternal investment in future reproduction. However, and as expected from the entangled effects of parental antagonism and co-adaptation, these effects critically depended on postnatal interactions with caring females and maternally inherited effects expressed in offspring. Our results demonstrate that parent–offspring co-adaptation and parental antagonism are entangled key drivers in the evolution of family life that cannot be fully understood in isolation. PMID:22810433

  14. Investigating the genetic architecture of conditional strategies using the environmental threshold model.

    PubMed

    Buzatto, Bruno A; Buoro, Mathieu; Hazel, Wade N; Tomkins, Joseph L

    2015-12-22

    The threshold expression of dichotomous phenotypes that are environmentally cued or induced comprise the vast majority of phenotypic dimorphisms in colour, morphology, behaviour and life history. Modelled as conditional strategies under the framework of evolutionary game theory, the quantitative genetic basis of these traits is a challenge to estimate. The challenge exists firstly because the phenotypic expression of the trait is dichotomous and secondly because the apparent environmental cue is separate from the biological signal pathway that induces the switch between phenotypes. It is the cryptic variation underlying the translation of cue to phenotype that we address here. With a 'half-sib common environment' and a 'family-level split environment' experiment, we examine the environmental and genetic influences that underlie male dimorphism in the earwig Forficula auricularia. From the conceptual framework of the latent environmental threshold (LET) model, we use pedigree information to dissect the genetic architecture of the threshold expression of forceps length. We investigate for the first time the strength of the correlation between observable and cryptic 'proximate' cues. Furthermore, in support of the environmental threshold model, we found no evidence for a genetic correlation between cue and the threshold between phenotypes. Our results show strong correlations between observable and proximate cues and less genetic variation for thresholds than previous studies have suggested. We discuss the importance of generating better estimates of the genetic variation for thresholds when investigating the genetic architecture and heritability of threshold traits. By investigating genetic architecture by means of the LET model, our study supports several key evolutionary ideas related to conditional strategies and improves our understanding of environmentally cued decisions. PMID:26674955

  15. Cover Cropping Alters the Diet of Arthropods in a Banana Plantation: A Metabarcoding Approach

    PubMed Central

    Mollot, Gregory; Duyck, Pierre-François; Lefeuvre, Pierre; Lescourret, Françoise; Martin, Jean-François; Piry, Sylvain; Canard, Elsa; Tixier, Philippe

    2014-01-01

    Plant diversification using cover crops may promote natural regulation of agricultural pests by supporting alternative prey that enable the increase of arthropod predator densities. However, the changes in the specific composition of predator diet induced by cover cropping are poorly understood. Here, we hypothesized that the cover crop can significantly alter the diet of predators in agroecosystems. The cover crop Brachiaria decumbens is increasingly used in banana plantations to control weeds and improve physical soil properties. In this paper, we used a DNA metabarcoding approach for the molecular analysis of the gut contents of predators (based on mini-COI) to identify 1) the DNA sequences of their prey, 2) the predators of Cosmopolites sordidus (a major pest of banana crops), and 3) the difference in the specific composition of predator diets between a bare soil plot (BSP) and a cover cropped plot (CCP) in a banana plantation. The earwig Euborellia caraibea, the carpenter ant Camponotus sexguttatus, and the fire ant Solenopsis geminata were found to contain C. sordidus DNA at frequencies ranging from 1 to 7%. While the frequencies of predators positive for C. sordidus DNA did not significantly differ between BSP and CCP, the frequency at which E. caraibea was positive for Diptera was 26% in BSP and 80% in CCP; the frequency at which C. sexguttatus was positive for Jalysus spinosus was 14% in BSP and 0% in CCP; and the frequency at which S. geminata was positive for Polytus mellerborgi was 21% in BSP and 3% in CCP. E. caraibea, C. sexguttatus and S. geminata were identified as possible biological agents for the regulation of C. sordidus. The detection of the diet changes of these predators when a cover crop is planted indicates the possible negative effects on pest regulation if predators switch to forage on alternative prey. PMID:24695585

  16. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    PubMed Central

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman; Wu, Si; Brewer, Heather M.; Gogarten, J. Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-01-01

    The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompα) and the porin OmpB (or Ompβ). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant β-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had β-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath. PMID:22768259

  17. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    SciTech Connect

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman R.; Wu, Si; Brewer, Heather M.; Gogarten, J Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-06-29

    The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompa) and the porin OmpB (or Ompb). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant b-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had b-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  18. POLYPEPTIDE AND POLYSACCHARIDE PROCESSING IN HYPERTHERMOPHILIC MICROORGANISMS

    SciTech Connect

    KELLY, ROBERT M.

    2008-12-22

    This project focused on the microbial physiology and biochemistry of heterotrophic hyperthermophiles with respect to mechanisms by which these organisms process polypeptides and polysaccharides under normal and stressed conditions. Emphasis is on two model organisms, for which completed genome sequences are available: Pyrococcus furiosus (growth Topt of 98°C), an archaeon, and Thermotoga maritima (growth Topt of 80°C), a bacterium. Both organisms are obligately anaerobic heterotrophs that reduce sulfur facultatively. Whole genome cDNA spotted microarrays were used to follow transcriptional response to a variety of environmental conditions in order to identify genes encoding proteins involved in the acquisition, synthesis, processing and utilization of polypeptides and polysaccharides. This project provided new insights into the physiological aspects of hyperthermophiles as these relate to microbial biochemistry and biological function in high temperature habitats. The capacity of these microorganisms to produce biohydrogen from renewable feedstocks makes them important for future efforts to develop biofuels.

  19. Proteolysis in hyperthermophilic microorganisms

    DOE PAGESBeta

    Ward, Donald E.; Shockley, Keith R.; Chang, Lara S.; Levy, Ryan D.; Michel, Joshua K.; Conners, Shannon B.; Kelly, Robert M.

    2002-01-01

    Proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. Genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. In this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus Pyrococcus , the crenarchaeote Sulfolobus solfataricus , and the bacterium Thermotoga maritima . An overview of the proteases in these organisms is given based on those proteases that have been characterized and on putativemore » proteases that have been identified from genomic sequences, but have yet to be characterized. The analysis revealed both similarities and differences in the mechanisms utilized for proteolysis by each of these hyperthermophiles and indicated how these mechanisms relate to proteolysis in less thermophilic cells and organisms.« less

  20. In situ nitrogen generation removes wax from flowlines

    SciTech Connect

    Khalil, C.N.

    1996-07-01

    Formation of paraffin (wax) in cold deepwater flowlines is a major problem for offshore operators of such facilities. Petrobras faces this problem continuously in its deepwater operations in the Campos basin, offshore Brazil. Since 1990, through its Petrobras Research Center (CENPES), the company has developed, extensively field tested, and recently commercialized, a novel technique for chemically removing such wax depositions. The process involves mixing and introducing to the line, two inorganic salts and organic solvents. The ensuing chemical reaction--which both generates nitrogen and heats the inside of the blocked flowline--allows the solvent to dissolve and dislodge the buildup, which is then flushed from the line. The process is called the Nitrogen Generation System (SGN). Petrobras/CENPES has recently formed a joint venture with the Brazilian service company Maritima Navegacao e Engenharia Ltda. to offer SGN services worldwide.

  1. Proteolysis in hyperthermophilic microorganisms

    PubMed Central

    Ward, Donald E.; Shockley, Keith R.; Chang, Lara S.; Levy, Ryan D.; Michel, Joshua K.; Conners, Shannon B.; Kelly, Robert M.

    2002-01-01

    Proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. Genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. In this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus Pyrococcus, the crenarchaeote Sulfolobus solfataricus, and the bacterium Thermotoga maritima. An overview of the proteases in these organisms is given based on those proteases that have been characterized and on putative proteases that have been identified from genomic sequences, but have yet to be characterized. The analysis revealed both similarities and differences in the mechanisms utilized for proteolysis by each of these hyperthermophiles and indicated how these mechanisms relate to proteolysis in less thermophilic cells and organisms. PMID:15803660

  2. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling

    PubMed Central

    Podgornaia, Anna I.; Casino, Patricia; Marina, Alberto; Laub, Michael T.

    2013-01-01

    Summary Two-component signal transduction systems typically involve a sensor histidine kinase that specifically phosphorylates a single, cognate response regulator. This protein-protein interaction relies on molecular recognition via a small set of residues in each protein. To better understand how these residues determine the specificity of kinase-substrate interactions, we rationally rewired the interaction interface of a Thermotoga maritima two-component system, HK853-RR468, to match that found in a different two-component system, E. coli PhoR-PhoB. The rewired proteins interacted robustly with each other, but no longer interacted with the parent proteins. Analysis of the crystal structures of the wild-type and mutant protein complexes, along with a systematic mutagenesis study, reveals how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions, protein evolution, and the design of novel protein interfaces. PMID:23954504

  3. Upon Further Review: VI. An Examination of Previous Lightcurve Analysis from the Palmer Divide Observatory

    NASA Astrophysics Data System (ADS)

    Warner, Brian D.

    2011-04-01

    Updated results of lightcurve analysis are given for 31 asteroids previously reported from the Palmer Divide Observatory (PDO). The original images were remeasured to obtain new data sets using the latest version of MPO Canopus photometry software, analysis tools, and revised techniques for linking observing runs that ranged from several days to several weeks. Moderately to significantly different results were found for: 301 Bavaria, 436 Patricia, 507 Laodica, 549 Jessonda, 585 Bilkis, 596 Scheila, 607 Jenny, 630 Euphemia, 875 Nymphe, 912 Maritima, 926 Imhilde, 1177 Gonnessia, 1203 Nanna, 1333 Cevenola, 1679 Nevanlinna, 1796 Riga, 2000 Herschel, 2266 Tchaikovsky, 2460 Mitlincoln, 2494 Inge, 3915 Fukushima, 3940 Larion, 4091 Lowe, 4209 Briggs, 4431 Holeungholee, 4690 Strasbourg, 5390 Huichiming, 5940 Feliksobolev, (16558) 1991 VQ2, (18108) 2000 NT5, and (45646) 2000 EE45. This is expected to be the final paper in a current series that has examined results obtained during the initial years of the asteroid lightcurve program at PDO.

  4. Feeding ecology of waterfowl wintering on evaporation ponds in California

    USGS Publications Warehouse

    Euliss, N.H., Jr.; Jarvis, R.L.; Gilmer, D.S.

    1991-01-01

    We examined the feeding ecology of Northern Pintails (Anas acuta), Northern Shovelers (A. clypeata), and Ruddy Ducks (Oxyura jamaicensis) wintering on drainwater evaporation ponds in California from 1982 through 1984. Pintails primarily consumed midges (Chironomidae) (39.3%) and widegeongrass (Ruppia maritima) nutlets (34.6%). Shovelers and Ruddy Ducks consumed 92.5% and 90.1% animal matter, respectively. Water boatmen (Corixidae) (51.6%), rotifers (Rotatoria) (20.4%), and copepods (Copepoda) (15.2%) were the most important Shoveler foods, and midges (49.7%) and water boatmen (36.0%) were the most important foods of Ruddy Ducks. All three species were opportunistic foragers, shifting their diets seasonally to the most abundant foods given their behavioral and morphological attributes.

  5. A redescription of Rhysida celeris (Humbert & Saussure, 1870), with a proposal of eight new synonyms (Scolopendromorpha, Scolopendridae, Otostigminae).

    PubMed

    Chagas-Júnior, Amazonas

    2013-01-01

    Seven species of the genus Rhysida Wood, 1862 from Venezuela and one subspecies from Peru described by Manuel Angel González Sponga and Wolfgang Bücherl respectively, are revised. Rhysida caripensis González-Sponga, 2002, Rhysida neoespartana González-Sponga, 2002, Rhysida guayanica González-Sponga, 2002, Rhysida maritima González-Sponga, 2002, Rhysida monaguensis González-Sponga, 2002, Rhysida porlamarensis González-Sponga 2002, Rhysida sucupanensis González-Sponga, 2002 and Rhysida celeris andina Bücherl, 1953 are junior synonyms of Rhysida celeris (Humbert & Saussure, 1870), which is redescribed and illustrated for the first time. Its geographic distribution is updated and a map showing its distribution is presented. PMID:23653497

  6. Nutrient levels modify saltmarsh responses to increased inundation in different soil types.

    PubMed

    Wong, Joanne X W; Van Colen, Carl; Airoldi, Laura

    2015-03-01

    Saltmarshes have been depleted historically, and cumulative stressors threaten their future persistence. We examined experimentally how nutrient availability (high vs. low) affects the responses of Spartina maritima to increased inundation in two mineral soil types (low vs. medium organic). Increased inundation, one of the effects of accelerated sea level rise, had negative effects on most plant growth parameters, but the magnitude varied with soil and nutrient levels, and between plants from different locations. Average differences between inundation treatments were largest at high nutrient conditions in low organic matter soils. We conclude that saltmarsh vegetation would be more drastically affected by increased inundation in low than in medium organic matter soils, and especially in estuaries already under high nutrient availability. This knowledge enhances the prediction of changes at the foreshore of saltmarshes related to sea level rise, and the development of site-specific conservation strategies. PMID:25594372

  7. Diversity of beet curly top Iran virus isolated from different hosts in Iran.

    PubMed

    Gharouni Kardani, Sara; Heydarnejad, Jahangir; Zakiaghl, Mohammad; Mehrvar, Mohsen; Kraberger, Simona; Varsani, Arvind

    2013-06-01

    Beet curly top Iran virus (BCTIV) is a major pathogen of sugar beet in Iran. In order to study diversity of BCTIV, we sampled 68 plants in Iran during the summer of 2010 with curly top disease symptoms on beans (Phaseolus vulgaris), cowpeas (Vigna unguiculata), tomatoes (Solanum lycopersicum L.), sea beets (Beta vulgaris subsp. maritima), and sugar beets (Beta vulgaris). Plant samples showing leaf curling, yellowing, and/or swelling of veins on the lower leaf surfaces were collected from various fields in Khorasan Razavi, Northern Khorasan (north-eastern Iran), East Azarbayejan, West Azarbayejan (north-western Iran), and Fars (southern Iran) provinces. Using rolling circle amplification coupled with restriction digests, cloning, and Sanger sequencing, we determined the genomes of nine new BCTIV isolates from bean, cowpea, tomato, sea beet, and sugar beet in Iran. Our analysis reveals ~11 % diversity amongst BCTIV isolates and we detect evidence of recombination within these genomes. PMID:23329008

  8. Wetland plants as indicators of heavy metal contamination.

    PubMed

    Phillips, D P; Human, L R D; Adams, J B

    2015-03-15

    In this study metal accumulating abilities of three emergent macrophytes (Phragmites australis, Typha capensis and Spartina maritima) were investigated in the urbanised Swartkops Estuary. Plants and sediment samples were collected at seven sites along the banks of the main channel and in adjacent canals. Sediments and plant organs were analysed, by means of atomic absorption spectrometry, for four elements (Cd, Cu, Pb, and Zn). Metal concentrations in the sediments of adjacent canals were found to be substantially higher than those at sites along the banks of the estuary. These differences were reflected in the plant organs for Pb and Zn, but not for Cu and Cd. All three species exhibited significantly higher concentrations of metals in their roots. These species are therefore suitable for use as indicators of the presence and level of heavy metal contaminants in estuaries. PMID:25599629

  9. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

    NASA Technical Reports Server (NTRS)

    Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

    1989-01-01

    Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

  10. Which plant for which skin disease? Part 2: Dermatophytes, chronic venous insufficiency, photoprotection, actinic keratoses, vitiligo, hair loss, cosmetic indications.

    PubMed

    Reuter, Juliane; Wölfle, Ute; Korting, Hans Christian; Schempp, Christoph

    2010-11-01

    This paper continues our review of scientifically evaluated plant extracts in dermatology. After plants effective against dermatophytes, botanicals with anti-edema effects in chronic venous insufficiency are discussed. There is good evidence from randomized clinical studies that plant extracts from grape vine leaves (Vitis vinifera), horse chestnut (Aesculus hippocastanum), sea pine (Pinus maritima) and butcher's broom (Ruscus aculeatus) can reduce edema in chronic venous insufficiency. Plant extracts from witch hazel (Hamamelis virginiana), green tea (Camellia sinensis), the fern Polypodium leucotomos and others contain antioxidant polyphenolic compounds that may protect the skin from sunburn and photoaging when administered topically or systemically. Extracts from the garden spurge (Euphorbia peplus) and from birch bark (Betula alba) have been shown to be effective in the treatment of actinic keratoses in phase II studies. Some plant extracts have also been investigated in the treatment of vitiligo, various forms of hair loss and pigmentation disorders, and in aesthetic dermatology. PMID:20707877

  11. Biochemical Characterization and Structural Analysis of a Bifunctional Cellulase/Xylanase from Clostridium thermocellum*

    PubMed Central

    Yuan, Shuo-Fu; Wu, Tzu-Hui; Lee, Hsiao-Lin; Hsieh, Han-Yu; Lin, Wen-Ling; Yang, Barbara; Chang, Chih-Kang; Li, Qian; Gao, Jian; Huang, Chun-Hsiang; Ho, Meng-Chiao; Guo, Rey-Ting; Liang, Po-Huang

    2015-01-01

    We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities. PMID:25575592

  12. Food habits and distribution of wintering canvasbacks, Aythya valisineria, on Chesapeake Bay

    USGS Publications Warehouse

    Perry, M.C.; Uhler, F.M.

    1988-01-01

    Baltic clams (Macoma balthica) were the predominant food items of 323 canvasbacks (Aythya valisineria) collected throughout Chesapeake Bay during 1970-1979. Natural vegetation constituted 4% of the food volume. Widgeongrass (Ruppia maritima) and redhead grass (Potamogeton perfoliatus) constituted the greatest percent volume and frequency of occurrence among the plant species, whereas wild celery (Vallisneria americana) constituted only a trace of the food volume. These results contrast with historical records of food habits of canvasbacks in Chesapeake Bay. Canvasback population estimates during the 1970?s were examined to detect annual and seasonal changes in distribution. Linear regression analyses of winter canvasback populations in the bay showed a significant decline in the upper-bay and middle-bay populations, but no significant changes in the lower-bay and Potomac River populations. The changes in winter distribution and abundance of the canvasback appear related to changes in natural food availability, which is the result of altered environmental conditions.

  13. RNA-activated DNA cleavage by the Type III-B CRISPR-Cas effector complex.

    PubMed

    Estrella, Michael A; Kuo, Fang-Ting; Bailey, Scott

    2016-02-15

    The CRISPR (clustered regularly interspaced short palindromic repeat) system is an RNA-guided immune system that protects prokaryotes from invading genetic elements. This system represents an inheritable and adaptable immune system that is mediated by multisubunit effector complexes. In the Type III-B system, the Cmr effector complex has been found to cleave ssRNA in vitro. However, in vivo, it has been implicated in transcription-dependent DNA targeting. We show here that the Cmr complex from Thermotoga maritima can cleave an ssRNA target that is complementary to the CRISPR RNA. We also show that binding of a complementary ssRNA target activates an ssDNA-specific nuclease activity in the histidine-aspartate (HD) domain of the Cmr2 subunit of the complex. These data suggest a mechanism for transcription-coupled DNA targeting by the Cmr complex and provide a unifying mechanism for all Type III systems. PMID:26848046

  14. The method of integrated kinetics and its applicability to the exo-glycosidase-catalyzed hydrolysis of p-nitrophenyl glycosides.

    PubMed

    Borisova, Anna S; Reddy, Sumitha K; Ivanen, Dina R; Bobrov, Kirill S; Eneyskaya, Elena V; Rychkov, Georgy N; Sandgren, Mats; Stålbrand, Henrik; Sinnott, Michael L; Kulminskaya, Anna A; Shabalin, Konstantin A

    2015-08-14

    In the present work we suggest an efficient method, using the whole time course of the reaction, whereby parameters kcat, Km and product KI for the hydrolysis of a p-nitrophenyl glycoside by an exo-acting glycoside hydrolase can be estimated in a single experiment. Its applicability was demonstrated for three retaining exo-glycoside hydrolases, β-xylosidase from Aspergillus awamori, β-galactosidase from Penicillium sp. and α-galactosidase from Thermotoga maritima (TmGalA). During the analysis of the reaction course catalyzed by the TmGalA enzyme we had observed that a non-enzymatic process, mutarotation of the liberated α-d-galactose, affected the reaction significantly. PMID:26005928

  15. Cooperative action of alpha-glucanotransferase and maltogenic amylase for an improved process of isomaltooligosaccharide (IMO) production.

    PubMed

    Lee, Hyun-Soo; Auh, Joong-Hyuck; Yoon, Hyun-Geun; Kim, Myo-Jeong; Park, Jin-Hee; Hong, Seung-Suh; Kang, Min-Hyung; Kim, Tae-Jip; Moon, Tae-Wha; Kim, Jung-Wan; Park, Kwan-Hwa

    2002-05-01

    Maltogenic amylase and alpha-glucanotransferase (alpha-GTase) were employed in an effort to develop an efficient process for the production of isomaltooligosaccharides (IMOs). Bacillus stearothermophilus maltogenic amylase (BSMA) and alpha-GTase from Thermotoga maritima were overexpressed in Escherichia coli using overexpression vectors. An IMO mixture containing 58% of various IMOs was produced from liquefied corn syrup by the hydrolyzing and transglycosylation activities of BSMA alone. When BSMA and alpha-GTase were reacted simultaneously, the IMO content increased to 68% and contained relatively larger IMOs compared with the products obtained by the reaction without alpha-GTase. Time course analysis of the IMO production suggested that BSMA hydrolyzed maltopentaose and maltohexaose most favorably into maltose and maltotriose and transferred the resulting molecules simultaneously to acceptor molecules to form IMOs. alpha-GTase transferred donor sugar molecules to the hydrolysis products such as maltose and maltotriose to form maltopentaose, which was then rehydrolyzed by BSMA as a favorable substrate. PMID:11982404

  16. Feasibility of using hyperaccumulating plants to bioremediate metal-contaminated soil

    SciTech Connect

    Kelly, R.J.; Guerin, T.F.

    1995-12-31

    A feasibility study was carried out to determine whether selected plants were capable of hyperaccumulating anthropogenic sources of metals found in soils from three contaminated sites. A trial was conducted using the previously reported hyperaccumulators, Armeria maritima (thrift), Impatiens balsamina (balsam), Alyssum saxatile (gold dust), and the control species, Brassica oleracea (cabbage). Although none of these plants showed any substantial hyperaccumulation of Cu, Zn, Pb, and Cd, it was established that there is an optimum period in the life-cycle of these plants in which the metal concentration reaches a maximum. This period was dependent on the metal, soil, and plant type. The current paper describes the data obtained for Zn and Cu uptake by thrift.

  17. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    PubMed Central

    Martinez-Hackert, Erik; Hendrickson, Wayne A.

    2009-01-01

    SUMMARY Trigger factor (TF) is a molecular chaperone that famously binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. This is the first atomic-level structure of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding and suggests a role for TF in the biogenesis of protein complexes. PMID:19737520

  18. Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone

    SciTech Connect

    Martinez-Hackert, E.; Hendrickson, W

    2009-01-01

    Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.

  19. In silico method for modelling metabolism and gene product expression at genome scale

    SciTech Connect

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  20. Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1.

    PubMed

    Furusawa, Go; Lau, Nyok-Sean; Shu-Chien, Alexander Chong; Jaya-Ram, Annette; Amirul, Al-Ashraf Abdullah

    2015-02-01

    The genus Aureispira consisting of two species, Aureispira marina and Aureispira maritima is an arachidonic acid-producing bacterium and produces secondary metabolites. In this study, we isolated a new Aureispira strain, Aureispira sp. CCB-QB1 from coastal area of Penang, Malaysia and the genome sequence of this strain was determined. The draft genome of this strain is composed of 185 contigs for 7,370,077 bases with 35.6% G+C content and contains 5911 protein-coding genes and 76 RNA genes. Linoleoyl-CoA desaturase, the key gene in arachidonic acid biosynthesis, is present in the genome. It was found that this strain uses mevalonate pathway for the synthesis of geranylgeranyl diphosphate (GGPP), which is precursor of diterpenoid, and novel pathway via futalosine for the synthesis of menaquinones. This is the first draft genome sequence of a member of the genus Aureispira. PMID:25468060

  1. Radical scavenging, antioxidant and antimicrobial activities of halophytic species.

    PubMed

    Meot-Duros, Laetitia; Le Floch, Gaëtan; Magné, Christian

    2008-03-01

    For the first time, both antioxidant and antimicrobial activities are simultaneously reported in halophytic plants, particularly on polar fractions. Chloroformic and methanolic extracts of the halophytes Eryngium maritimum L., Crithmum maritimum L. and Cakile maritima Scop. were tested for their antimicrobial activities against 12 bacterial and yeast strains. In addition, radical scavenging and antioxidant activities were assessed, as well as total phenol contents. Only one bacterial strain (Listeria monocytogenes) was not inhibited by plants extracts, and apolar (chloroformic) fractions were generally more active than polar (methanolic) ones. Eryngium maritimum presented the weakest radical scavenging activity (ABTS IC(50)=0.28 mg ml(-1)), as well as the lowest total phenol content (16.4 mg GAE g(-1) DW). However, the three halophytic species had relatively strong total antioxidant activities (from 32.7 to 48.6 mg ascorbate equivalents g (-1) DW). Consequences on the potential use of these plants in food or cosmetic industry are discussed. PMID:18164885

  2. Intrinsic stability of Brassicaceae plasma membrane in relation to changes in proteins and lipids as a response to salinity.

    PubMed

    Chalbi, Najla; Martínez-Ballesta, Ma Carmen; Youssef, Nabil Ben; Carvajal, Micaela

    2015-03-01

    Changes in plasma membrane lipids, such as sterols and fatty acids, have been observed as a result of salt stress. These alterations, together with modification of the plasma membrane protein profile, confer changes in the physical properties of the membrane to be taken into account for biotechnological uses. In our experiments, the relationship between lipids and proteins in three different Brassicaceae species differing in salinity tolerance (Brassica oleracea, B. napus and Cakile maritima) and the final plasma membrane stability were studied. The observed changes in the sterol (mainly an increase in sitosterol) and fatty acid composition (increase in RUFA) in each species led to physical adaptation of the plasma membrane to salt stress. The in vitro vesicles stability was higher in the less tolerant (B. oleracea) plants together with low lipoxygenase activity. These results indicate that the proteins/lipids ratio and lipid composition is an important aspect to take into account for the use of natural vesicles in plant biotechnology. PMID:25544590

  3. Influence of biological, environmental and technical factors on phenolic content and antioxidant activities of Tunisian halophytes.

    PubMed

    Ksouri, Riadh; Megdiche, Wided; Falleh, Hanen; Trabelsi, Nejla; Boulaaba, Mondher; Smaoui, Abderrazak; Abdelly, Chedly

    2008-11-01

    Halophyte ability to withstand salt-triggered oxidative stress is governed by multiple biochemical mechanisms that facilitate retention and/or acquisition of water, protect chloroplast functioning, and maintain ion homeostasis. Most essential traits include the synthesis of osmolytes, specific proteins, and antioxidant molecules. This might explain the utilization of some halophytes as traditional medicinal and dietary plants. The present study aimed at assessing the phenolic content and antioxidant activities of some Tunisian halophytes (Cakile maritima, Limoniastrum monopetalum, Mesembryanthemum crystallinum, M. edule, Salsola kali, and Tamarix gallica), depending on biological (species, organ and developmental stage), environmental, and technical (extraction solvent) factors. The total polyphenol contents and antioxidant activities (DPPH and superoxide radicals scavenging activities, and iron chelating and reducing powers) were strongly affected by the above-cited factors. Such variability might be of great importance in terms of valorising these halophytes as a source of naturally secondary metabolites, and the methods for phenolic and antioxidant production. PMID:18940702

  4. Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada

    PubMed Central

    Saarela, Jeffery M.

    2012-01-01

    Abstract Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves. PMID:22461730

  5. Biohydrogenesis in the Thermotogales

    SciTech Connect

    Kelly, Robert M

    2014-12-13

    The production and consumption of molecular hydrogen drives the physiology and bioenergetics of many microorganisms in hydrothermal environments. As such, the potential of these microorganisms as model systems to probe fundamental issues related to biohydrogen production merits consideration. It is important to understand how carbon/energy sources relate to the disposition of reducing power and, ultimately, the formation of molecular hydrogen by high temperature microorganisms. This project focused on bacteria in the thermophilic order Thermotogales, fermentative anaerobes that produce H2 from simple and complex carbohydrates. The major thrusts of the project are summarized in the Objectives listed below: OBJECTIVE 1: Examine the regulation of substrate catabolic proteins and pathways as this relates to carbon partitioning, disposition of reducing power, and H2 generation in Thermotoga maritima. OBJECTIVE 2: Apply classical genetics and develop molecular genetic tools for Thermotoga species to dissect catabolic and regulatory pathways related to sugar metabolism and H2 evolution. OBJECTIVE 3: Thermotogales biodiversity arises from adaptive specialization that expands on a conserved minimal genome; physiological characterization of selected novel traits will be done to expand understanding of biohydrogenesis. Four species within the genus Thermotoga were examined to understand similarities and differences in the mechanisms by which simple and complex carbohydrates were utilized and converted to molecular hydrogen. Although the core genome of these four species represented 75% of open reading frames (ORFs), there were significant differences in carbohydrate utilization patterns. New ABC transporters were identified within the Thermotogales through genomic and biochemical analysis. Molecular genetics tools were developed to examine Thermotoga maritima physiology. Cell lines were created in which both H2 and acetate levels were elevated on a per cell basis relative to the wild type, while lactate remained undetectable. Genome resequencing indicated that the primary genetic target for these phenotypic changes was the ATP binding component of a maltose ABC transporter. High temperature anaerobic [14C]-maltose transport assays demonstrated maltose uptake was reduced in the H2 overproducing cell lines. This suggested normal rates of maltose transport in the wild type organism lead to a metabolic imbalance that limited H2 synthesis. The microbial ecology of T. maritima was examined through functional genomics experiments. Under low nutrient conditions, T. maritima was observed to produce a range of putative peptides, some of which were related to α-carbon cyclic peptides produced by Bacillus subtilus. Finally, the role of ‘toga’ in these novel microorganisms was shown to involve association with insoluble growth substrates. The ‘toga’ distends from the cytoplasmic membrane-enclosed portion of the cells as they enter the late exponential/stationary phase of growth. Some of the genes encoding toga-associated proteins were up-regulated during this phase of growth and the distension is caused by continued growth of the toga, and not shrinkage of the cytoplasmic aspect of the cells. This increase in cell surface area may have selective value to provide a larger anchor for polysaccharide hydrolytic enzymes during a time of nutritional stress. This project led to many interesting insights about the Thermotogales that have both scientific and technological implications. Ongoing work will leverage these developments to further elucidate many interesting features of these novel microorganisms.

  6. A redescription of Rhysida celeris (Humbert & Saussure, 1870), with a proposal of eight new synonyms (Scolopendromorpha, Scolopendridae, Otostigminae)

    PubMed Central

    Chagas-Júnior, Amazonas

    2013-01-01

    Abstract Seven species of the genus Rhysida Wood, 1862 from Venezuela and one subspecies from Peru described by Manuel Angel González Sponga and Wolfgang Bücherl respectively, are revised. Rhysida caripensis González-Sponga, 2002, Rhysida neoespartana González-Sponga, 2002, Rhysida guayanica González-Sponga, 2002, Rhysida maritima González-Sponga, 2002, Rhysida monaguensis González-Sponga, 2002, Rhysida porlamarensis González-Sponga 2002, Rhysida sucupanensis González-Sponga, 2002 and Rhysida celeris andina Bücherl, 1953 are junior synonyms of Rhysida celeris (Humbert & Saussure, 1870), which is redescribed and illustrated for the first time. Its geographic distribution is updated and a map showing its distribution is presented. PMID:23653497

  7. Inorganic pyrophosphatases: one substrate, three mechanisms.

    PubMed

    Kajander, Tommi; Kellosalo, Juho; Goldman, Adrian

    2013-06-27

    Soluble inorganic pyrophosphatases (PPases) catalyse an essential reaction, the hydrolysis of pyrophosphate to inorganic phosphate. In addition, an evolutionarily ancient family of membrane-integral pyrophosphatases couple this hydrolysis to Na(+) and/or H(+) pumping, and so recycle some of the free energy from the pyrophosphate. The structures of the H(+)-pumping mung bean PPase and the Na(+)-pumping Thermotoga maritima PPase solved last year revealed an entirely novel membrane protein containing 16 transmembrane helices. The hydrolytic centre, well above the membrane, is linked by a charged "coupling funnel" to the ionic gate about 20Å away. By comparing the active sites, fluoride inhibition data and the various models for ion transport, we conclude that membrane-integral PPases probably use binding of pyrophosphate to drive pumping. PMID:23684653

  8. Evaluation of phytotoxicity of seaport sediments aged artificially by rotary leaching in the framework of a quarry deposit scenario.

    PubMed

    Bedell, J-P; Ferro, Y; Bazin, C; Perrodin, Y

    2014-09-15

    In the framework of an ecological risk assessment of seaport sediments for terrestrial ecosystems when deposited in quarries, we simulated the "ageing" of sediments exposed to rain. This experiment highlighted an inflection point at the solid/liquid ratio 1/25, after which the extraction of pollutants increases moderately. The raw sediments studied inhibited the germination of Lolium perenne and Armeria maritima (a halophytic species) seeds. Furthermore, they affected the early development of L.perenne. The same sediments, leached at a ratio of 1/25, presented a reduction of acute (germination) and chronic (growth) phytotoxicity. The bioconcentration factors of the metals studied decreased with the leached sediment, except for Cu which was still clearly identified in root parts. Thus rotary leaching tests and phytotoxicity bioassays can be used to provide an initial assessment of the ability of plants, particularly halophytes, to colonize deposits of dredged seaport sediments. PMID:25110051

  9. In silico method for modelling metabolism and gene product expression at genome scale

    PubMed Central

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, nathan E.; Orth, Jeffrey D.; Schrimpe-Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua n.; Zengler, Karsten; Palsson, Bernhard O.

    2013-01-01

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism. PMID:22760628

  10. Non-complexed four cascade enzyme mixture: simple purification and synergetic co-stabilization.

    PubMed

    Myung, Suwan; Zhang, Y-H Percival

    2013-01-01

    Cell-free biosystems comprised of synthetic enzymatic pathways would be a promising biomanufacturing platform due to several advantages, such as high product yield, fast reaction rate, easy control and access, and so on. However, it was essential to produce (purified) enzymes at low costs and stabilize them for a long time so to decrease biocatalyst costs. We studied the stability of the four recombinant enzyme mixtures, all of which originated from thermophilic microorganisms: triosephosphate isomerase (TIM) from Thermus thermophiles, fructose bisphosphate aldolase (ALD) from Thermotoga maritima, fructose bisphosphatase (FBP) from T. maritima, and phosphoglucose isomerase (PGI) from Clostridium thermocellum. It was found that TIM and ALD were very stable at evaluated temperature so that they were purified by heat precipitation followed by gradient ammonia sulfate precipitation. In contrast, PGI was not stable enough for heat treatment. In addition, the stability of a low concentration PGI was enhanced by more than 25 times in the presence of 20 mg/L bovine serum albumin or the other three enzymes. At a practical enzyme loading of 1000 U/L for each enzyme, the half-life time of free PGI was prolong to 433 h in the presence of the other three enzymes, resulting in a great increase in the total turn-over number of PGI to 6.2×10(9) mole of product per mole of enzyme. This study clearly suggested that the presence of other proteins had a strong synergetic effect on the stabilization of the thermolabile enzyme PGI due to in vitro macromolecular crowding effect. Also, this result could be used to explain why not all enzymes isolated from thermophilic microorganisms are stable in vitro because of a lack of the macromolecular crowding environment. PMID:23585905

  11. Functional analysis of centipede development supports roles for Wnt genes in posterior development and segment generation.

    PubMed

    Hayden, Luke; Schlosser, Gerhard; Arthur, Wallace

    2015-01-01

    The genes of the Wnt family play important and highly conserved roles in posterior growth and development in a wide range of animal taxa. Wnt genes also operate in arthropod segmentation, and there has been much recent debate regarding the relationship between arthropod and vertebrate segmentation mechanisms. Due to its phylogenetic position, body form, and possession of many (11) Wnt genes, the centipede Strigamia maritima is a useful system with which to examine these issues. This study takes a functional approach based on treatment with lithium chloride, which causes ubiquitous activation of canonical Wnt signalling. This is the first functional developmental study performed in any of the 15,000 species of the arthropod subphylum Myriapoda. The expression of all 11 Wnt genes in Strigamia was analyzed in relation to posterior development. Three of these genes, Wnt11, Wnt5, and WntA, were strongly expressed in the posterior region and, thus, may play important roles in posterior developmental processes. In support of this hypothesis, LiCl treatment of S. maritima embryos was observed to produce posterior developmental defects and perturbations in AbdB and Delta expression. The effects of LiCl differ depending on the developmental stage treated, with more severe effects elicited by treatment during germband formation than by treatment at later stages. These results support a role for Wnt signalling in conferring posterior identity in Strigamia. In addition, data from this study are consistent with the hypothesis of segmentation based on a "clock and wavefront" mechanism operating in this species. PMID:25627713

  12. Stability of endoglucanases from mesophilic fungus and thermophilic bacterium in acidified polyols.

    PubMed

    Chong, Barrie Fong; Harrison, Mark D; O'Hara, Ian M

    2014-01-01

    Recent developments in chemical pretreatments of lignocellulosic biomass using polyols as co-solvents (e.g., glycerol and ethylene glycol) at temperatures less than 100°C may allow the effective use of thermostable and non-thermostable cellulases in situ during the saccharification process. The potential of biomass saccharifying enzymes, endoglucanases (EG) from a thermophilic bacterium (Thermotoga maritima) and a mesophilic fungus (Trichoderma longibrachiatum), to retain their activity in aqueous buffer, acidified glycerol, and acidified ethylene glycol used as co-solvents at pretreatment temperatures at or below 100°C were examined. The results show that despite its origin, T. longibrachiatum EG (Tl-EG) retained 75% of its activity after exposure to 100°C for 5 min in aqueous buffer while T. maritima EG (Tm-EG) retained only 5% activity. However, at 90°C both enzymes retained over 87% of their activity. In acidified (0.1% (w/w) H2SO4) glycerol, Tl-EG retained similar activity (80%) to that obtained in glycerol alone, while Tm-EG retained only 35%. With acidified ethylene glycol under these conditions, both Tl-EG and Tm-EG retained 36% of their activity. The results therefore show that Tl-EG is more stable in both acidified glycerol and ethylene glycol than Tm-EG. A preliminary kinetic study showed that pure glycerol improved the thermal stability of Tl-EG but destabilized Tm-EG, relative to the buffer solution. The half-lives of both Tl-EG and Tm-EG are 4.5 min in acidified glycerol, indicating that the effectiveness of these enzymes under typical pretreatment times of greater than 15 min will be considerably diminished. Attempts have been made to explain the differences in the results obtained between the two enzymes. PMID:24910337

  13. Structure of the ribosomal interacting GTPase YjeQ from the enterobacterial species Salmonella typhimurium

    SciTech Connect

    Nichols, C. E.; Johnson, C.; Lamb, H. K.; Lockyer, M.; Charles, I. G.; Hawkins, A. R.; Stammers, D. K.

    2007-11-01

    The X-ray crystal structure of the GTPase YjeQ from S. typhimurium is presented and compared with those of orthologues from T. maritima and B. subtilis. The YjeQ class of P-loop GTPases assist in ribosome biogenesis and also bind to the 30S subunit of mature ribosomes. YjeQ ribosomal binding is GTP-dependent and thought to specifically direct protein synthesis, although the nature of the upstream signal causing this event in vivo is as yet unknown. The attenuating effect of YjeQ mutants on bacterial growth in Escherichia coli makes it a potential target for novel antimicrobial agents. In order to further explore the structure and function of YjeQ, the isolation, crystallization and structure determination of YjeQ from the enterobacterial species Salmonella typhimurium (StYjeQ) is reported. Whilst the overall StYjeQ fold is similar to those of the previously reported Thematoga maritima and Bacillus subtilis orthologues, particularly the GTPase domain, there are larger differences in the three OB folds. Although the zinc-finger secondary structure is conserved, significant sequence differences alter the nature of the external surface in each case and may reflect varying signalling pathways. Therefore, it may be easier to develop YjeQ-specific inhibitors that target the N- and C-terminal regions, disrupting the metabolic connectivity rather than the GTPase activity. The availability of coordinates for StYjeQ will provide a significantly improved basis for threading Gram-negative orthologue sequences and in silico compound-screening studies, with the potential for the development of species-selective drugs.

  14. A comparative study of the early osmotic, ionic, redox and hormonal signaling response in leaves and roots of two halophytes and a glycophyte to salinity.

    PubMed

    Ellouzi, Hasna; Ben Hamed, Karim; Hernández, Iker; Cela, Jana; Müller, Maren; Magné, Christian; Abdelly, Chedly; Munné-Bosch, Sergi

    2014-12-01

    Salt stress is one of the most important abiotic stress factors affecting plant growth and productivity in natural ecosystems. In this study, we aimed at determining possible differences between salt tolerant and salt sensitive species in early (within 72 h) salt stress response in leaves and roots. To this purpose, we subjected three Brassicaceae species, namely two halophytes-Cakile maritima and Thellungiella salsuginea--and a glycophyte--Arabidopsis thaliana- to short-term salt stress (400 mM NaCl). The results indicate that the halophytes showed a differential osmotic and ionic response together with an early and transient oxidative burst, which was characterized by enhanced hydrogen peroxide levels and subsequent activation of antioxidant defenses in both leaves and roots. In addition, the halophytes displayed enhanced accumulation of abscisic acid, jasmonic acid (JA) and ACC (aminocyclopropane-1-carboxylic acid, the precursor of ethylene) in leaves and roots, as compared to A. thaliana under salt stress. Moreover, the halophytes showed enhanced expression of ethylene response factor1 (ERF1), the convergence node of the JA and ethylene signaling pathways in both leaves and roots upon exposure to salt stress. In conclusion, we show that the halophytes C. maritima and T. salsuginea experience an early oxidative burst, improved antioxidant defenses and hormonal response not only in leaves but also in roots, in comparison to the glycophyte A. thaliana. This differential signaling response converging, at least in part, into increased ERF1 expression in both above- and underground tissues seems to underlay, at least in part, the enhanced tolerance of the two studied halophytes to salt stress. PMID:25156490

  15. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests

    PubMed Central

    O?dziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J. A.; Khalili, M.; Arnautova, Y. A.; Jagielska, A.; Makowski, M.; Schafroth, H. D.; Ka?mierkiewicz, R.; Ripoll, D. R.; Pillardy, J.; Saunders, J. A.; Kang, Y. K.; Gibson, K. D.; Scheraga, H. A.

    2005-01-01

    Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of ? and ?+? proteins [6070 residues with C? rms deviation (rmsd) <6 ]. However, for ?+? proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two ? and three ?+?, with sizes of 53235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue ?+? protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3- C? rmsd. So far this protein is the largest ?+? protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly ?-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 rmsd, except the 32 C-terminal residues, most of which form a ?-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction. PMID:15894609

  16. Ligand-induced conformational changes in a thermophilic ribose-binding protein

    SciTech Connect

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.

    2009-05-21

    Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (appTm value is 108 C) than the mesophilic Escherichia coli homolog (ecRBP) (appTm value is 56 C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.

  17. Transportable data from non-target arthropod field studies for the environmental risk assessment of genetically modified maize expressing an insecticidal double-stranded RNA.

    PubMed

    Ahmad, Aqeel; Negri, Ignacio; Oliveira, Wladecir; Brown, Christopher; Asiimwe, Peter; Sammons, Bernard; Horak, Michael; Jiang, Changjian; Carson, David

    2016-02-01

    As part of an environmental risk assessment, the potential impact of genetically modified (GM) maize MON 87411 on non-target arthropods (NTAs) was evaluated in the field. MON 87411 confers resistance to corn rootworm (CRW; Diabrotica spp.) by expressing an insecticidal double-stranded RNA (dsRNA) transcript and the Cry3Bb1 protein and tolerance to the herbicide glyphosate by producing the CP4 EPSPS protein. Field trials were conducted at 14 sites providing high geographic and environmental diversity within maize production areas from three geographic regions including the U.S., Argentina, and Brazil. MON 87411, the conventional control, and four commercial conventional reference hybrids were evaluated for NTA abundance and damage. Twenty arthropod taxa met minimum abundance criteria for valid statistical analysis. Nine of these taxa occurred in at least two of the three regions and in at least four sites across regions. These nine taxa included: aphid, predatory earwig, lacewing, ladybird beetle, leafhopper, minute pirate bug, parasitic wasp, sap beetle, and spider. In addition to wide regional distribution, these taxa encompass the ecological functions of herbivores, predators and parasitoids in maize agro-ecosystems. Thus, the nine arthropods may serve as representative taxa of maize agro-ecosystems, and thereby support that analysis of relevant data generated in one region can be transportable for the risk assessment of the same or similar GM crop products in another region. Across the 20 taxa analyzed, no statistically significant differences in abundance were detected between MON 87411 and the conventional control for 123 of the 128 individual-site comparisons (96.1 %). For the nine widely distributed taxa, no statistically significant differences in abundance were detected between MON 87411 and the conventional control. Furthermore, no statistically significant differences were detected between MON 87411 and the conventional control for 53 out of 56 individual-site comparisons (94.6 %) of NTA pest damage to the crop. In each case where a significant difference was observed in arthropod abundance or damage, the mean value for MON 87411 was within the reference range and/or the difference was not consistently observed across collection methods and/or sites. Thus, the differences were not representative of an adverse effect unfamiliar to maize and/or were not indicative of a consistent plant response associated with the GM traits. Results from this study support a conclusion of no adverse environmental impact of MON 87411 on NTAs compared to conventional maize and demonstrate the utility of relevant transportable data across regions for the ERA of GM crops. PMID:26433587

  18. Mother and offspring fitness in an insect with maternal care: phenotypic trade-offs between egg number, egg mass and egg care

    PubMed Central

    2014-01-01

    Background Oviparous females have three main options to increase their reproductive success: investing into egg number, egg mass and/or egg care. Although allocating resources to either of these three components is known to shape offspring number and size, potential trade-offs among them may have key impacts on maternal and offspring fitness. Here, we tested the occurrence of phenotypic trade-offs between egg number, egg mass and maternal expenditure on egg care in the European earwig, Forficula auricularia, an insect with pre- and post-hatching forms of maternal care. In particular, we used a series of laboratory observations and experiments to investigate whether these three components non-additively influenced offspring weight and number at hatching, and whether they were associated with potential costs to females in terms of future reproduction. Results We found negative associations between egg number and mass as well as between egg number and maternal expenditure on egg care. However, these trade-offs could only be detected after statistically correcting for female weight at egg laying. Hatchling number was not determined by single or additive effects among the three life-history traits, but instead by pairwise interactions among them. In particular, offspring number was positively associated with the number of eggs only in clutches receiving high maternal care or consisting of heavy eggs, and negatively associated with mean egg mass in clutches receiving low care. In contrast, offspring weight was positively associated with egg mass only. Finally, maternal expenditure on egg care reduced their future reproduction, but this effect was only detected when mothers were experimentally isolated from their offspring at egg hatching. Conclusions Overall, our study reveals simultaneous trade-offs between the number, mass and care of eggs. It also demonstrates that these factors interact in their impact on offspring production, and that maternal expenditure on egg care possibly shapes female future reproduction. These findings emphasize that studying reproductive success requires consideration of phenotypic trade-offs between egg-number, egg mass and egg care in oviparous species. PMID:24913927

  19. The multiple target use of spirodiclofen (Envidor 240 SC) in IPM pomefruit in Belgium.

    PubMed

    De Maeyer, Luk; Geerinck, Rik

    2009-01-01

    Envidor 240 SC, active ingredient spirodiclofen is a broad spectrum acaricide acting via lipid biosynthesis inhibition (LBI) with no cross resistance to currently available acaricides and with additional insecticidal properties. Envidor is positive IPM listed but in frame of resistance management limited to one application per season. In pear growing Envidor constitutes an important tool in pear sucker control in a tandem strategy with abamectine. Being totally selective on predatory bugs Anthocoris nemoralis, Envidor installs a favourable low prey/predator ratio avoiding any damage of further 3rd or 4th Psylla generations. The application of Envidor on the second Psylla generation coincides with the migration of Lepidosaphes ulmi scales and with the spread of rustmites Epitremerus pyri on which season long control is achieved. On apples, Envidor settled as an important tool for scales control especially on the wood but recently its acaricidal use revivals. This is induced by the withdrawal of totylfluanid with its regulating mite control and with the further efficacy decline of registered METI-acaricides. Even with full introduction of Typhlodromus pyri, mites and rustmites may unexpectedly flear up. On Typhlodromus pyri, Envidor is IOBC 2 classified (slightly harmful) but the favourable low prey/predator ratio and within season recovery make it full IPM compatible. On Aculus schlechtendali, apple rustmite with a short generation cyclus, the larval and fecundity effects of Envidor lead to an explicit knock down efficacy. On mixed populations of Panonychus ulmi with longer generation cyclus, Envidor shows a slow initial effect with culminating efficacy after 2-3 weeks and a long lasting efficacy of more than 100 days, avoiding any leaf or consequent fruit damage. High rain fastness and the right positioning at 30-50 % hatching of winter eggs make of Envidor a very consistent correction acaride. The addition of a surfactant is not recommended for mite control. Up to now, no shifting in susceptibility of Envidor on Panonychus ulmi or Tetranychus urticae is found in Belgian orchards. Since Envidor combines both in apples and pears an efficacy on multiple pests occurring simultaneously after flowering, with a good selectivity profile on predators, parasitoïds, syrphids, lacewings and earwigs, it remains a most important tool in modern IPM pomefruit. PMID:20218531

  20. USE OF GREEN MANURE CROPS AND SUGAR BEET VARIETIES TO CONTROL HETERODERA BETAE.

    PubMed

    Raaijmakers, E

    2014-01-01

    Although it is less studied than the white beet cyst nematode (Heterodera schachtii), the yellow beet cyst nematode (H. betae) has been found in many countries in Europe. For example in The Netherlands, France and Spain. H. betae causes yield losses on sandy soils. A high infestation can result in loss of complete plants. In The Netherlands, this nematode is especially found in the south eastern and north eastern part, where it occurs on 18% and 5% of the fields, respectively. From a project of the Dutch Sugar beet Research Institute IRS (SUSY) on factors explaining differences in sugar yield, this nematode was one of the most important factors reducing sugar yields on sandy soils. Until 2008, the only way to control H. betae was by reducing the number of host crops in the crop rotation. Host crops are crops belonging to the families of Cruciferae, Chenopodiaceae, Polygonaceae, Caryophyllaceae and Leguminosea. In order to find more control measures, research was done to investigate the host status of different green manure crops and the resistance and tolerance of different sugar beet varieties to H. betae. White mustard (Sinapis alba) and oil seed radish (Raphanus sativus spp. oleiferus) varieties resistant to H. schachtii were investigated for their resistance against H. betae. A climate room trial and a field trial with white mustard and oil seed radish were conducted in 2007 and 2008, respectively. Results show that H. betae could multiply on susceptible white mustard and susceptible oil seed radish, but not on the H. schachtii resistant varieties. In climate room trials in 2009, 2010 and 2011 and field trials in 2010, 2011 and 2012, the effect of different sugar beet varieties on the multiplication of H. betae and the effect of H. betae on yield at different infestation levels was investigated. Sugar beet varieties with resistance genes to H. schachtii (from Beta procumbens or B. maritima) were selected. Varieties with resistance genes from these sources were not totally resistant to H. betae, but limited the multiplication of this nematode in comparison with susceptible varieties considerably. Only the varieties with resistance genes from B. maritima gave higher yields in comparison with susceptible varieties. Growing these varieties was already profitable from very light infestation levels (75 eggs and larvae/100 ml soil) of H. betae. Therefore, resistant cruciferous green manure crops and resistant and tolerant sugar beet varieties are good tools for growers to control H. betae. PMID:26084110

  1. New crystal forms of Diocleinae lectins in the presence of different dimannosides

    SciTech Connect

    Moreno, Frederico Bruno Mendes Batista; Bezerra, Gustavo Arruda; Oliveira, Taianá Maia de; Souza, Emmanuel Prata de; Rocha, Bruno Anderson Matias da; Benevides, Raquel Guimarães; Delatorre, Plínio; Cavada, Benildo Sousa; Azevedo, Walter Filgueira Jr de

    2006-11-01

    The crystallization and preliminary X-ray data of Canavalia gladiata lectin (CGL) and C. maritima lectin (CML) complexed with Man(α1-2)Man(α1)OMe, Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe in two crystal forms [the complexes with Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe crystallized in space group P3{sub 2} and those with Man(α1-2)Man(α1)OMe crystallized in space group I222], which differed from those of the native proteins (P2{sub 1}2{sub 1}2 for CML and C222 for CGL), are reported. Studying the interactions between lectins and sugars is important in order to explain the differences observed in the biological activities presented by the highly similar proteins of the Diocleinae subtribe. Here, the crystallization and preliminary X-ray data of Canavalia gladiata lectin (CGL) and C. maritima lectin (CML) complexed with Man(α1-2)Man(α1)OMe, Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe in two crystal forms [the complexes with Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe crystallized in space group P3{sub 2} and those with Man(α1-2)Man(α1)OMe crystallized in space group I222], which differed from those of the native proteins (P2{sub 1}2{sub 1}2 for CML and C222 for CGL), are reported. The crystal complexes of ConA-like lectins with Man(α1-4)Man(α1)OMe are reported here for the first time.

  2. Experimental observations on sediment resuspension within submerged model canopies under oscillatory flow

    NASA Astrophysics Data System (ADS)

    Ros, Àlex; Colomer, Jordi; Serra, Teresa; Pujol, Dolors; Soler, Marianna; Casamitjana, Xavier

    2014-12-01

    A set of laboratory experiments were conducted to study the effect of submerged aquatic vegetation in sediment resuspension under progressive waves. Three vegetation models (rigid, flexible and real plants of Ruppia maritima), six wave frequencies (in the range F=0.6-1.6 Hz) and four plant densities (Solid Plant Fractions, SPF in the range of 1-10%) were used. The sediment bed properties corresponded to a salt marsh wetland with a bimodal particle size distribution with two particle populations (population 1: particle diameters in the range of 2.5 to 6.0 μm, and population 2: particle diameters in the range of 6.0 to 100 μm). Within the canopy, wave velocities were attenuated for all the canopies studied and for all the frequencies analyzed. The change in the TKE (ΔTKE) compared with the case without plants was studied. For the rigid canopy model, in comparison to the unimpeded experiment, an increase in ΔTKE inside the canopy for smaller frequencies (F=0.6-1.2 Hz) was observed together with stem Reynolds numbers Rep above 250. As a result, sediment resuspension for both sediment populations was higher than that of the unimpeded experiment. However, at higher frequencies (F=1.4 and 1.6 Hz) and higher plant densities (SPF=5%, 7.5% and 10%), the ΔTKE inside the canopy decreased, coinciding with stem Reynolds number Rep below 250. As a result, sediment resuspension for larger canopy densities and larger frequencies was reduced. For the flexible vegetation model, in comparison with the unimpeded experiment, a reduction in the ΔTKE inside the canopy was nearly always found. Resuspended sediment concentrations were found to decrease as flexible canopy densities increased. For the flexible vegetation the stem Reynolds number was Rep<250 and no production of ΔTKE was observed. The real case of a canopy of R. maritima behaved similarly to the flexible model canopy.

  3. Tidal events and salt-marsh structure influence black mangrove (Avicennia germinans) recruitment across an ecotone.

    PubMed

    Peterson, Jennifer M; Bell, Susan S

    2012-07-01

    Field experiments were conducted at a black mangrove-salt-marsh ecotone in southwest Florida (U.S.A.) to investigate retention of propagules of the black mangrove, Avicennia germinans, by salt-marsh plants as a mechanism of facilitation operating on recruitment success at landward boundaries. Buoyant A. germinans propagules are dispersed by tides, and stranding is required for establishment; therefore, processes that enable stranding should facilitate mangrove recruitment. We expected the physical structure of salt-marsh vegetation to define propagule retention capacity, and we predicted that salt-marsh plants with distinct growth forms would differentially retain propagules. Experimental monoculture plots (1 m2) of salt-marsh plants with different growth forms (Sporobolus virginicus [grass], Sesuvium portulacastrum [succulent forb], and Batis maritima [succulent scrub]) were created, and A. germinans propagules were emplaced into these plots and monitored over time. For comparison, propagules were also placed into natural polyculture plots (1 m2). Polyculture plots contained at least two of the salt-marsh plant taxa selected for monoculture treatments, and S. virginicus was always present within these polyculture plots. Natural polyculture plots retained 59.3% +/- 11.0% (mean +/- SE) of emplaced propagules. Monocultures varied in their propagule retention capacities with plots of S. virginicus retaining on average 65.7% +/- 11.5% of transplanted propagules compared to 7.2% +/- 1.8% by B. maritima and 5.0% +/- 1.9% by S. portulacastrum. Plots containing S. virginicus retained a significantly greater percentage of emplaced propagules relative to the two succulent salt-marsh taxa. Furthermore, propagule entrapment, across all treatments, was strongly correlated with salt-marsh structure (r2 = 0.6253, P = 0.00001), which was estimated using an indirect quantitative metric (lateral obstruction) calculated from digital images of plots. Overall, our findings imply that entrapment of propagules by salt-marsh plants may be facilitative if propagules are dispersed beyond the established tree line by spring or storm tides, and that facilitation may be sustained over time. We conclude that salt-marsh ecotone permeability may modulate landward encroachment by A. germinans, and that interactions among the early life history stages of black mangroves and neighboring plants may direct community responses to climate change. PMID:22919911

  4. Biosynthesis, Translocation, and Accumulation of Betaine in Sugar Beet and Its Progenitors in Relation to Salinity 12

    PubMed Central

    Hanson, Andrew D.; Wyse, Roger

    1982-01-01

    Like other halophytic chenopods, sugar beet (Beta vulgaris L.) can accumulate high betaine levels in shoots and roots. N,N,N-trimethylglycine impedes sucrose crystallization and so lowers beet quality. The objective of this research was to examine the genetic variability and physiological significance of betaine accumulation in sugar beet and its relatives. Three cultivated genotypes of B. vulgaris and two genotypes of the wild progenitor B. maritima L. were grown with and without gradual salinization (final NaCl concentration = 150 millimolar). At 6 weeks old, all five genotypes had moderately high betaine levels in shoots and roots when unsalinized (averages for all genotypes: shoots = 108 micromoles per gram dry weight; roots = 99 micromoles per gram dry weight). Salinization raised betaine levels of shoots and roots 2- to 3-fold, but did not greatly depress shoot or root growth. The genotype WB-167—an annual B. maritima type—always had approximately 40% lower betaine levels in roots than the other four genotypes, although the betaine levels in the shoots were not atypically low. The site and pathway of betaine synthesis were investigated in young, salinized sugar beet plants by: (a) supplying 1 micromole [14C]ethanolamine to young leaf blades or to the taproot sink of intact plants; (b) supplying tracer [14C]formate to discs of leaf, hypocotyl, and taproot tissues in darkness. Conversion of both 14C precursors to betaine was active only in leaf tissue. Very little 14C appeared in the phospholipid phosphatidylcholine before betaine was heavily labeled; this was in marked contrast to the labeling patterns in salinized barley. Phosphorylcholine was a prominent early 14C metabolite of both [14C]ethanolamine and [14C]formate in all tissues of sugar beet. Betaine translocation was examined in young plants of sugar beet and WB-167 by applying tracer [methyl-14C]betaine to a young expanded leaf and determining the distribution of 14C after 3 days. In all cases, extensive 14C translocation to young leaves and taproot sink occurred; neither in the fed leaf nor in sink organs were any 14C metabolites of betaine detected. PMID:16662637

  5. Spatial and temporal habitat partitioning by zooplankton in the Bornholm Basin (central Baltic Sea)

    NASA Astrophysics Data System (ADS)

    Schulz, Jan; Peck, Myron A.; Barz, Kristina; Schmidt, Jörn Oliver; Hansen, Frank C.; Peters, Janna; Renz, Jasmin; Dickmann, Miriam; Mohrholz, Volker; Dutz, Jörg; Hirche, Hans-Jürgen

    2012-12-01

    The deep basins in the Baltic Sea such as the Bornholm Basin (BB) are subject to seasonal changes in the strength of physico-chemical stratification. These depth-related changes in key abiotic factors are strong drivers of habitat partitioning by the autochthonous zooplankton community. Species-specific ecophysiological preferences often result in both seasonal and inter-annual changes in vertical abundance that, when combined with depth-specific water currents, also lead to horizontal differences in spatial distribution. The present study documented the seasonal and depth-specific changes in the abundance and species composition of zooplankton in the BB based upon broad-scale survey data: 832 vertically-resolved (10 m) multinet samples collected at nine stations between March 2002 and May 2003. Changes in the zooplankton community were significantly correlated with changes in ambient hydrography. Each of five taxa (Bosmina coregoni maritima, Acartia spp., Pseudocalanus spp., Temora longicornis, Synchaeta spp.) contributed >10% to the zooplankton community composition. The appearance of cladocerans was mainly correlated with the phenology of thermocline development in the spring. The cladoceran B. coregoni maritima was a dominant member of this community during the warmest periods, preferring the surface waters above the thermocline. Copepods exhibited distinct, ontogenetic and seasonal changes in their distribution. The rotifers (Synchaeta sp.) were the most abundant zooplankton in May. Based on a multivariate approach and the evaluation of vertical distribution patterns, five major habitat utilisation modes were identified that were based, to a large extent, on the dynamics of thermal and haline stratification of the Baltic Sea. Our statistical analysis of one of the most thorough datasets collected on Baltic zooplankton in recent decades reveals some of the factors that make this stratified system highly dynamic with respect to the spatial overlap between predators and prey. As fish and gelatinous plankton often feed in distinct layers and/or exhibit feeding migrations, the inhomogeneous distribution of potential prey can result in a spatial mismatch. Based on the five modes identified at the community level for zooplankton, we discuss how climate-driven hydrographic variability may influence the strength of trophic coupling within the Bornholm Basin.

  6. Unique biosynthesis of dehydroquinic acid?

    PubMed

    Woodard, Ronald W

    2004-10-01

    A search of the genomic sequences of the thermophilic microorganisms Aquifex aeolicus, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii for the first seven enzymes (aroG, B, D, E, K, A, and C ) involved in the shikimic acid biosynthetic pathway reveal two key enzymes are missing. The first enzyme in the pathway, 3-deoxy-d-arabino-heptulosonic acid 7-phosphate synthase (aroG) and the second enzyme in the pathway, 5-dehydroquinic acid synthase (aroB) are "missing." The remaining five genes for the shikimate pathway in these organism are present and are similar to the corresponding Escherichia coli genes. The genomic sequences of the thermophiles Pyrococcus abyssi and Thermotoga maritima contain the aroG and aroB genes. Several fungi such as Aspergillus fumigatus, Aspergillus nidulans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pneumocystis carinii f. sp. carinii, and Neurospora crassa contain the gene aroM, a pentafunctional enzyme whose overall activity is equivalent to the combined catalytic activities of proteins expressed by aroB, D, E, K, and A genes. Two of these fungi also lack an aroG gene. A discussion of potential reasons for these missing enzymes is presented. PMID:15381397

  7. The Structure of a Soluble Chemoreceptor Suggests a Mechanism for Propagating Conformational Signals

    SciTech Connect

    Pollard, Abiola M.; Bilwes, Alexandrine M.; Crane, Brian R.; Cornell

    2009-09-02

    Transmembrane chemoreceptors, also known as methyl-accepting chemotaxis proteins (MCPs), translate extracellular signals into intracellular responses in the bacterial chemotaxis system. MCP ligand binding domains control the activity of the CheA kinase, situated {approx}200 {angstrom} away, across the cytoplasmic membrane. The 2.17 {angstrom} resolution crystal structure of a Thermotoga maritima soluble receptor (Tm14) reveals distortions in its dimeric four-helix bundle that provide insight into the conformational states available to MCPs for propagating signals. A bulge in one helix generates asymmetry between subunits that displaces the kinase-interacting tip, which resides more than 100 {angstrom} away. The maximum bundle distortion maps to the adaptation region of transmembrane MCPs where reversible methylation of acidic residues tunes receptor activity. Minor alterations in coiled-coil packing geometry translate the bulge distortion to a >25 {angstrom} movement of the tip relative to the bundle stalks. The Tm14 structure discloses how alterations in local helical structure, which could be induced by changes in methylation state and/or by conformational signals from membrane proximal regions, can reposition a remote domain that interacts with the CheA kinase.

  8. Reconstruction of the Chemotaxis Receptor-Kinase Assembly

    SciTech Connect

    Park,S.; Borbat, P.; Gonzalez-Bonet, G.; Bhatnagar, J.; Pollard, A.; Freed, J.; Bilwes, A.; Crane, B.

    2006-01-01

    In bacterial chemotaxis, an assembly of transmembrane receptors, the CheA histidine kinase and the adaptor protein CheW processes environmental stimuli to regulate motility. The structure of a Thermotoga maritima receptor cytoplasmic domain defines CheA interaction regions and metal ion-coordinating charge centers that undergo chemical modification to tune receptor response. Dimeric CheA-CheW, defined by crystallography and pulsed ESR, positions two CheWs to form a cleft that is lined with residues important for receptor interactions and sized to clamp one receptor dimer. CheW residues involved in kinase activation map to interfaces that orient the CheW clamps. CheA regulatory domains associate in crystals through conserved hydrophobic surfaces. Such CheA self-contacts align the CheW receptor clamps for binding receptor tips. Linking layers of ternary complexes with close-packed receptors generates a lattice with reasonable component ratios, cooperative interactions among receptors and accessible sites for modification enzymes.

  9. Bi-phasic composition of trans-root electrical potential in roots of Plantago species: involvement of spatially separated electrogenic pumps.

    PubMed

    de Boer, A H; Prins, H B; Zanstra, P E

    1983-04-01

    The effect of oxygen on the trans-root potential (TRP) of excised roots in Plantago media L. and P. maritima L. was investigated. Two distinct reactions were found. In some experiments (type A roots) the reaction of TRP to anoxia was bi-phasic, and this reaction fits well into a model, assuming the presence of two spatially separated proton pump sites in the roots: one at the plasmalemma of epidermal and cortical cells and the other at the symplast/xylem interface. The two pumps work in opposite directions. In other experiments (type B roots) no hyperpolarization as a response to anoxia at the inner symplast membrane was observed. There is evidence that the inner pump is also present in these roots, but only in an inactive or electroneutral state. It is concluded that O2-deficiency prevails more often in the central part of the root than in epidermal and cortical cells, when roots are brought gradually under anoxia. This causes the pump located at the symplast/xylem interface to be inhibited more quickly than the other at decreasing O2-concentrations in the bathing solution. PMID:24264156

  10. Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support

    PubMed Central

    Tibhe, Jagdish D; Fu, Hui; Noël, Timothy; Wang, Qi; Meuldijk, Jan

    2013-01-01

    Summary Threonine aldolase (TA) from Thermotoga maritima was immobilized on an Eupergit support by both a direct and an indirect method. The incubation time for the direct immobilization method was optimized for the highest amount of enzyme on the support. By introducing the immobilized TA in a packed-bed microreactor, a flow synthesis of phenylserine was developed, and the effects of temperature and residence time were studied in particular. Calculations of the Damköhler number revealed that no mass transfer limitations are given in the micro-interstices of the packed bed. The yield does not exceed 40% and can be rationalized by the natural equilibrium as well as product inhibition which was experimentally proven. The flow synthesis with the immobilized enzyme was compared with the corresponding transformation conducted with the free enzyme. The product yield was further improved by operating under slug flow conditions which is related to the very short residence time distribution. In all cases 20% diastereomeric excess (de) and 99% enantiomeric excess (ee) were observed. A continuous run of the reactant solution was carried out for 10 hours in order to check enzyme stability at higher temperature. Stable operation was achieved at 20 minute residence time. Finally, the productivity of the reactor was calculated, extrapolated to parallel run units, and compared with data collected previously. PMID:24204429

  11. Biomimetic assembly and activation of [FeFe]-hydrogenases.

    PubMed

    Berggren, G; Adamska, A; Lambertz, C; Simmons, T R; Esselborn, J; Atta, M; Gambarelli, S; Mouesca, J-M; Reijerse, E; Lubitz, W; Happe, T; Artero, V; Fontecave, M

    2013-07-01

    Hydrogenases are the most active molecular catalysts for hydrogen production and uptake, and could therefore facilitate the development of new types of fuel cell. In [FeFe]-hydrogenases, catalysis takes place at a unique di-iron centre (the [2Fe] subsite), which contains a bridging dithiolate ligand, three CO ligands and two CN(-) ligands. Through a complex multienzymatic biosynthetic process, this [2Fe] subsite is first assembled on a maturation enzyme, HydF, and then delivered to the apo-hydrogenase for activation. Synthetic chemistry has been used to prepare remarkably similar mimics of that subsite, but it has failed to reproduce the natural enzymatic activities thus far. Here we show that three synthetic mimics (containing different bridging dithiolate ligands) can be loaded onto bacterial Thermotoga maritima HydF and then transferred to apo-HydA1, one of the hydrogenases of Chlamydomonas reinhardtii algae. Full activation of HydA1 was achieved only when using the HydF hybrid protein containing the mimic with an azadithiolate bridge, confirming the presence of this ligand in the active site of native [FeFe]-hydrogenases. This is an example of controlled metalloenzyme activation using the combination of a specific protein scaffold and active-site synthetic analogues. This simple methodology provides both new mechanistic and structural insight into hydrogenase maturation and a unique tool for producing recombinant wild-type and variant [FeFe]-hydrogenases, with no requirement for the complete maturation machinery. PMID:23803769

  12. Paleobiology of the Sand Beneath the Valders Diamicton at Valders, Wisconsin

    USGS Publications Warehouse

    Maher, L.J., Jr.; Miller, N.G.; Baker, R.G.; Curry, B. Brandon; Mickelson, D.M.

    1998-01-01

    Previously undescribed pollen, plant macrofossils, molluscs, and ostracodes were recovered from a 2.5-m-thick glaciolacustrine unit of silty sand and clay at Valders, Wisconsin. The interstadial sediment was deposited about 12,200 14C yr B.P. after retreat of the Green Bay lobe that deposited diamicton of the Horicon Formation, and before advance of the Lake Michigan lobe that deposited the red-brown diamicton of the Valders Member of the Kewaunee Formation. Fluctuations of abundance of Candona subtriangulata, Cytherissa lacustris, and three other species define four ostracode biozones in the lower 1.7 m, suggesting an open lake environment that oscillated in depth and proximity to glacial ice. Pollen is dominated by Picea and Artemisia, but the low percentages of many other types of longdistance origin suggest that the terrestrial vegetation was open and far from the forest border. The upper part of the sediment, a massive sand deposited in either a shallow pond or a sluggish stream, contains a local concentration of plant macrofossils. The interpretation of a cold open environment is supported by the plant macrofossils of more than 20 species, dominated by those of open mineral soils (Arenaria rubella, Cerastium alpinum type, Silene acaulis, Sibbaldia procumbens, Dryas integrifolia, Vaccinium uliginosum var. alpinum, Armeria maritima, etc.) that in North America occur largely in the tundra and open tundra-forest ecotone of northern Canada. Ice-wedge casts occur in the sand. ?? 1998 University of Washington.

  13. Mercury in sediments and vegetation in a moderately contaminated salt marsh (Tagus Estuary, Portugal).

    PubMed

    Canário, João; Vale, Carlos; Poissant, Laurier; Nogueira, Marta; Pilote, Martin; Branco, Vasco

    2010-01-01

    Depth variations of total mercury (Hg) and methylmercury (MeHg) concentrations were studied in cores from non-colonized sediments, sediments colonized by Halimione portulacoides, Sarcocorniafruticosa and Spartina maritima and belowground biomass, in a moderately contaminated salt marsh (Tagus Estuary, Portugal). Concentrations in belowground biomass exceeded up to 3 (Hg) and 15 (MeHg) times the levels in sediments, and up to 198 (Hg) and 308 (MeHg) times those found in aboveground parts. Methylmercury in colonized sediments reached 3% of the total Hg, 50 times above the maximum values found in non-colonized sediments. The absence of correlations between total Hg concentrations in sediments and the corresponding MeHg levels suggested that methylation was only dependent on the environmental and microbiological factors. The analysis of belowground biomass at high-depth resolution (2 cm) provided evidence that Hg and MeHg were actively absorbed from sediments, with higher enrichment factors at layers where higher microbial activity was probably occurring. The results obtained in this study indicated that the biotransformation of Hg to the toxic MeHg could increase the toxicity of plant-colonized sediments. PMID:21179951

  14. Effects of Posidonia oceanica beach-cast on germination, growth and nutrient uptake of coastal dune plants.

    PubMed

    Del Vecchio, Silvia; Marbà, Núria; Acosta, Alicia; Vignolo, Clara; Traveset, Anna

    2013-01-01

    Seagrass meadows play an important role in marine ecosystems. A part of seagrass production is also exported to adjacent coastal terrestrial systems, possibly influencing their functioning. In this work we experimentally analyzed the effect of Posidonia oceanica beach-cast on plant germination, growth, and nutrient uptake of two plant species (Cakile maritima and Elymus farctus) that grow on upper beaches and fore dunes along the Mediterranean coasts. We compared plants growing in simple sand (control) with those growing in a substrate enriched with P. oceanica wrack (treatment) in laboratory. P. oceanica wrack doubled the N substrate pool and kept the substrate humid. Plants growing in the treated substrate grew faster, were twice as large as those growing in the control substrate, while tissues were enriched in N and P (Cakile by the 1.3 fold in N and 2.5 fold in P; Elymus by 1.5 fold in N and 2 fold in P). Our results suggest a positive effect of seagrass litter for the enhancing of dune species, highlighting its role for the conservation of coastal dune ecosystems. PMID:23894678

  15. Structure and electrostatic property of cytoplasmic domain of ZntB transporter.

    SciTech Connect

    Tan, K.; Sather, A.; Robertson, J. L.; Moy, S.; Roux, B.; Joachimiak, A.; Biosciences Division; Cornell Univ.; Univ. of Chicago

    2009-10-01

    ZntB is the distant homolog of CorA Mg{sup 2+} transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn{sup 2+} and Cd{sup 2+}, but not Mg{sup 2+}. Here, we report the 1.90 {angstrom} crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn{sup 2+} or Cd{sup 2+} binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl{sup -} ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl{sup -} ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport.

  16. A Structural Basis for Mg(2+) Homeostasis and the CorA Translocation Cycle

    SciTech Connect

    Payandeh,J.; Pai, E.

    2006-01-01

    We describe the CorA Mg{sup 2+} transporter homologue from Thermotoga maritima in complex with 12 divalent cations at 3.7 {angstrom} resolution. One metal is found near the universally conserved GMN motif, apparently stabilized within the transmembrane region. This portion of the selectivity filter might discriminate between the size and preferred coordination geometry of hydrated substrates. CorA may further achieve specificity by requiring the sequential dehydration of substrates along the length of its {approx}55 {angstrom} long pore. Ten metal sites identified within the cytoplasmic funnel domain are linked to long extensions of the pore helices and regulate the transport status of CorA. We have characterized this region as an intrinsic divalent cation sensor and provide evidence that it functions as a Mg{sup 2+}-specific homeostatic molecular switch. A proteolytic protection assay, biophysical data, and comparison to a soluble domain structure from Archaeoglobus fulgidus have revealed the potential reaction coordinate for this diverse family of transport proteins.

  17. Crystallization and preliminary X-ray diffraction analysis of the magnesium transporter CorA

    SciTech Connect

    Payandeh, Jian; Pai, Emil F.

    2006-02-01

    Full-length and soluble domains of the integral membrane protein CorA have been expressed, purified and crystallized. X-ray diffraction data have been collected and analyzed. The full-length integral membrane protein CorA from Thermotoga maritima (TmCorA{sub 1–351}) has been expressed in Escherichia coli and purified without membrane isolation. TmCorA{sub 1–351} crystallized in the monoclinic space group C2, with unit-cell parameters a = 214.25, b = 86.30, c = 181.53 Å, β = 112.23°. Native crystals diffracted to 3.7 Å using synchrotron radiation, but selenomethionine-substituted crystals rarely diffracted to better than 5.0 Å. All full-length protein crystals were highly mosaic and produced anisotropic diffraction patterns. To aid in crystallographic phasing, soluble domain constructs were screened and the periplasmic domain of CorA from Archaeoglobus fulgidus (AfCorA{sub 1–263}) was crystallized in the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 101.17, c = 142.87 Å. Native and SeMet-substituted AfCorA{sub 1–263} crystals diffracted to ∼3.0 Å using synchrotron radiation.

  18. Crystallization and Preliminary X-ray Diffraction Analysis of the Magnesium Transporter CorA

    SciTech Connect

    Payandeh,J.; Pai, E.

    2006-01-01

    The full-length integral membrane protein CorA from Thermotoga maritima (TmCorA{sub 1-351}) has been expressed in Escherichia coli and purified without membrane isolation. TmCorA{sub 1-351} crystallized in the monoclinic space group C2, with unit-cell parameters a = 214.25, b = 86.30, c = 181.53 Angstroms, {beta} = 112.23 degrees . Native crystals diffracted to 3.7 Angstroms using synchrotron radiation, but selenomethionine-substituted crystals rarely diffracted to better than 5.0 Angstroms. All full-length protein crystals were highly mosaic and produced anisotropic diffraction patterns. To aid in crystallographic phasing, soluble domain constructs were screened and the periplasmic domain of CorA from Archaeoglobus fulgidus (AfCorA1-263) was crystallized in the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 101.17, c = 142.87 Angstroms. Native and SeMet-substituted AfCorA{sub 1-263} crystals diffracted to {approx}3.0 Angstroms using synchrotron radiation.

  19. A βα-barrel built by the combination of fragments from different folds

    PubMed Central

    Bharat, Tanmay A. M.; Eisenbeis, Simone; Zeth, Kornelius; Höcker, Birte

    2008-01-01

    Combinatorial assembly of protein domains plays an important role in the evolution of proteins. There is also evidence that protein domains have come together from stable subdomains. This concept of modular assembly could be used to construct new well folded proteins from stable protein fragments. Here, we report the construction of a chimeric protein from parts of a (βα)8-barrel enzyme from histidine biosynthesis pathway (HisF) and a protein of the (βα)5-flavodoxin-like fold (CheY) from Thermotoga maritima that share a high structural similarity. We expected this construct to fold into a full (βα)8-barrel. Our results show that the chimeric protein is a stable monomer that unfolds with high cooperativity. Its three-dimensional structure, which was solved to 3.1 Å resolution by x-ray crystallography, confirms a barrel-like fold in which the overall structures of the parent proteins are highly conserved. The structure further reveals a ninth strand in the barrel, which is formed by residues from the HisF C terminus and an attached tag. This strand invades between β-strand 1 and 2 of the CheY part closing a gap in the structure that might be due to a suboptimal fit between the fragments. Thus, by a combination of parts from two different folds and a small arbitrary fragment, we created a well folded and stable protein. PMID:18632584

  20. A beta alpha-barrel built by the combination of fragments from different folds.

    PubMed

    Bharat, Tanmay A M; Eisenbeis, Simone; Zeth, Kornelius; Höcker, Birte

    2008-07-22

    Combinatorial assembly of protein domains plays an important role in the evolution of proteins. There is also evidence that protein domains have come together from stable subdomains. This concept of modular assembly could be used to construct new well folded proteins from stable protein fragments. Here, we report the construction of a chimeric protein from parts of a (betaalpha)(8)-barrel enzyme from histidine biosynthesis pathway (HisF) and a protein of the (betaalpha)(5)-flavodoxin-like fold (CheY) from Thermotoga maritima that share a high structural similarity. We expected this construct to fold into a full (betaalpha)(8)-barrel. Our results show that the chimeric protein is a stable monomer that unfolds with high cooperativity. Its three-dimensional structure, which was solved to 3.1 A resolution by x-ray crystallography, confirms a barrel-like fold in which the overall structures of the parent proteins are highly conserved. The structure further reveals a ninth strand in the barrel, which is formed by residues from the HisF C terminus and an attached tag. This strand invades between beta-strand 1 and 2 of the CheY part closing a gap in the structure that might be due to a suboptimal fit between the fragments. Thus, by a combination of parts from two different folds and a small arbitrary fragment, we created a well folded and stable protein. PMID:18632584

  1. Allosteric Inhibitors at the Heterodimer Interface of Imidazole Glycerol Phosphate Synthase

    NASA Astrophysics Data System (ADS)

    Snoeberger, Ning-Shiuan Nicole

    Imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima is a heterodimeric enzyme composed of the HisH and HisF proteins. It is attractive as a pathological target since it is absent in mammals but found in plant and opportunistic human pathogens. IGPS was experimentally determined to be a V-type allosteric enzyme that is involved in an essential biosynthetic pathway of microorganisms. The enzyme catalyzes the hydrolysis of glutamine to form NH3 in the HisH protein, followed by cyclization of NH3 with N'-[(5'-phosphoribulosyl)imino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) in the HisF subunit, forming imidazole glycerol phosphate (IGP) and 5-aminoimidazole-4-carboxamide ribotide (AICAR) that enter the histidine and purine biosynthetic pathways. Allosteric motions induced upon the binding of the effector PRFAR to HisF propagate through the non-covalent HisH/HisF interface and synchronize catalytic activity at the two distant active sites. However, the nature of the allosteric pathway and the feasibility of manipulating signal transduction by using allosteric drug-like molecules remain to be established. Molecular docking studies of commercial drugs at the HisH/HisF interface were used to identify stable candidates with a potential allosteric effect on the reaction mechanism. Molecular dynamic simulations and calculations of NMR chemical shifts were combined to elucidate the allosteric pathway of IGPS.

  2. Composition, abundance, biomass, and production of macrofauna in a New England estuary: comparisons among eelgrass meadows and other nursery habitats

    USGS Publications Warehouse

    Heck, K.L., Jr.; Able, K.W.; Roman, C.T.; Fahay, M.P.

    1995-01-01

    Quantitative suction sampling was used to characterize and compare the species composition, abundance, biomass, and secondary production of macrofauna inhabiting intertidal mudflat and sandflat, eelgrass meadow, and saltmarshpool habitats in the Nauset Marsh complex, Cape Cod, Massachusetts (USA). Species richness and abundance were often greatest in eelgrass habitat, as was macroinvertebrate biomass and production. Most striking was the five to fifteen times greater rate of annual macrofaunal production in eelgrass habitat than elsewhere, with values ranging from approximately 23139 g AFDW m super(2) yr super(1). The marsh pool containing widgeon grass (Ruppia maritima) supported surprisingly low numbers of macroinvertebrates, probably due to stressfully low dissolved oxygen levels at night during the summer. Two species of macroinvertebrates, blue mussels (Mytilus edulis) and to a lesser extent bay scallops (Argopecten irradians), used eelgrass as 'nursery habitat.' Calculations showed that macroinvertebrate production is proportionally much greater than the amount of primary production attributable to eelgrass in the Nauset Marsh system, and that dramatic changes at all trophic levels could be expected if large changes in seagrass abundance should occur. This work further underscores the extraordinarily large impact that seagrass can have on both the structure and function of estuarine ecosystems.

  3. Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine

    PubMed Central

    e?kut?, Jolita; McCloskey, Diane E; Thomas, H Jeanette; Secrist, John A; Pegg, Anthony E; Ealick, Steven E

    2011-01-01

    Aminopropyltransferases are essential enzymes that form polyamines in eukaryotic and most prokaryotic cells. Spermidine synthase (SpdS) is one of the most well-studied enzymes in this biosynthetic pathway. The enzyme uses decarboxylated S-adenosylmethionine and a short-chain polyamine (putrescine) to make a medium-chain polyamine (spermidine) and 5?-deoxy-5?-methylthioadenosine as a byproduct. Here, we report a new spermidine synthase inhibitor, decarboxylated S-adenosylhomocysteine (dcSAH). The inhibitor was synthesized, and dose-dependent inhibition of human, Thermatoga maritima, and Plasmodium falciparum spermidine synthases, as well as functionally homologous human spermine synthase, was determined. The human SpdS/dcSAH complex structure was determined by X-ray crystallography at 2.0 resolution and showed consistent active site positioning and coordination with previously known structures. Isothermal calorimetry binding assays confirmed inhibitor binding to human SpdS with Kd of 1.1 0.3 ?M in the absence of putrescine and 3.2 0.1 ?M in the presence of putrescine. These results indicate a potential for further inhibitor development based on the dcSAH scaffold. PMID:21898642

  4. Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

    PubMed Central

    Konc, Janez; Hodošček, Milan; Ogrizek, Mitja; Trykowska Konc, Joanna; Janežič, Dušanka

    2013-01-01

    A challenge in structural genomics is prediction of the function of uncharacterized proteins. When proteins cannot be related to other proteins of known activity, identification of function based on sequence or structural homology is impossible and in such cases it would be useful to assess structurally conserved binding sites in connection with the protein's function. In this paper, we propose the function of a protein of unknown activity, the Tm1631 protein from Thermotoga maritima, by comparing its predicted binding site to a library containing thousands of candidate structures. The comparison revealed numerous similarities with nucleotide binding sites including specifically, a DNA-binding site of endonuclease IV. We constructed a model of this Tm1631 protein with a DNA-ligand from the newly found similar binding site using ProBiS, and validated this model by molecular dynamics. The interactions predicted by the Tm1631-DNA model corresponded to those known to be important in endonuclease IV-DNA complex model and the corresponding binding free energies, calculated from these models were in close agreement. We thus propose that Tm1631 is a DNA binding enzyme with endonuclease activity that recognizes DNA lesions in which at least two consecutive nucleotides are unpaired. Our approach is general, and can be applied to any protein of unknown function. It might also be useful to guide experimental determination of function of uncharacterized proteins. PMID:24244144

  5. Comparison of Three Ionic Liquid-Tolerant Cellulases by Molecular Dynamics

    PubMed Central

    Jaeger, Vance; Burney, Patrick; Pfaendtner, Jim

    2015-01-01

    We have employed molecular dynamics to investigate the differences in ionic liquid tolerance among three distinct family 5 cellulases from Trichoderma viride, Thermogata maritima, and Pyrococcus horikoshii. Simulations of the three cellulases were conducted at a range of temperatures in various binary mixtures of the ionic liquid 1-ethyl-3-methyl-imidazolium acetate with water. Our analysis demonstrates that the effects of ionic liquids on the enzymes vary in each individual case from local structural disturbances to loss of much of one of the enzyme’s secondary structure. Enzymes with more negatively charged surfaces tend to resist destabilization by ionic liquids. Specific and unique structural changes in the enzymes are induced by the presence of ionic liquids. Disruption of the secondary structure, changes in dynamical motion, and local changes in the binding pocket are observed in less tolerant enzymes. Ionic-liquid-induced denaturation of one of the enzymes is indicated over the 500 ns timescale. In contrast, the most tolerant cellulase behaves similarly in water and in ionic-liquid-containing mixtures. Unlike the heuristic approaches that attempt to predict enzyme stability using macroscopic properties, molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme’s behavior induced by ionic liquids and other mixed solvents. Using these insights, we propose specific experimentally testable hypotheses regarding the origin of activity loss for each of the systems investigated in this study. PMID:25692593

  6. One-Pot Biosynthesis of High-Concentration α-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes.

    PubMed

    Zhou, Wei; You, Chun; Ma, Hongwu; Ma, Yanhe; Zhang, Y-H Percival

    2016-03-01

    α-Glucose 1-phosphate (G1P) is synthesized from 5% (w/v) corn starch and 1 M phosphate mediated by α-glucan phosphorylase (αGP) from the thermophilic bacterium Thermotoga maritima at pH 7.2 and 70 °C. To increase G1P yield from corn starch containing branched amylopectin, a hyper-thermostable isoamylase from Sulfolobus tokodaii was added for simultaneous starch gelatinization and starch-debranching hydrolysis at 85 °C and pH 5.5 before αGP use. The pretreatment of isoamylase increased G1P titer from 120 mM to 170 mM. To increase maltose and maltotriose utilization, the third thermostable enzyme, 4-glucanotransferase (4GT) from Thermococcus litoralis, was added during the late stage of G1P biotransformation, further increasing G1P titer to 200 mM. This titer is the highest G1P level obtained on starch or its derived products (maltodextrin and soluble starch). This study suggests that in vitro multienzyme biotransformation has an advantage of great engineering flexibility in terms of space and time compared with microbial fermentation. PMID:26832825

  7. Crystal structure of a two-subunit TrkA octameric gating ring assembly

    DOE PAGESBeta

    Deller, Marc C.; Johnson, Hope A.; Miller, Mitchell D.; Spraggon, Glen; Elsliger, Marc -André; Wilson, Ian A.; Lesley, Scott A.; Ye, Sheng

    2015-03-31

    The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K⁺ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K⁺ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K⁺ ions acrossmore » the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K⁺ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K⁺ gating ring assemblies.« less

  8. The effect of nitrogen loading on a brackish estuarine faunal community: A stable isotope approach

    USGS Publications Warehouse

    Keats, R.A.; Osher, L.J.; Neckles, H.A.

    2004-01-01

    Coastal ecosystems worldwide face increased nutrient enrichment from shoreline and watershed development and atmospheric pollution. We investigated the response of the faunal community of a small microtidal estuary dominated by Ruppia maritima (widgeon grass) in Maine, United States, to increased nitrogen loading using an in situ mesocosm enrichment experiment. Community response was characterized by assessing quantitative shifts in macroin-vertebrate community composition and identifying changes in food web structure using stable carbon and nitrogen isotope ratios of producers and consumers. The community was dominated by brackish water invertebrates including midge larvae, oligochaetes, damselfly larvae, amphipods, and ostracods. Experimental nutrient additions resulted in significantly lower densities of herbivorous chironomids and predatory damselflies and greater densities of deposit feeding oligochaetes. Grazing midge larvae (Chironomidae: Dicrotendipes, Cricotopus) consumed epiphytic algae under both natural and enriched conditions. Deposit feeding Chironomus was dependent on allochthonous sources of detritus under natural conditions and exhibited a shift to autochthonous sources of detritus under enriched conditions. Predatory Enallagma primarily consumed grazing chironomids under all but the highest loading conditions. Experimental nutrient loading resulted in an increase in generalist deposit feeders dependent on autochthonous sources of detritus.

  9. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum

    PubMed Central

    Kazanov, Marat D.; Li, Xiaoqing; Gelfand, Mikhail S.; Osterman, Andrei L.; Rodionov, Dmitry A.

    2013-01-01

    Large and functionally heterogeneous families of transcription factors have complex evolutionary histories. What shapes specificities toward effectors and DNA sites in paralogous regulators is a fundamental question in biology. Bacteria from the deep-branching lineage Thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (ROK) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. We applied an integrated genomic approach to study functions and specificities of regulators from this family. A comparative analysis of 11 Thermotogae genomes revealed novel mechanisms of transcriptional regulation of the sugar utilization networks, DNA-binding motifs and specific functions. Reconstructed regulons for seven groups of ROK regulators were validated by DNA-binding assays using purified recombinant proteins from the model bacterium Thermotoga maritima. All tested regulators demonstrated specific binding to their predicted cognate DNA sites, and this binding was inhibited by specific effectors, mono- or disaccharides from their respective sugar catabolic pathways. By comparing ligand-binding domains of regulators with structurally characterized kinases from the ROK family, we elucidated signature amino acid residues determining sugar-ligand regulator specificity. Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family. PMID:23209028

  10. CheYs acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli

    PubMed Central

    Fraiberg, Milana; Afanzar, Oshri; Cassidy, C. Keith; Gabashvili, Alexandra; Schulten, Klaus; Levin, Yishai; Eisenbach, Michael

    2015-01-01

    Summary Stimulation of Escherichia coli with acetate elevates the acetylation level of the chemotaxis response regulator CheY. This elevation, in an unknown mechanism, activates CheY to generate clockwise rotation. Here, using quantitative selective reaction monitoring mass spectrometry and high-resolution targeted mass spectrometry, we identified K91 and K109 as the major sites whose acetylation level in vivo increases in response to acetate. Employing single and multiple lysine replacements in CheY, we found that K91 and K109 are also the sites mainly responsible for acetate-dependent clockwise generation. Furthermore, we showed that clockwise rotation is repressed when residue K91 is non-modified, as evidenced by an increased ability of CheY to generate clockwise rotation when K91 was acetylated or replaced by specific amino acids. Using molecular dynamics simulations we show that K91 repression is manifested in the conformational dynamics of the ?4?4 loop, shifted towards an active state upon mutation. Removal of ?4?4 loop repression may represent a general activation mechanism in CheY, pertaining also to the canonical phosphorylation activation pathway as suggested by crystal structures of active and inactive CheY from Thermotoga maritima. By way of elimination we further suggest that K109 acetylation is actively involved in generating clockwise rotation. PMID:25388160

  11. Crystal structure of a two-subunit TrkA octameric gating ring assembly

    SciTech Connect

    Deller, Marc C.; Johnson, Hope A.; Miller, Mitchell D.; Spraggon, Glen; Elsliger, Marc -André; Wilson, Ian A.; Lesley, Scott A.; Ye, Sheng

    2015-03-31

    The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K⁺ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K⁺ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K⁺ ions across the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K⁺ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K⁺ gating ring assemblies.

  12. Air pollution effects on the ultrastructure of Phlomis fruticosa mesophyll cells

    SciTech Connect

    Psaras, G.K.; Christodoulakis, N.S.

    1987-04-01

    Plant physiologists and environmental scientists suggest that a basic effect of air pollution on plants leads towards the minimization of their productivity. On the other hand the action of individual pollutants on intact plants has been studied from biochemical as well as structural viewpoint. Thus the study of plant responses to SO/sub 2/ exposure revealed that this agent causes acute and chronic injury. Chronic injury results in chlorosis and subsequent necrosis due to destruction of chlorophylls and final chloroplast lysis. It has been documented that ultrastructural characteristics of leaves are affected prior to any visible injury. Electron microscope examination of SO/sub 2/ fumigated plant-attached leaves of Vicia faba revealed chloroplast thylakoids starting to swell whilst photosynthesis rate was drastically reduced. The first light microscope-detected effects of air pollution on the leaf structure of plants common in natural ecosystems of Athens metropolitan area, have been reported. A chlorosis phenomenon in Urginea maritima leaves as well as an indication of detrimental effects of Phlomis fruticosa mesophyll chloroplasts were documented. In this work further investigation has been undertaken in order to elucidate the precise effects of air pollution on the ultrastructure of the photosynthesizing mesophyll cells.

  13. Allatostatins C, double C and triple C, the result of a local gene triplication in an ancestral arthropod.

    PubMed

    Veenstra, Jan A

    2016-05-01

    Allatostatin C is the arthropod homolog of vertebrate somatostatin. The gene went through a local gene triplification leading to the existence of three genes coding such peptides, allatostatins C, CC and CCC. All three genes are still present in several chelicerates, such as the horseshoe crab Limulus polyphemus, several spiders and the scorpion Mesobuthus martensii, the myriapod Strigamia maritima, as well as at least two insect species, Locusta migratoria and Athalia rosae, a sawfly. All three peptides have well conserved primary structures and peptides can easily be classified as either allatostatin C, CC or CCC. In most insect species only two of the genes have been preserved. In many species, these are CC and CCC, but in Diptera, Lepidoptera and Coleoptera it are allatostatins C and CC that are still present. In some arthropod species two or even all three genes can still be found closely associated in the genome and are present on the same scaffold showing that a local amplification was at the origin of these genes. PMID:27102937

  14. [Impacts of Ochotona pallasi disturbance on alpine grassland community characteristics].

    PubMed

    Zhao, Guo-qin; Li, Guang-yong; Ma, Wen-hu; Zhao, Dian-zhi; Li, Xiao-yan

    2013-08-01

    Plateau pika is the main fossorial mammal in the alpine grassland in Qinghai Lake Watershed of Northwest China. Based on the field investigation data from 18 alpine grassland quadrats in the Watershed, and by using redundancy analysis (RDA) and the surface fitting offered by 'R-Vegan' , the disturbance intensity of plateau pika (Ochotona pallasi) was classified as four levels. In order to explore the impacts of plateau pika disturbance on the alpine grassland ecosystem and its grazing quality, the community characteristics under different disturbance intensities by plateau pika were analyzed, and a conceptual model about the alpine grassland community succession was proposed. The results showed that with the increase of the disturbance intensity, the dominant species changed from Juncus roemerianus to Poa pratensis and Laux maritima. When the disturbance was small, the community had high quantitative values of coverage, aboveground biomass, biodiversity, and species richness, but the proportion of weeds was also high. When the disturbance was large, the quantitative values were the lowest, while the proportion of weeds was the highest. When the disturbance was moderate, the community had relatively high quantitative values, and the proportion of grasses and sedges was the highest. It was concluded that the community' s characteristic values under low plateau pika disturbance intensity were high but the grazing quality was low, while high disturbance intensity resulted in the grassland degradation. Therefore, the disturbance intensity in the threshold could maintain the stability of alpine grassland ecosystem and improve its grazing quality. PMID:24380328

  15. Chemical and in vitro assessment of Alaskan coastal vegetation antioxidant capacity.

    PubMed

    Kellogg, Joshua; Lila, Mary Ann

    2013-11-20

    Alaska Native (AN) communities have utilized tidal plants and marine seaweeds as food and medicine for generations, yet the bioactive potential of these resources has not been widely examined. This study screened six species of Alaskan seaweed ( Fucus distichus , Saccharina latissima , Saccharina groenlandica , Alaria marginata , Pyropia fallax , and Ulva lactuca ) and one tidal plant ( Plantago maritima ) for antioxidant activity. Total polyphenolic content (TPC) was determined, and chemical antioxidant capacity was assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferrous ion chelating, and nitric oxide (NO) inhibition assays. In vitro inhibition of radical oxygen species (ROS) generation and NO synthesis was evaluated in a RAW 264.7 macrophage culture. Greatest TPC (557.2 μg phloroglucinol equivalents (PGE)/mg extract) was discovered in the ethyl acetate fraction of F. distichus, and highest DDPH scavenging activity was exhibited by F. distichus and S. groenlandica fractions (IC50 = 4.29-5.12 μg/mL). These results support the potential of Alaskan coastal vegetation, especially the brown algae, as natural sources of antioxidants for preventing oxidative degeneration and maintaining human health. PMID:24147955

  16. Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates

    SciTech Connect

    Hamilton-Brehm, Scott; Vishnivetskaya, Tatiana A; Allman, Steve L; Mielenz, Jonathan R; Elkins, James G

    2012-01-01

    Flow cytometry (FCM) techniques have been developed for sorting mesophilic organisms, but the difficulty increases if the target microbes are thermophilic anaerobes. We demonstrate a reliable, high-throughput method of screening thermophilic anaerobic organisms using FCM and 96-well plates for growth on biomass-relevant substrates. The method was tested using the cellulolytic thermophiles Clostridium ther- mocellum (Topt = 55 C), Caldicellulosiruptor obsidiansis (Topt = 78 C) and the fermentative hyperthermo- philes, Pyrococcus furiosus (Topt = 100 C) and Thermotoga maritima (Topt = 80 C). Multi-well plates were incubated at various temperatures for approximately 72 120 h and then tested for growth. Positive growth resulting from single cells sorted into individual wells containing an anaerobic medium was verified by OD600. Depending on the growth substrate, up to 80 % of the wells contained viable cultures, which could be transferred to fresh media. This method was used to isolate thermophilic microbes from Rabbit Creek, Yellowstone National Park (YNP), Wyoming. Substrates for enrichment cultures including crystalline cellulose (Avicel), xylan (from Birchwood), pretreated switchgrass and Populus were used to cultivate organisms that may be of interest to lignocellulosic biofuel production.

  17. Ecological correlates of variable organ sizes and fat loads in the most northerly-wintering shorebirds

    USGS Publications Warehouse

    Ruthrauff, Daniel R.; Dekinga, Anne; Gill, R.E., Jr.; Summers, R.W.; Piersma, Theunis

    2013-01-01

    Shorebirds at northern latitudes during the nonbreeding season typically carry relatively large lipid stores and exhibit an up-regulation of lean tissues associated with digestion and thermogenesis. Intraspecific variation in these tissues across sites primarily reflects differences in environmental conditions. Rock (Calidris ptilocnemis (Coues, 1873)) and Purple (Calidris maritima (Brünnich, 1764)) sandpipers are closely related species having the most northerly nonbreeding distributions among shorebirds, living at latitudes up to 61°N in Cook Inlet, Alaska, and up to 71°N in northern Norway, respectively. Cook Inlet is the coldest known site used by nonbreeding shorebirds, and the region’s mudflats annually experience extensive coverage of foraging sites by sea and shore-fast ice. Accordingly, Rock Sandpipers increase their fat stores to nearly 20% of body mass during winter. In contrast, Purple Sandpipers exploit predictably ice-free rocky intertidal foraging sites and maintain low (<6.5%) fat stores. Rock Sandpipers increase the mass of lean tissues from fall to winter, including contour feathers, stomach, and liver components. They also have greater lean pectoralis and supracoracoideus muscle and liver and kidney tissues compared with Purple Sandpipers in winter. This demonstrates a combined emphasis on digestive processes and thermogenesis, whereas Purple Sandpipers primarily augment organs associated with digestive processes. The high winter fat loads and increased lean tissues of Rock Sandpipers in Cook Inlet reflect the region’s persistent cold and abundant but sporadically unavailable food resources.

  18. A study of antioxidant activity, enzymatic inhibition and in vitro toxicity of selected traditional sudanese plants with anti-diabetic potential

    PubMed Central

    2014-01-01

    Background Diabetes mellitus is a chronic metabolic disease with life-threatening complications. Despite the enormous progress in conventional medicine and pharmaceutical industry, herbal-based medicines are still a common practice for the treatment of diabetes. This study evaluated ethanolic and aqueous extracts of selected Sudanese plants that are traditionally used to treat diabetes. Methods Extraction was carried out according to method described by Sukhdev et. al. and the extracts were tested for their glycogen phosphorylase inhibition, Brine shrimp lethality and antioxidant activity using (DPPH) radical scavenging activity and iron chelating activity. Extracts prepared from the leaves of Ambrosia maritima, fruits of Foeniculum vulgare and Ammi visnaga, exudates of Acacia Senegal, and seeds of Sesamum indicum and Nigella sativa. Results Nigella sativa ethanolic extract showed no toxicity on Brine shrimp Lethality Test, while its aqueous extract was toxic. All other extracts were highly toxic and ethanolic extracts of Foeniculum vulgare exhibited the highest toxicity. All plant extracts with exception of Acacia senegal revealed significant antioxidant activity in DPPH free radical scavenging assay. Conclusions These results highly agree with the ethnobotanical uses of these plants as antidiabetic. This study endorses further studies on plants investigated, to determine their potential for type 2 diabetes management. Moreover isolation and identification of active compounds are highly recommended. PMID:24885334

  19. Mesohaline submerged aquatic vegetation survey along the U.S. gulf of Mexico coast, 2000: A stratified random approach

    USGS Publications Warehouse

    Carter, J.; Merino, J.H.; Merino, S.L.

    2009-01-01

    Estimates of submerged aquatic vegetative (SAV) along the U.S. Gulf of Mexico (Gulf) generally focus on seagrasses. In 2000, we attempted a synoptic survey of SAV in the mesohaline (5-20 ppt) zone of estuarine and nearshore areas of the northeastern Gulf. Areas with SAV were identified from existing aerial 1992 photography, and a literature review was used to select those areas that were likely to experience mesohaline conditions during the growing season. In 2000, a drought year, we visited 217 randomly selected SAV beds and collected data on species composition and environmental conditions. In general, sites were either clearly polyhaline (2: 20 ppt) or oligohaline (S 5 ppt), with only five sites measuring between 5 and 20 ppt. Ruppia maritima L. (13-35 ppt, n = 28) was the only species that occurred in mesohaline salinities. Halodule wrightii Asch. occurred in 73% of the beds. The nonindigenous Myriophyllum spicatum L. was present in four locations with salinities below 3 ppt. No nonindigenous macroalgae were identified, and no nonindigenous angiosperms occurred in salinities above 3 ppt. Selecting sample locations based on historical salinity data was not a successful strategy for surveying SAV in mesohaline systems, particularly during a drought year. Our ability to locate SAV beds within 50 m of their aerially located position 8 yr later demonstrates some SAV stability in the highly variable conditions of the study area. ?? 2009 by the Marine Environmental Silences Consortium of Alabama.

  20. Functional adaptations of the bacterial chaperone trigger factor to extreme environmental temperatures.

    PubMed

    Godin-Roulling, Amandine; Schmidpeter, Philipp A M; Schmid, Franz X; Feller, Georges

    2015-07-01

    Trigger factor (TF) is the first molecular chaperone interacting cotranslationally with virtually all nascent polypeptides synthesized by the ribosome in bacteria. Thermal adaptation of chaperone function was investigated in TFs from the Antarctic psychrophile Pseudoalteromonas haloplanktis, the mesophile Escherichia coli and the hyperthermophile Thermotoga maritima. This series covers nearly all temperatures encountered by bacteria. Although structurally homologous, these TFs display strikingly distinct properties that are related to the bacterial environmental temperature. The hyperthermophilic TF strongly binds model proteins during their folding and protects them from heat-induced misfolding and aggregation. It decreases the folding rate and counteracts the fast folding rate imposed by high temperature. It also functions as a carrier of partially folded proteins for delivery to downstream chaperones ensuring final maturation. By contrast, the psychrophilic TF displays weak chaperone activities, showing that these functions are less important in cold conditions because protein folding, misfolding and aggregation are slowed down at low temperature. It efficiently catalyses prolyl isomerization at low temperature as a result of its increased cellular concentration rather than from an improved activity. Some chaperone properties of the mesophilic TF possibly reflect its function as a cold shock protein in E. coli. PMID:25389111

  1. Vegetation dynamics in impounded marshes along the Indian River Lagoon, Florida, USA

    NASA Astrophysics Data System (ADS)

    Rey, Jorge R.; Crossman, Roy A.; Kain, Tim R.

    1990-05-01

    Data are presented on the vegetation dynamics of two impounded marshes along the Indian River Lagoon, in east-central Florida, USA. Vegetation in one of the marshes (IRC 12) was totally eliminated by overflooding and by hypersaline conditions (salinities over 100 ppt) that developed there in 1979 after the culvert connecting the marsh with the lagoon was closed. Over 20% recovery of the herbaceous halophytes Salicornia virginica, S. bigelovii, and Batis maritima was observed at that site after the culvert was reopened in 1982, but total cover in the marsh remains well below the original 75%. No recovery of mangroves was observed at this site. The second site (SLC 24), while remaining isolated from the lagoon during much of the study, did not suffer the complete elimination of vegetation experienced at the first site. At this location, mangroves increased in cover and frequency with a concomitant decrease in herbaceous halophytes. Considerable damage to the vegetation was evident at IRC 12 when the impoundment was closed and flooded for mosquito control in 1986. Although the damage was temporary, its occurrence emphasizes the need of planning and constant monitoring and adjustment of management details as conditions within particular marshes change. Storms and hurricanes may be important in promoting a replacement of black mangroves by red mangroves in closed impoundments because the former cannot tolerate pneumatophore submergence for long periods of time.

  2. Metal speciation in salt marsh sediments: Influence of halophyte vegetation in salt marshes with different morphology

    NASA Astrophysics Data System (ADS)

    Pedro, Sílvia; Duarte, Bernardo; Raposo de Almeida, Pedro; Caçador, Isabel

    2015-12-01

    Salt marshes provide environmental conditions that are known to affect metal speciation in sediments. The elevational gradient along the marsh and consequent differential flooding are some of the major factors influencing halophytic species distribution and coverage due to their differential tolerance to salinity and submersion. Different species, in turn, also have distinct influences on the sediment's metal speciation, and its metal accumulation abilities. The present work aimed to evaluate how different halophyte species in two different salt marshes could influence metal partitioning in the sediment at root depth and how that could differ from bare sediments. Metal speciation in sediments around the roots (rhizosediments) of Halimione portulacoides, Sarcocornia fruticosa and Spartina maritima was determined by sequentially extracting operationally defined fractions with solutions of increasing strength and acidity. Rosário salt marsh generally showed higher concentrations of all metals in the rhizosediments. Metal partitioning was primarily related to the type of metal, with the elements' chemistry overriding the environment's influence on fractionation schemes. The most mobile elements were Cd and Zn, with greater availability being found in non-vegetated sediments. Immobilization in rhizosediments was predominantly influenced by the presence of Fe and Mn oxides, as well as organic complexes. In the more mature of both salt marshes, the differences between vegetated and non-vegetated sediments were more evident regarding S. fruticosa, while in the younger system all halophytes presented significantly different metal partitioning when compared to that of mudflats.

  3. Expression patterns of Wnt genes in the venom claws of centipedes.

    PubMed

    Hayden, Luke; Arthur, Wallace

    2013-01-01

    The venom claws of centipedes, also known as forcipules, represent an evolutionary novelty that must have arisen in the centipede stem species, as they are not found in any other myriapods. The developmental-genetic changes that are involved in the origin of novelties are of considerable interest. It has previously been shown that centipede forcipules have a unique Hox code. However, this is a combinatorial code: no single Hox gene has a forcipule-specific expression. Here, we focus on Wnt genes. Two genes of this family show forcipule-specific expression in the "model centipede" Strigamia maritima: Wnt7 and Wnt11. For Wnt7, this forcipular expression zone seems to be a new one, which has arisen in evolution subsequently to other expression zones of the same gene. However, for Wnt11, the forcipule-specific expression probably arose by reduction of a more general pattern that originally included most or all of the limbs of an ancestral myriapod. Thus the developmental-genetic basis of the evolutionary change that turned the first pair of walking legs into venom claws is complex, involving different types of change in expression pattern. This sort of complexity is likely to be the case regarding evolutionary changes in morphology in general. Whether the origins of those features that can be considered as novelties are different in terms of their developmental-genetic basis from more routine evolutionary changes remains an open question. PMID:24074281

  4. Spatial and seasonal variation in heavy metals in interstitial water of salt marsh soils.

    PubMed

    Otero, Xosé L; Macías, Felipe

    2002-01-01

    The composition of interstitial water collected from a salt marsh in NW Spain showed clear seasonal and spatial variations associated with redox cycles of Fe and S. In the summer, salinity increased in all soils as a consequence of the increase in evapotranspiration. The pH and concentrations of heavy metals also differed with season, but not all environments showed the same variations. Soils not colonized by plants had the highest pH and lowest heavy metal concentrations in the summer. These results support the idea that higher temperatures lead to an increase in the activity of sulfate-reducing bacteria, which in turn leads to an increase in alkalinity and concentration of sulfides in the water. Trace metals tend to precipitate with sulfides under these conditions and are removed from the interstitial water. In contrast, in the soils colonized by Spartina maritima, the oxidation of metal sulfides during the summer led to a decrease in pH and an increase in the metal concentrations in the interstitial water. The results obtained concur with those found for seasonal variations in metal sulfides in soils from the same salt marsh. PMID:12395829

  5. Trophic plasticity of the gastropod Hydrobia ulvae within an intertidal bay (Roscoff, France): A stable isotope evidence

    NASA Astrophysics Data System (ADS)

    Riera, P.

    2010-01-01

    The study investigated the trophic ecology of the gastropod Hydrobia ulvae in different habitat types within an intertidal bay. The results point out two major trophic pathways involving H.ulvae in this bay. On the one hand, in sandy/muddy sediments Hydrobia derives most of its energy from allochtonous detritus derived from Enteromorpha sp and the total SOM pool. In addition, in these sediments, the phototrophic purple bacteria mats played a substantial trophic role in the diet of Hydrobia. On the other hand, in a Spartina maritima marsh, the gastropod appears firstly dependent of autochtonous detritus derived from this plant. The minor contribution of microphytobenthos to the diet of Hydrobia is consistent with a relatively low presence of epipelic diatoms at the sampling sites. These results provide evidence that the trophic ecology of H.ulvae inhabiting intertidal sediments is quite plastic and does not necessarily rely primarly on microphytobenthos. Consequently, in a single bay, the small spatial scale variability in the origin and availability of detritus have direct implications on the food incorporation by H.ulvae.

  6. Screening of 18 species for digestate phytodepuration.

    PubMed

    Pavan, Francesca; Breschigliaro, Simone; Borin, Maurizio

    2015-02-01

    This experiment assesses the aptitude of 18 species in treating the digestate liquid fraction (DLF) in a floating wetland treatment system. The pilot system was created in NE Italy in 2010 and consists of a surface-flow system with 180 floating elements (Tech-IA®) vegetated with ten halophytes and eight other wetland species. The species were transplanted in July 2011 in basins filled with different proportions of DLF/water (DLF/w); periodic increasing of the DLF/w ratio was imposed after transplanting, reaching the worst conditions for plants in summer 2012 (highest EC value 7.3 mS cm/L and NH4-N content 225 mg/L). It emerged that only Cynodon dactylon, Typha latifolia, Elytrigia atherica, Halimione portulacoides, Salicornia fruticosa, Artemisia caerulescens, Spartina maritima and Puccinellia palustris were able to survive under the system conditions. Halophytes showed higher dry matter production than other plants. The best root development (up to 40-cm depth) was recorded for Calamagrostis epigejos, Phragmites australis, T. latifolia and Juncus maritimus. The highest nitrogen (10-15 g/m(2)) and phosphorus (1-4 g/m(2)) uptakes were obtained with P. palustris, Iris pseudacorus and Aster tripolium. In conclusion, two halophytes, P. palustris and E. atherica, present the highest potential to be used to treat DLF in floating wetlands. PMID:25005162

  7. A role for [Fe4S4] clusters in tRNA recognition—a theoretical study

    PubMed Central

    Stiebritz, Martin T.

    2014-01-01

    Over the past several years, structural studies have led to the unexpected discovery of iron–sulfur clusters in enzymes that are involved in DNA replication/repair and protein biosynthesis. Although these clusters are generally well-studied cofactors, their significance in the new contexts often remains elusive. One fascinating example is a tryptophanyl-tRNA synthetase from the thermophilic bacterium Thermotoga maritima, TmTrpRS, that has recently been structurally characterized. It represents an unprecedented connection among a primordial iron–sulfur cofactor, RNA and protein biosynthesis. Here, a possible role of the [Fe4S4] cluster in tRNA anticodon-loop recognition is investigated by means of density functional theory and comparison with the structure of a human tryptophanyl-tRNA synthetase/tRNA complex. It turns out that a cluster-coordinating cysteine residue, R224, and polar main chain atoms form a characteristic structural motif for recognizing a putative 5′ cytosine or 5′ 2-thiocytosine moiety in the anticodon loop of the tRNA molecule. This motif provides not only affinity but also specificity by creating a structural and energetical penalty for the binding of other bases, such as uracil. PMID:24753428

  8. Purification and properties of multiple isoforms of a novel thiol methyltransferase involved in the production of volatile sulfur compounds from Brassica oleracea.

    PubMed

    Attieh, J; Sparace, S A; Saini, H S

    2000-08-15

    Five functional isoforms of a novel plant thiol methyltransferase from the leaves of cabbage (Brassica oleracea L.) were purified to electrophoretic homogeneity. Pooled, partly purified preparations of the enzyme were previously shown to methylate thiol compounds released upon the hydrolysis of glucosinolates. The enzyme could also accept halide ions as substrates. The estimated molecular masses of the purified isoforms ranged between 26 and 31 kDa. The three most abundant isoforms of the enzyme could all catalyze the S-adenosyl-l-methionine-dependent methylation of thiocyanate, a number of organic thiols and iodide. However, the kinetic properties of these forms toward various substrates differed widely. None of the isoforms examined methylated the O- and N-equivalents of the thiol substrates. The three isoforms also had distinct pH optima, covering the range from 5 to 9. Their kinetic analysis indicated that they shared a sequential substrate binding mechanism and an Ordered Bi Bi mechanism for substrate binding and product release. Partial internal amino acid sequence from one isoform showed high similarity to an Arabidopsis EST of unknown function, and to a recently cloned methyl chloride transferase from Batis maritima. The differences in the pH optima and kinetic properties of the isoforms suggest that each may methylate a specific substrate or a narrow group of substrates under cellular conditions. PMID:10933880

  9. Antioxidant Potential of Bark Extracts from Boreal Forest Conifers.

    PubMed

    Legault, Jean; Girard-Lalancette, Karl; Dufour, Dominic; Pichette, André

    2013-01-01

    The bark of boreal forest conifers has been traditionally used by Native Americans to treat various ailments and diseases. Some of these diseases involve reactive oxygen species (ROS) that can be prevented by the consumption of antioxidants such as phenolic compounds that can be found in medicinal plants. In this study, ultrasonic assisted extraction has been performed under various solvent conditions (water:ethanol mixtures) on the bark of seven boreal forest conifers used by Native Americans including: Pinus strobus, Pinus resinosa, Pinus banksiana, Picea mariana, Picea glauca, Larix laricina, and Abies balsamea. The total phenolic content, as well as ORACFL potency and cellular antioxidant activity (IC50), were evaluated for all bark extracts, and compared with the standardized water extract of Pinus maritima bark (Pycnogenol), which showed clinical efficiency to prevent ROS deleterious effects. The best overall phenolic extraction yield and antioxidant potential was obtained with Picea glauca and Picea mariana. Interestingly, total phenolic content of these bark extracts was similar to Pycnogenol but their antioxidant activity were higher. Moreover, most of the extracts did not inhibit the growth of human skin fibroblasts, WS1. A significant correlation was found between the total phenolic content and the antioxidant activity for water extracts suggesting that these compounds are involved in the activity. PMID:26784337

  10. A rare case of a natural contact zone in Morocco between an autopolyploid and an allopolyploid of Centaurea aspera with sterile tetraploid hybrids.

    PubMed

    Garmendia, A; Ferriol, M; Juarez, J; Zając, A; Kałużny, K; Merle, H

    2015-05-01

    A new contact zone between Centaurea aspera and Centaurea seridis was found in Morocco. Chromosome counts and flow cytometry showed that both taxa were tetraploid (4x = 44). A literature review and morphometric analysis established that C. aspera corresponds to the autopolyploid C. aspera subsp. gentilii and C. seridis corresponds to the allopolyploid C. seridis var. auriculata. This contact area was compared with the homologous contact zones in Spain formed by the diploid C. aspera subsp. stenophylla and the tetraploid C. seridis subsp. maritima. Natural hybrids between parental species were frequent in both areas. In Spain, hybrids were triploid (from reduced gametes A and gamete AB), highly sterile and exerted a 'triploid block'. In Morocco, cytometry showed that hybrids were tetraploid and, therefore, probably fertile, but all the capitula lacked achenes. It is likely that the resulting genome of the new tetraploid hybrid (AAAB), through the fusion of reduced gametes AA (from subsp. gentilii) and AB (from var. auriculata), could explain irregularities in meiosis through formation of aneuploid gametes and, therefore, infertility of the hybrid. Moroccan sterile tetraploid hybrids develop, but have the identical irregularities to Spanish triploids, probably due to the odd number of homologous chromosomes. The new hybrid is first described as C. x subdecurrens nothosubsp. paucispinus. In addition, distribution and ecological traits are analysed. PMID:25363815

  11. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments.

    PubMed

    Nesbø, Camilla L; S Swithers, Kristen; Dahle, Håkon; Haverkamp, Thomas H A; Birkeland, Nils-Kåre; Sokolova, Tatiana; Kublanov, Ilya; Zhaxybayeva, Olga

    2015-07-01

    Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development. PMID:25500512

  12. High-resolution screening combined with HPLC-HRMS-SPE-NMR for identification of potential health-promoting constituents in sea aster and searocket--new Nordic food ingredients.

    PubMed

    Wubshet, Sileshi G; Schmidt, Jeppe S; Wiese, Stefanie; Staerk, Dan

    2013-09-11

    Sea aster (Aster tripolium L.) and searocket (Cakile maritima Scop.), potential ingredients in the New Nordic Diet, were analyzed by high-resolution radical scavenging and high-resolution α-glucosidase inhibition assays. Results from the two bioactivity profiles were used to guide subsequent structural analysis toward constituents with potential health-promoting effects. Structural analysis was performed by high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction and automated tube transfer nuclear magnetic resonance spectroscopy, that is, HPLC-HRMS-SPE-ttNMR. High-resolution mass spectrometry together with detailed analysis of one- and two-dimensional proton detected NMR experiments enabled unambiguous assignment of the targeted analytes. This revealed a series of caffeoyl esters (1, 2, 5), flavonoid glycosides (3, 4, 6, 11-15), flavonoids (7-9), sinapate esters (10, 16, 17), and sinapinic acid (18) associated with radical scavenging and/or α-glucosidase inhibition. In vitro assays implemented in this study showed that sea aster holds potential as a future functional food ingredient for lowering postprandial blood glucose level for diabetics, but further investigations are needed to prove the effect in vivo. PMID:23962163

  13. Palynological analysis of camelid coprolites: seasonality in the use of the site Cerro Casa de Piedra 7 (Santa Cruz, Argentina)

    NASA Astrophysics Data System (ADS)

    Velázquez, Nadia Jimena; Burry, Lidia Susana; Fugassa, Martín Horacio; Civalero, María Teresa; Aschero, Carlos Alberto

    2014-01-01

    Palynological, palaeoparasitological and paleobotanical studies of coprolites found in archaeological sites from Perito Moreno National Park (47°57‧S72°05‧W) yielded information on diet, palaeoenvironment and health. These studies allowed adding evidence to the reconstruction of life history of the hunter-gatherers that inhabited Patagonia during the Holocene. We examined the season of the year when camelid Lama guanicoe coprolites (5400 ± 64 yr 14C BP to 9640 ± 190 yr 14C BP) were deposited at Cerro Casa de Piedra 7 (site CCP7). The study used palynological evidence and comparison with pollen spectra of modern feces collected during summer, fall, winter and spring of 2010. The dominant types were: pollen of Nothofagus, Empetrum rubrum, Asteraceae subfam. Asteroideae, Nassauvia, Caryophyllaceae and Poaceae; fern spores; remains of Eimeria macusaniensis; and plant remains of Poaceae, Festuca pallescens, Stipa speciosa, Armeria maritima, Gaultheria mucronata and E. rubrum. Pollen spectra of modern and fossil feces were used for multivariate analysis. Coprolites associated to fall and winter modern feces. These results and those obtained from pollen concentration values and the presence of pollen types indicators of seasonality, allowed the determination of summer, fall and winter coprolites. However, caution must be taken with the seasonality results of coprolites dated earlier than 9000 years BP since the environmental conditions differed from now. The site was probably a camelid shelter during the unfavorable seasons.

  14. From bacterial to human dihydrouridine synthase: automated structure determination

    SciTech Connect

    Whelan, Fiona Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  15. Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

    PubMed

    Gao, Honghai; Huang, Jianmin; Barany, Francis; Cao, Weiguo

    2007-01-01

    Endonuclease V (endo V) recognizes a broad range of aberrations in DNA such as deaminated bases or mismatches. It nicks DNA at the second phosphodiester bond 3' to a deaminated base or a mismatch. Endonuclease V obtained from Thermotoga maritima preferentially cleaves purine mismatches in certain sequence context. Endonuclease V has been combined with a high-fidelity DNA ligase to develop an enzymatic method for mutation scanning. A biochemical screening of site-directed mutants identified mutants in motifs III and IV that altered the base preferences in mismatch cleavage. Most profoundly, a single alanine substitution at Y80 position switched the enzyme to essentially a C-specific mismatch endonuclease, which recognized and cleaved A/C, C/A, T/C, C/T and even the previously refractory C/C mismatches. Y80A can also detect the G13D mutation in K-ras oncogene, an A/C mismatch embedded in a G/C rich sequence context that was previously inaccessible using the wild-type endo V. This investigation offers insights on base recognition and active site organization. Protein engineering in endo V may translate into better tools in mutation recognition and cancer mutation scanning. PMID:17130153

  16. Improving small-angle X-ray scattering data for structural analyses of the RNA world.

    PubMed

    Rambo, Robert P; Tainer, John A

    2010-03-01

    Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNA(val), and yeast tRNA(phe) that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways. PMID:20106957

  17. Ritual plants of Muslim graveyards in northern Israel

    PubMed Central

    Dafni, Amots; Lev, Efraim; Beckmann, Sabine; Eichberger, Christian

    2006-01-01

    This article surveys the botanical composition of 40 Muslim graveyards in northern Israel, accompanied by an ethnobotanical study of the folkloristic traditions of the use of these plants in cemeteries. Three groups of plants were found to be repeated systematically and were also recognized for their ritual importance: aromatics herbs (especially Salvia fruticosa and Rosmarinus officinalis), white flowered plants (mainly Narcissus tazetta, Urginea maritima, Iris spp. and Pancratium spp.) and Cupressus sempervirens as the leading cemetery tree. As endemic use we can indicate the essential role of S. fruticosa as the main plant used in all human rites of passage symbolizing the human life cycle. The rosemary is of European origin while the use of basil is of Indian influence. The use of white flowers as cemeteries plants reflects an old European influence and almost the same species are used or their congeners. Most of the trees and shrubs that are planted in Muslim cemeteries in Israel have the same use in ancient as well in modern European cultures. In conclusion, our findings on the occurrence of plants in graveyards reflect the geographic situation of Israel as a crossroads in the cultural arena between Asia and Europe. Most of the traditions are common to the whole Middle East showing high relatedness to the classical world as well as to the present-day Europe. PMID:16961931

  18. Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8

    PubMed Central

    Suzuki, Sakiko; Yanai, Hisaaki; Kanagawa, Mayumi; Tamura, Satoko; Watanabe, Yuzo; Fuse, Kyotaro; Baba, Seiki; Sampei, Gen-ichi; Kawai, Gota

    2012-01-01

    The crystal structure of PurL from Thermus thermophilus HB8 (TtPurL; TTHA1519) was determined in complex with an adenine nucleotide, PO4 3− and Mg2+ at 2.35 Å resolution. TtPurL consists of 29 α-helices and 28 β-strands, and one loop is disordered. TtPurL consists of four domains, A1, A2, B1 and B2, and the structures of the A1–B1 and A2–B2 domains were almost identical to each other. Although the sequence identity between TtPurL and PurL from Thermotoga maritima (TmPurL) is higher than that between TtPurL and the PurL domain of the large PurL from Salmonella typhimurium (StPurL), the secondary structure of TtPurL is much more similar to that of StPurL than to that of TmPurL. PMID:22232163

  19. A role for [Fe4S4] clusters in tRNA recognition--a theoretical study.

    PubMed

    Stiebritz, Martin T

    2014-05-01

    Over the past several years, structural studies have led to the unexpected discovery of iron-sulfur clusters in enzymes that are involved in DNA replication/repair and protein biosynthesis. Although these clusters are generally well-studied cofactors, their significance in the new contexts often remains elusive. One fascinating example is a tryptophanyl-tRNA synthetase from the thermophilic bacterium Thermotoga maritima, TmTrpRS, that has recently been structurally characterized. It represents an unprecedented connection among a primordial iron-sulfur cofactor, RNA and protein biosynthesis. Here, a possible role of the [Fe4S4] cluster in tRNA anticodon-loop recognition is investigated by means of density functional theory and comparison with the structure of a human tryptophanyl-tRNA synthetase/tRNA complex. It turns out that a cluster-coordinating cysteine residue, R224, and polar main chain atoms form a characteristic structural motif for recognizing a putative 5' cytosine or 5' 2-thiocytosine moiety in the anticodon loop of the tRNA molecule. This motif provides not only affinity but also specificity by creating a structural and energetical penalty for the binding of other bases, such as uracil. PMID:24753428

  20. Isolation, characterization, and survival strategies of Thermotoga sp. strain PD524, a hyperthermophile from a hot spring in Northern Thailand.

    PubMed

    Kanoksilapatham, Wirojne; Keawram, Porranee; Gonzalez, Juan M; Robb, Frank T

    2015-07-01

    A hyperthermophilic Thermotoga sp. strain PD524 was isolated from a hot spring in Northern Thailand. Cells were long-curved rods (0.5-0.6 × 2.5-10 μm) surrounded by a typical outer membrane toga. Strain PD524 is aero-tolerant at 4 °C but is aero-sensitive at 80 °C. A heat resistant subpopulation was observed in late-stationary phase. Cells from late-stationary phase were revealed remarkably less sensitive to 0.001 % SDS treatment than cells from exponential phase. The temperature range for growth was 70-85 °C (opt. temp. 80 °C), pH range was 6-8.5 (opt. pH 7.5-8.0), and NaCl range of 0 to <10 g/L (opt. 0.5 g/L). Glucose, sucrose, maltose, fructose, xylose, mannose, arabinose, trehalose, starch, and cellobiose were utilized as growth substrates. Growth was inhibited by S(o). Growth yield was stimulated by SO 4 (=) but not by S2O 3 (=) and NO3 (-). Analysis of 16S rRNA gene sequence (KF164213) of strain PD524 revealed closest similarity (96 %) to Thermotoga maritima MSB8(T), T. neapolitana NES(T), T. petrophila RKU-1(T), and T. naphthophila RKU-10(T). PMID:26101016

  1. A legacy of contrasting spatial genetic structure on either side of the Atlantic-Mediterranean transition zone in a marine protist.

    PubMed

    Lowe, Chris D; Martin, Laura E; Montagnes, David J S; Watts, Phillip C

    2012-12-18

    The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change. PMID:23213247

  2. Novel α-L-Fucosidases from a Soil Metagenome for Production of Fucosylated Human Milk Oligosaccharides.

    PubMed

    Lezyk, Mateusz; Jers, Carsten; Kjaerulff, Louise; Gotfredsen, Charlotte H; Mikkelsen, Maria D; Mikkelsen, Jørn D

    2016-01-01

    This paper describes the discovery of novel α-L-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. Seven novel α-L-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in E. coli as recombinant 6xHis-tagged proteins. All seven fucosidases belong to glycosyl hydrolase family 29 (GH 29). Six of the seven α-L-fucosidases were substrate-inhibited, moderately thermostable and most hydrolytically active in the pH range 6-7, when tested with para-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as the substrate. In contrast, one fucosidase (Mfuc6) exhibited a high pH optimum and an unusual sigmoidal kinetics towards pNP-Fuc substrate. When tested for trans-fucosylation activity using pNP-Fuc as donor, most of the enzymes were able to transfer fucose to pNP-Fuc (self-condensation) or to lactose. With the α-L-fucosidase from Thermotoga maritima and the metagenome-derived Mfuc5, different fucosyllactose variants including the principal fucosylated HMO 2'-fucosyllactose were synthesised in yields of up to ~6.4%. Mfuc5 was able to release fucose from xyloglucan and could also use it as a fucosyl-donor for synthesis of fucosyllactose. This is the first study describing the use of glycosyl hydrolases for the synthesis of genuine fucosylated human milk oligosaccharides. PMID:26800369

  3. Impacts of the 1998 and 2010 mass coral bleaching events on the Western Gulf of Thailand

    NASA Astrophysics Data System (ADS)

    Sutthacheep, Makamas; Yucharoen, Mathinee; Klinthong, Wanlaya; Pengsakun, Sittiporn; Sangmanee, Kanwara; Yeemin, Thamasak

    2013-11-01

    A long-term study of coral reef ecology in the Gulf of Thailand provides a good opportunity to examine the temporal variation on the impact of mass coral bleaching at those reef sites. We compared the bleaching and mortality of corals between the mass bleaching events in 1998 and 2010 at a coral community in the Western Gulf of Thailand. The aim was to identify the coral species which were most likely to suffer from (and to be able to tolerate) changes in seawater temperature. Significant differences in the susceptibility of the coral taxa to bleaching events between the years 1998 and 2010 and among coral species were documented. Bleaching was significantly different between the most dominant corals. Diploastrea heliopora was the most resistant coral to bleaching in both years. Some coral species showed more resistance to bleaching in 2010. The coral mortality following the mass bleaching events in 1998 and 2010 varied significantly between the years and the coral taxa. Mortality of some dominant coral taxa was also lower in 2010. Seven coral species, i.e. Astreopora myriophthalma, Pachyseris rugosa, Turbinaria mesenterina, Goniastrea pectinata, Favia pallida, F. maritima, Favites halicora, Platygyra daedalea and Galaxea fascicularis, were tolerant to the coral bleaching events. An ecosystem-based approach to managing coral reefs in the Gulf of Thailand is needed to identify appropriate marine protected area networks and to strengthen marine and coastal resource policies in order to build coral reef resilience.

  4. The biological soil crusts of the San Nicolas Island: Enigmatic algae from a geographically isolated ecosystem

    USGS Publications Warehouse

    Flechtner, V.R.; Johansen, J.R.; Belnap, J.

    2008-01-01

    Composite soil samples from 7 sites on San Nicolas Island were evaluated quantitatively and qualitatively for the presence of cyanobacteria and eukaryotic microalgae. Combined data demonstrated a rich algal flora with 19 cyanobacterial and 19 eukaryotic microalgal genera being identified, for a total of 56 species. Nine new species were identified and described among the cyanobacteria and the eukaryotic microalgae that were isolated: Leibleinia edaphica, Aphanothece maritima, Chroococcidiopsis edaphica, Cyanosarcina atroveneta, Hassallia californica, Hassallia pseudoramosissima, Microchaete terrestre, Palmellopsis californiens, and Pseudotetracystis compactis. Distinct distributional patterns of algal taxa existed among sites on the island and among soil algal floras of western North America. Some algal taxa appeared to be widely distributed across many desert regions, including Microcoleus vaginatus, Nostoc punctiforme, Nostoc paludosum, and Tolypothrix distorta, Chlorella vulgaris, Diplosphaera cf. chodatii, Myrmecia astigmatica, Myrmecia biatorellae, Hantzschia amphioxys, and Luticola mutica. Some taxa share a distinctly southern distribution with soil algae from southern Arizona, southern California, and Baja California (e.g., Scenedesmus deserticola and Eustigmatos magnus). The data presented herein support the view that the cyanobacterial and microalgal floras of soil crusts possess significant biodiversity, much of it previously undescribed.

  5. Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.

    PubMed

    Smith, Craig D; Carson, Mike; Friedman, Alan M; Skinner, Matthew M; Delucas, Lawrence; Chantalat, Laurent; Weise, Lance; Shirasawa, Takuji; Chattopadhyay, Debashish

    2002-03-01

    Spontaneous formation of isoaspartyl residues (isoAsp) disrupts the structure and function of many normal proteins. Protein isoaspartyl methyltransferase (PIMT) reverts many isoAsp residues to aspartate as a protein repair process. We have determined the crystal structure of human protein isoaspartyl methyltransferase (HPIMT) complexed with adenosyl homocysteine (AdoHcy) to 1.6-A resolution. The core structure has a nucleotide binding domain motif, which is structurally homologous with the N-terminal domain of the bacterial Thermotoga maritima PIMT. Highly conserved residues in PIMTs among different phyla are placed at positions critical to AdoHcy binding and orienting the isoAsp residue substrate for methylation. The AdoHcy is completely enclosed within the HPIMT and a conformational change must occur to allow exchange with adenosyl methionine (AdoMet). An ordered sequential enzyme mechanism is supported because C-terminal residues involved with AdoHcy binding also form the isoAsp peptide binding site, and a change of conformation to allow AdoHcy to escape would preclude peptide binding. Modeling experiments indicated isoAsp groups observed in some known protein crystal structures could bind to the HPIMT active site. PMID:11847284

  6. In vitro enzymatic modification of puerarin to puerarin glycosides by maltogenic amylase.

    PubMed

    Li, Dan; Park, Sung-Hoon; Shim, Jae-Hoon; Lee, Hee-Seob; Tang, Shuang-Yan; Park, Cheon-Seok; Park, Kwan-Hwa

    2004-12-01

    Puerarin (daidzein 8-C-glucoside), the most abundant isoflavone in Puerariae radix, is prescribed to treat coronary heart disease, cardiac infarction, problems in ocular blood flow, sudden deafness, and alcoholism. However, puerarin cannot be given by injection due to its low solubility in water. To increase its solubility, puerarin was transglycosylated using various enzymes. Bacillus stearothermophilus maltogenic amylase (BSMA) was the most effective transferase used compared with Thermotoga maritima maltosyl transferase (TMMT), Thermus scotoductus 4-alpha-glucanotransferase (TS4alphaGTase), and Bacillus sp. I-5 cyclodextrin glucanotransferase (BSCGTase). TMMT and TS4alphaGTase lacked acceptor specificity for puerarin, which lacks an O-glucoside linkage between D-glucose and 7-OH-daidzein. The yield exceeded 70% when reacting 1% puerarin (acceptor), 3.0% soluble starch (donor), and 5U/100 microL BSMA at 55 degrees C for 45 min. The two major transfer products of the BSMA reaction were purified using C(18) and GPC chromatography. Their structures were identified as alpha-d-glucosyl-(1-->6)-puerarin and alpha-D-maltosyl-(1-->6)-puerarin using ESI+ TOF MS-MS and 13C NMR spectroscopy. The solubility of the transfer products was 14 and 168 times higher than that of puerarin, respectively. PMID:15542087

  7. Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

    PubMed Central

    Ahmed, Wareed; Bhat, Anuradha Gopal; Leelaram, Majety Naga; Menon, Shruti; Nagaraja, Valakunja

    2013-01-01

    Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn2+ fingers from the mycobacterial topoI could be associated with Zn2+ export and homeostasis. PMID:23771144

  8. Fluorescence in insects

    NASA Astrophysics Data System (ADS)

    Welch, Victoria L.; Van Hooijdonk, Eloise; Intrater, Nurit; Vigneron, Jean-Pol

    2012-10-01

    Fluorescent molecules are much in demand for biosensors, solar cells, LEDs and VCSEL diodes, therefore, considerable efforts have been expended in designing and tailoring fluorescence to specific technical applications. However, naturally occurring fluorescence of diverse types has been reported from a wide array of living organisms: most famously, the jellyfish Aequorea victoria, but also in over 100 species of coral and in the cuticle of scorpions, where it is the rule, rather than the exception. Despite the plethora of known insect species, comparatively few quantitative studies have been made of insect fluorescence. Because of the potential applications of natural fluorescence, studies in this field have relevance to both physics and biology. Therefore, in this paper, we review the literature on insect fluorescence, before documenting its occurrence in the longhorn beetles Sternotomis virescens, Sternotomis variabilis var. semi rufescens, Anoplophora elegans and Stellognatha maculata, the tiger beetles Cicindela maritima and Cicindela germanica and the weevil Pachyrrhynchus gemmatus purpureus. Optical features of insect fluorescence, including emitted wavelength, molecular ageing and naturally occurring combinations of fluorescence with bioluminescence and colour-producing structures are discussed.

  9. A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes.

    PubMed

    Mazola, Yuliet; Guirola, Osmany; Palomares, Sucel; Chinea, Glay; Menéndez, Carmen; Hernández, Lázaro; Musacchio, Alexis

    2015-09-01

    Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima β-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed β-propeller catalytic domain (31 %) and the C-terminal β-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the β-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability. PMID:26267297

  10. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes.

    PubMed

    Jan, Pierre-Loup; Gracianne, Cécile; Fournet, Sylvain; Olivier, Eric; Arnaud, Jean-François; Porte, Catherine; Bardou-Valette, Sylvie; Denis, Marie-Christine; Petit, Eric J

    2016-03-01

    The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (N e ), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only 1 year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having N e close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex-ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance. PMID:26989440

  11. Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species.

    PubMed

    Roy, Shradha; Ueda, Minoru; Kadowaki, Koh-ichi; Tsutsumi, Nobuhiro

    2010-01-01

    The ribosomal protein S16 (RPS16), the product of the rps16, is generally encoded in the chloroplast genomes of flowering plants. However, it has been reported that chloroplast-encoded RPS16 in mono- and dicotyledonous plants has been substituted by the product of nuclear-encoded rps16, which was transferred from the mitochondria to the nucleus before the early divergence of angiosperms. Current databases show that the chloroplast-encoded rps16 has become a pseudogene in four species of the Brassicaceae (Aethionema grandiflorum, Arabis hirsuta, Draba nemorosa, and Lobularia maritima). Further analysis of Arabidopsis thaliana and its close relatives has shown that pseudogenization has also occurred via the loss of its splicing capacity (Arabidopsis thaliana and Olimarabidopsis pumila). In contrast, the spliced product of chloroplast-encoded rps16 is observed in close relatives of Arabidopsis thaliana (Arabidopsis arenosa, Arabidopsis lyrata, and Crucihimalaya lasiocarpa). In this study, we identified the different functional status of rps16 in several chloroplast genomes in the genus Arabidopsis and its close relatives. Our results strongly suggest that nuclear- and chloroplast-encoded rps16 genes coexisted for at least 126 million years. We raise the possibility of the widespread pseudogenization of rps16 in the angiosperm chloroplast genomes via the loss of its splicing capacity, even when the rps16 encoded in the chloroplast genome is transcriptionally active. PMID:21317544

  12. Molecular Diagnostics, Taxonomy, and Phylogeny of the Stem Nematode Ditylenchus dipsaci Species Complex Based on the Sequences of the Internal Transcribed Spacer-rDNA.

    PubMed

    Subbotin, Sergei A; Madani, Mehrdad; Krall, Eino; Sturhan, Dieter; Moens, Maurice

    2005-11-01

    ABSTRACT The stem nematode Ditylenchus dipsaci is of great economic importance worldwide as a parasite of agricultural crops and horticultural plants. The internal transcribed spacer (ITS) of rDNA from 23 populations of the D. dipsaci complex from various host plants were amplified and sequenced. Seven previously studied populations were also included in the study. The phylogenetic analysis of the full ITS and ITS2 sequence alignments using minimum evolution, maximum parsimony, and Bayesian inference under the complex model of DNA evolution revealed trees with two main clades: (i) D. dipsaci sensu stricto with diploid chromosome numbers and comprising most isolates from agricultural, ornamental, and several wild plants, and (ii) Ditylenchus spp. with polyploid chromosome numbers, reproductively isolated from diploid populations, and subdivided into six subclades ("giant race" from Vicia faba, Ditylenchus species parasitizing various Asteraceae, and a Ditylenchus sp. from Plantago maritima). Using the energy minimization approach and comparative sequence analysis, it has been found that the secondary structure of ditylenchid ITS2 is organized in three main domains. The importance of knowledge on the RNA structure for phylogenetic analysis is discussed. Conventional polymerase chain reaction (PCR) and real-time PCR with SYBR green dye I with a species specific primer have been developed for detection and quantification of D. dipsaci sensu stricto Validation tests revealed a rather high correlation between real numbers of fourth-stage juveniles of the stem nematodes in a sample and expected numbers detected by real-time PCR. Problems of accuracy of quantification are discussed. PMID:18943362

  13. Phylogenetic Analyses of Meloidogyne Small Subunit rDNA

    PubMed Central

    De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

    2002-01-01

    Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species. PMID:19265950

  14. Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

    PubMed Central

    Dekhtyar, Michael; Morin, Amelie; Sakanyan, Vehary

    2008-01-01

    Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I σ70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the α subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the σ70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance. PMID:18471287

  15. A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules

    PubMed Central

    Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried

    2015-01-01

    A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis. PMID:26355961

  16. Structure of the Entire Cytoplasmic Portion of a Sensor Histidine-kinase Protein

    SciTech Connect

    Marina,A.; Waldburger, C.; Hendrickson, W.

    2005-01-01

    The large majority of histidine kinases (HKs) are multifunctional enzymes having autokinase, phosphotransfer and phosphatase activities, and most of these are transmembrane sensor proteins. Sensor HKs possess conserved cytoplasmic phosphorylation and ATP-binding kinase domains. The different enzymatic activities require participation by one or both of these domains, implying the need for different conformational states. The catalytic domains are linked to the membrane through a coiled-coil segment that sometimes includes other domains. We describe here the first crystal structure of the complete cytoplasmic region of a sensor HK, one from the thermophile Thermotoga maritima in complex with ADP{beta}N at 1.9 Angstrom resolution. The structure reveals previously unidentified functions for several conserved residues and reveals the relative disposition of domains in a state seemingly poised for phosphotransfer. The structure thereby inspires hypotheses for the mechanisms of autophosphorylation, phosphotransfer and response-regulator dephosphorylation, and for signal transduction through the coiled-coil segment. Mutational tests support the functional relevance of interdomain contacts.

  17. Rising from the Sea: Correlations between Sulfated Polysaccharides and Salinity in Plants

    PubMed Central

    Aquino, Rafael S.; Grativol, Clicia; Mourão, Paulo A. S.

    2011-01-01

    High salinity soils inhibit crop production worldwide and represent a serious agricultural problem. To meet our ever-increasing demand for food, it is essential to understand and engineer salt-resistant crops. In this study, we evaluated the occurrence and function of sulfated polysaccharides in plants. Although ubiquitously present in marine algae, the presence of sulfated polysaccharides among the species tested was restricted to halophytes, suggesting a possible correlation with salt stress or resistance. To test this hypothesis, sulfated polysaccharides from plants artificially and naturally exposed to different salinities were analyzed. Our results revealed that the sulfated polysaccharide concentration, as well as the degree to which these compounds were sulfated in halophytic species, were positively correlated with salinity. We found that sulfated polysaccharides produced by Ruppia maritima Loisel disappeared when the plant was cultivated in the absence of salt. However, subjecting the glycophyte Oryza sativa Linnaeus to salt stress did not induce the biosynthesis of sulfated polysaccharides but increased the concentration of the carboxylated polysaccharides; this finding suggests that negatively charged cell wall polysaccharides might play a role in coping with salt stress. These data suggest that the presence of sulfated polysaccharides in plants is an adaptation to high salt environments, which may have been conserved during plant evolution from marine green algae. Our results address a practical biological concept; additionally, we suggest future strategies that may be beneficial when engineering salt-resistant crops. PMID:21552557

  18. Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine

    SciTech Connect

    Še; #269; kut; #279; , Jolita; McCloskey, Diane E.; Thomas, H. Jeanette; Secrist III, John A.; Pegg, Anthony E.; Ealick, Steven E.

    2011-11-17

    Aminopropyltransferases are essential enzymes that form polyamines in eukaryotic and most prokaryotic cells. Spermidine synthase (SpdS) is one of the most well-studied enzymes in this biosynthetic pathway. The enzyme uses decarboxylated S-adenosylmethionine and a short-chain polyamine (putrescine) to make a medium-chain polyamine (spermidine) and 5'-deoxy-5'-methylthioadenosine as a byproduct. Here, we report a new spermidine synthase inhibitor, decarboxylated S-adenosylhomocysteine (dcSAH). The inhibitor was synthesized, and dose-dependent inhibition of human, Thermatoga maritima, and Plasmodium falciparum spermidine synthases, as well as functionally homologous human spermine synthase, was determined. The human SpdS/dcSAH complex structure was determined by X-ray crystallography at 2.0 {angstrom} resolution and showed consistent active site positioning and coordination with previously known structures. Isothermal calorimetry binding assays confirmed inhibitor binding to human SpdS with K{sub d} of 1.1 {+-} 0.3 {mu}M in the absence of putrescine and 3.2 {+-} 0.1 {mu}M in the presence of putrescine. These results indicate a potential for further inhibitor development based on the dcSAH scaffold.

  19. Paleobiology of the Sand Beneath the Valders Diamicton at Valders, Wisconsin

    NASA Astrophysics Data System (ADS)

    Maher, Louis J.; Miller, Norton G.; Baker, Richard G.; Curry, B. Brandon; Mickelson, David M.

    1998-03-01

    Previously undescribed pollen, plant macrofossils, molluscs, and ostracodes were recovered from a 2.5-m-thick glaciolacustrine unit of silty sand and clay at Valders, Wisconsin. The interstadial sediment was deposited about 12,200 14C yr B.P. after retreat of the Green Bay lobe that deposited diamicton of the Horicon Formation, and before advance of the Lake Michigan lobe that deposited the red-brown diamicton of the Valders Member of the Kewaunee Formation. Fluctuations of abundance of Candona subtriangulata, Cytherissa lacustris,and three other species define four ostracode biozones in the lower 1.7 m, suggesting an open lake environment that oscillated in depth and proximity to glacial ice. Pollen is dominated by Piceaand Artemisia,but the low percentages of many other types of long-distance origin suggest that the terrestrial vegetation was open and far from the forest border. The upper part of the sediment, a massive sand deposited in either a shallow pond or a sluggish stream, contains a local concentration of plant macrofossils. The interpretation of a cold open environment is supported by the plant macrofossils of more than 20 species, dominated by those of open mineral soils ( Arenaria rubella, Cerastium alpinumtype, Silene acaulis, Sibbaldia procumbens, Dryas integrifolia, Vaccinium uliginosumvar. alpinum, Armeria maritima,etc.) that in North America occur largely in the tundra and open tundra-forest ecotone of northern Canada. Ice-wedge casts occur in the sand.

  20. Analysis of 13 asteroid lightcurves obtained at the Palmer Divide Observatory

    NASA Astrophysics Data System (ADS)

    Warner, Brian D.

    2006-06-01

    The lightcurves for the following asteroids were obtained and then analyzed to find the synodic period and amplitude. 321 Florentina: 2.8711±0.0003h, 0.37±0.02m; 787 Moskva: 6.056±0.001h, 0.61±0.02m; 839 Valborg: 10.366±0.005h, 0.14±0.02m; 912 Maritima: 48.43±0.05h, >0.12±0.02m; 1176 Lucidor: 4.0791±0.0006h, 0.06±0.02m; 1862 Apollo: 3.0680±0.0002h, 0.30-1.20±0.02m; 2266 Tchaikovsky: 4.883±0.003h, 0.04±0.01m; 2951 Perepadin: 4.7808±0.0001h, 0.60±0.02m; 5108 Lubeck: 8.769±0.003, 0.43±0.02m; (17864) 1998 KK38: 6.56±0.01h, 0.17±0.02m; (18582) 1997 XK9: 114±10h, 0.94±0.02m; (20231) 1997 YK: 48.2±0.1h, >0.22±0.02m. Asteroid 868 Lova was also observed but its long period is only constrained as >24h.

  1. A thermostable exo-?-fructosidase immobilised through rational design.

    PubMed

    Martnez, Duniesky; Cutio-Avila, Bessy; Prez, Enrique Rosendo; Menndez, Carmen; Hernndez, Lzaro; Del Monte-Martnez, Alberto

    2014-02-15

    Thermotoga maritima exo-?-fructosidase (BfrA) secreted by a recombinant Pichia pastoris strain was optimally immobilised on Glyoxyl-Sepharose CL 4B using the Rational Design of Immobilised Derivatives (RDID) strategy. Covalent attachment of the N-glycosylated BfrA onto the activated support at pH 10 allowed total recovery of the loaded enzyme and its activity. The immobilisation process caused no variation in the catalytic properties of the enzyme and allowed further enhancement of the thermal stability. Complete inversion of cane sugar (2.04 M) in a batch stirred tank reactor at 60 C was achieved with a productivity of 22.2 g of substrate hydrolysed/gram of biocatalyst/hour. Half-life of the immobilised enzyme of 5 days at 60 C was determined in a continuously operated fixed-bed column reactor. Our results promote the applicability of the BfrA-immobilised biocatalyst for the complete hydrolysis of concentrated sucrose solutions under industrial conditions, especially at a high reaction temperature. PMID:24128552

  2. Marinomonas spartinae sp. nov., a novel species with plant-beneficial properties.

    PubMed

    Lucena, Teresa; Mesa, Jennifer; Rodriguez-Llorente, Ignacio D; Pajuelo, Eloisa; Caviedes, Miguel Ángel; Ruvira, María A; Pujalte, María J

    2016-04-01

    Two strains of Gram-stain-negative, chemo-organotrophic, aerobic and halophilic gammaproteobacteria, isolated from within the stem and roots of Spartina maritima in salt marshes from the south Atlantic Spanish coast, were found to represent a novel species in the genus Marinomonas through phylogenetic analysis of their 16S rRNA genes and phenotypic characterization. 16S rRNA gene sequences of the two strains shared < 96.2 % similarity with other Marinomonas species, with Marimonas alcarazii being the most similar in sequence. They required sodium ions for growth, were able to thrive at low (4 °C) temperatures and at salinities of 12-15 %, were unable to hydrolyse any tested macromolecule except casein, and grew with different monosaccharides, disaccharides, sugar alcohols, organic acids and amino acids. The novel species differed from other Marinomonas species in the use of several sole carbon sources, its temperature and salinity ranges for growth, ion requirements and cellular fatty acid composition, which included C16 : 0, C16 : 1 and C18 : 1 as major components and C10 : 0 3-OH, C12 : 0 and C12 : 0 3-OH as minor components. The name Marinomonas spartinae sp. nov. is proposed, with SMJ19T ( = CECT 8886T = KCTC 42958T) as the type strain. PMID:26821806

  3. Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly

    PubMed Central

    Deller, Marc C.; Johnson, Hope A.; Miller, Mitchell D.; Spraggon, Glen; Elsliger, Marc-André; Wilson, Ian A.; Lesley, Scott A.

    2015-01-01

    The TM1088 locus of T. maritima codes for two proteins designated TM1088A and TM1088B, which combine to form the cytosolic portion of a putative Trk K+ transporter. We report the crystal structure of this assembly to a resolution of 3.45 Å. The high resolution crystal structures of the components of the assembly, TM1088A and TM1088B, were also determined independently to 1.50 Å and 1.55 Å, respectively. The TM1088 proteins are structurally homologous to each other and to other K+ transporter proteins, such as TrkA. These proteins form a cytosolic gating ring assembly that controls the flow of K+ ions across the membrane. TM1088 represents the first structure of a two-subunit Trk assembly. Despite the atypical genetics and chain organization of the TM1088 assembly, it shares significant structural homology and an overall quaternary organization with other single-subunit K+ gating ring assemblies. This structure provides the first structural insights into what may be an evolutionary ancestor of more modern single-subunit K+ gating ring assemblies. PMID:25826626

  4. Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis

    PubMed Central

    Liu, Xiuying; Yin, Yan; Wu, Jinjun; Liu, Zhenfeng

    2014-01-01

    Phospholipids are elemental building-block molecules for biological membranes. Biosynthesis of phosphatidylinositol, phosphatidylglycerol and phosphatidylserine requires a central liponucleotide intermediate named cytidine-diphosphate diacylglycerol (CDP-DAG). The CDP-DAG synthetase (Cds) is an integral membrane enzyme catalysing the formation of CDP-DAG, an essential step for phosphoinositide recycling during signal transduction. Here we report the structure of the Cds from Thermotoga maritima (TmCdsA) at 3.4 Å resolution. TmCdsA forms a homodimer and each monomer contains nine transmembrane helices arranged into a novel fold with three domains. An unusual funnel-shaped cavity penetrates half way into the membrane, allowing the enzyme to simultaneously accept hydrophilic substrate (cytidine 5′-triphosphate (CTP)/deoxy-CTP) from cytoplasm and hydrophobic substrate (phosphatidic acid) from membrane. Located at the bottom of the cavity, a Mg2+-K+ hetero-di-metal centre coordinated by an Asp-Asp dyad serves as the cofactor of TmCdsA. The results suggest a two-metal-ion catalytic mechanism for the Cds-mediated synthesis of CDP-DAG at the membrane–cytoplasm interface. PMID:24968740

  5. Identification of plant viruses using one-dimensional gel electrophoresis and peptide mass fingerprints.

    PubMed

    Luo, H; Wylie, S J; Jones, M G K

    2010-05-01

    A generic assay to detect and partially characterize unknown viruses from plants was developed. Proteins extracted from virus-infected and uninfected plants were separated in one dimension by SDS polyacrylamide gel electrophoresis. Differentially expressed protein bands were eluted after trypsin digestion and resulting peptide fragments separated according to their mass by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Resulting peptide mass fingerprints (PMF) were compared with those in protein databases. The assay was used to identify three known viruses: the potyviruses Zucchini yellow mosaic virus and Turnip mosaic virus, and an alfamovirus Alfalfa mosaic virus. It was also used to identify a virus that manifested symptoms in wild Cakile maritima plants, tentatively identified as Pelargonium zonate spot virus (PZSV) (genus Anulavirus) by its PMF, and then confirmed by nucleotide sequencing. The detection of PZSV constitutes a first record of this virus in Australia and in this host. It is proposed that this rapid and simple assay is a useful approach for analysis of plant samples known to harbor viruses that could not be identified using antisera or nucleic acid-based assays. PMID:20170682

  6. Genetic structure of populations of Alternaria brassicicola suggests the occurrence of sexual recombination.

    PubMed

    Bock, Clive H; Thrall, Peter H; Burdon, Jeremy J

    2005-02-01

    Substantial polymorphism was detected between isolates from five populations of Alternaria brassicicola attacking Cakile maritima along the New South Wales coast of Australia, with a maximum of two genotypes being shared between population pairs. Of ten pair-wise population comparisons, six had no pathogen genotypes in common; only one genotype occurred five times, and most (93 %) were found only once. Although an UPGMA based on Nei's measure of genetic distance separated the five populations, a cluster analysis using individual isolates failed to group them according to population, indicating significant gene flow. An analysis of molecular variance indicated ca 14% of the variation occurred between populations, representing moderate population differentiation over the spatial scale of the study. Tests of the relative contribution of clonality and sexual recombination indicated low, albeit significant levels of linkage disequilibrium in all populations. The level of linkage disequilibrium, and the high genotype diversity, provides support for the contention that a hitherto unidentified sexual stage might be a significant factor in the life-cycle of A. brassicicola. PMID:15839106

  7. Use of digital multispectral videography to assess seagrass distribution in San Quintin Bay, Baja California, Mexico

    USGS Publications Warehouse

    Ward, D.H.; Tibbitts, T.L.; Morton, Alexandra; Carrera-Gonzalez, Eduardo; Kempka, R.

    2004-01-01

    Apparent threats to the spatial distribution of seagrass in San Quinti??n Bay prompted us to make a detailed assessment of habitats in the bay. Six coastal habitats and three seagrass subclasses were delineated using airborne digital multispectral videography (DMSV), Eelgrass, Zostera marina, was the predominant seagrass and covered 40% (1949 ha) of the areal extent of the bay in 1999. Eelgrass grew over a wide range of tidal depths from about -3.0 in mean lower low water (MLLW) to about 1.0 m MLLW, but greatest spatial extent occurred in intertidal areas -0.6 m to 1.0 m MLLW. Exposed-continuous (i.e., high density) eelgrass was the most abundant habitat in the bay. Widgeongrass, Ruppia maritima, was the only other seagrass present and covered 3% (136 ha) of the areal extent of the entire bay. Widgeongrass grew in single species stands in the upper intertidal (??? 0.4 MLLW) and intermixed with eelgrass at lower tidal depths. Overall accuracy of the six habitat classes and three subclasses in the DMSV map was relatively high at 84%. Our detailed map of San Quintin Bay can be used in future change detection analyses to monitor the health of seagrasses in the bay.

  8. Integration of an [FeFe]-hydrogenase into the anaerobic metabolism of Escherichia coli

    PubMed Central

    Kelly, Ciarán L.; Pinske, Constanze; Murphy, Bonnie J.; Parkin, Alison; Armstrong, Fraser; Palmer, Tracy; Sargent, Frank

    2015-01-01

    Biohydrogen is a potentially useful product of microbial energy metabolism. One approach to engineering biohydrogen production in bacteria is the production of non-native hydrogenase activity in a host cell, for example Escherichia coli. In some microbes, hydrogenase enzymes are linked directly to central metabolism via diaphorase enzymes that utilise NAD+/NADH cofactors. In this work, it was hypothesised that heterologous production of an NAD+/NADH-linked hydrogenase could connect hydrogen production in an E. coli host directly to its central metabolism. To test this, a synthetic operon was designed and characterised encoding an apparently NADH-dependent, hydrogen-evolving [FeFe]-hydrogenase from Caldanaerobacter subterranus. The synthetic operon was stably integrated into the E. coli chromosome and shown to produce an active hydrogenase, however no H2 production was observed. Subsequently, it was found that heterologous co-production of a pyruvate::ferredoxin oxidoreductase and ferredoxin from Thermotoga maritima was found to be essential to drive H2 production by this system. This work provides genetic evidence that the Ca.subterranus [FeFe]-hydrogenase could be operating in vivo as an electron-confurcating enzyme. PMID:26839796

  9. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis

    PubMed Central

    2015-01-01

    Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site many ångstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets. To demonstrate the utility of our program, we present a case study describing the allostery of HisH-HisF, an amidotransferase from T. maritima thermotiga. WISP and its VMD-based graphical user interface (GUI) can be downloaded from http://nbcr.ucsd.edu/wisp. PMID:24803851

  10. Laūq: A Sustained-Release Dosage Form for Respiratory Disorders in Traditional Persian Medicine.

    PubMed

    Karegar-Borzi, Hossein; Salehi, Mehdi; Rahimi, Roja

    2016-01-01

    Laūq is a pharmaceutical dosage form that had been mainly used for the treatment of various respiratory disorders in traditional Persian medicine. It is important from 2 aspects: a dosage form with efficient and optimum delivery of drugs to the respiratory tract and biological effects of its ingredients. Natural medicine in laūq has been demonstrated to act in respiratory disorders by their antitussive, antiallergic, anti-inflammatory, antioxidant, spasmolytic, and antibacterial activities. Some of these natural remedies act by most of the mentioned mechanisms such as Cydonia oblonga, Glycyrrhiza glabra, Crocus sativus, Hyssopus officinalis, Foeniculum vulgare, and honey. However, the evidence is limited including Cassia fistula, Papaver somniferum, and Drimia maritima. According to positive pharmacokinetic and pharmacodynamic aspects of laūqs, they may be considered as efficient dosage forms for delivery of drugs to the respiratory tract. For better compatibility of patients, it could be substituted laūqs with newer drug delivery systems like lozenges. PMID:26008751

  11. The structure of a bacterial DUF199 / WhiA protein: domestication of an invasive endonuclease

    PubMed Central

    Kaiser, Brett K.; Clifton, Matthew C.; Shen, Betty W.; Stoddard, Barry L.

    2009-01-01

    Proteins of the DUF199 family, present in all gram-positive bacteria and best characterized by the WhiA sporulation control factor in Streptomyces coelicolor, are thought to act as genetic regulators. The crystal structure of the DUF199/WhiA protein from Thermatoga maritima demonstrates that these proteins possess a bipartite structure, in which a degenerate N-terminal LAGLIDADG homing endonuclease (LHE) scaffold is tethered to a C-terminal helix-turn-helix (HTH) domain. The LHE domain has lost those residues critical for metal binding and catalysis, and also displays an extensively altered DNA-binding surface as compared to homing endonucleases. The HTH domain most closely resembles related regions of several bacterial sigma70 factors that bind the −35 regions of bacterial promoters. The structure illustrates how an invasive element might be transformed during evolution into a larger assemblage of protein folds that can participate in the regulation of a complex biological pathway. PMID:19836336

  12. Analysis of genetic structure and dispersal patterns in a population of sea beet.

    PubMed Central

    Tufto, J; Raybould, A F; Hindar, K; Engen, S

    1998-01-01

    A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio. PMID:9691051

  13. Effects of two plant extracts on larval leafminer Liriomyza trifolii (Diptera: Agromyzidae) in tomatoes.

    PubMed

    Civelek, H S; Weintraub, P G

    2004-10-01

    Aqueous extracts from two plants, Urginea maritima L. (Liliaceae) and Euphorbia myrsinites L. (Euphorbiaceae), were tested for their insecticidal activity against the leafminer Liriomyza trifolii (Burgess) on infested tomato, Lycopersicon esculentum Mill., plants in the laboratory and field. Two grams of plant material was extracted with 100 ml of water and then diluted 1:100, 1:50, and 1:25 with distilled water. Diluted plant extract was either applied to the infested tomato leaves or by soil drench and was compared with foliar application of cyromazine. All dilutions of both plant extracts caused significant control of the leafminer larvae and maintained populations below those of the nontreated control plants in all trials. Only at the most concentrated dilutions (1:25) were the plant extracts statistically similar to the cyromazine treatment. Furthermore, greenhouse yields from all of the foliar treatments were statistically similar to the cyromazine treatment and significantly better than the nontreated control. Four species of leafminer parasitoids were found in the greenhouse; however, the percentage of parasitism was significantly less in all treated replicates than in the nontreated control replicates. Aqueous extracts from these two plant extracts exhibited both translaminar and systemic activity and are potential candidates as new organic insecticides. PMID:15568346

  14. Biosynthesis of D-xylulose 5-phosphate from D-xylose and polyphosphate through a minimized two-enzyme cascade.

    PubMed

    Kim, Jae-Eung; Zhang, Y-H Percival

    2016-02-01

    Sugar phosphates cannot be produced easily by microbial fermentation because negatively-charged compounds cannot be secreted across intact cell membrane. D-xylulose 5-phosphate (Xu5P), a very expensive sugar phosphate, was synthesized from D-xylose and polyphosphate catalyzed by enzyme cascades in one pot. The synthetic enzymatic pathway comprised of xylose isomerase and xylulokinase was designed to produce Xu5P, along with a third enzyme, polyphosphate kinase, responsible for in site ATP regeneration. Due to the promiscuous activity of the ATP-based xylulokinase from a hyperthermophilic bacterium Thermotoga maritima on polyphosphate, the number of enzymes in the pathway was minimized to two without polyphosphate kinase. The reactions catalyzed by the two-enzyme and three-enzyme pathways were compared for Xu5P production, and the reaction conditions were optimized by examining effects of reaction temperature, enzyme ratio and substrate concentration. The optimized two-enzyme system produced 32 mM Xu5P from 50 mM xylose and polyphosphate after 36 h at 45°C. Biosynthesis of less costly Xu5P from D-xylose and polyphosphate could be highly feasible via this minimized two-enzyme pathway. Biotechnol. Bioeng. 2016;113: 275-282. © 2015 Wiley Periodicals, Inc. PMID:26241217

  15. Long day plants and the response to global warming: rapid evolutionary change in day length sensitivity is possible in wild beet.

    PubMed

    Van Dijk, H; Hautekèete, N

    2007-01-01

    Day length is a key factor in flowering induction in many plant species in a seasonal environment with flowering induction usually happening at shorter day lengths in lower latitudes. Now, the climate changes systematically at a considerable speed due to global warming. As a consequence, earlier flowering will be selected for in long day plants by favouring a lower threshold for day length sensitivity, on the condition of available genetic variability. Here, we show that there is considerable genetic variation for day length sensitivity in our study species, the seabeet Beta vulgaris subsp. maritima. In the northernmost natural populations without vernalization requirement, in southwest France, the necessary day length for flowering induction could be reduced by artificial selection in <10 generations from >13 h to <11 h, the latter value corresponding to populations in the Beta-species complex from Northern Africa and the eastern part of the Mediterranean tested under the same conditions. A quantitative genetic analysis provided evidence of a gradual change without detectable major genes. Additional experiments were carried out to separate the response to photoperiod from age and energy effects. A certain effect of energy availability has been found, whereas age effects could be excluded. These results indicate a considerable potential for evolutionary change in adjusting flowering time in a changing climate. PMID:17210028

  16. Food habits of diving ducks in the Carolinas

    USGS Publications Warehouse

    Perry, M.C.; Uhler, F.M.

    1982-01-01

    Food habits analyses were conducted on 264 diving ducks (7 species) from North and South Carolina during the 1970'S. The Baltic clam (Macoma balthica) was the predominant food among canvasbacks (Aythya valisineria) from the Pamlico River area, whereas sago pondweed (Potamogeton pectinatus) predominated in birds from impoundments in North and South Carolina. Shoalgrass (Halodule beaudettei) formed 100% of the gullet food and 99% of the gizzard food in redheads (Aythya americana) from Pamlico Sound. Lesser scaup (Aythya affinis) in North Carolina had fed predominantly on mollusks (Mulinia lateralis and Rangia cuneata), whereas widgeon grass (Ruppia maritima) was the predominant food in birds from South Carolina. In North Carolina, ring-necked ducks (Aythya collaris) fed mainly on vegetation, and greater scaup (Aythya marila), bufflehead (Bucephala albeola), and ruddy ducks (Oxyura jamaicensis) fed mainly on Mulinia lateralis. Food habits data from this study when compared with historical food habits of these species indicate that most diving duck species were feeding more on invertebrates and less on submerged aquatic vegetation than in the past. North and South Carolina have a diverse food supply and appear to offer waterfowl adequate wintering habitat based on these food habits studies. Present trends in wintering habitat, however, could adversely affect diving duck populations in the future.

  17. Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor.

    PubMed

    Ferris, Hedda U; Zeth, Kornelius; Hulko, Michael; Dunin-Horkawicz, Stanislaw; Lupas, Andrei N

    2014-06-01

    Bacterial chemotaxis receptors are elongated homodimeric coiled-coil bundles, which transduce signals generated in an N-terminal sensor domain across 15-20nm to a conserved C-terminal signaling subdomain. This signal transduction regulates the activity of associated kinases, altering the behavior of the flagellar motor and hence cell motility. Signaling is in turn modulated by selective methylation and demethylation of specific glutamate and glutamine residues in an adaptation subdomain. We have determined the structure of a chimeric protein, consisting of the HAMP domain from Archaeoglobus fulgidus Af1503 and the methyl-accepting domain of Escherichia coli Tsr. It shows a 21nm coiled coil that alternates between two coiled-coil packing modes: canonical knobs-into-holes and complementary x-da, a variant form related to the canonical one by axial rotation of the helices. Comparison of the obtained structure to the Thermotoga maritima chemoreceptor TM1143 reveals that they adopt different axial rotation states in their adaptation subdomains. This conformational change is presumably induced by the upstream HAMP domain and may modulate the affinity of the chemoreceptor to the methylation-demethylation system. The presented findings extend the cogwheel model for signal transmission to chemoreceptors. PMID:24680785

  18. Recognition of the Helical Structure of β-1,4-Galactan by a New Family of Carbohydrate-binding Modules*

    PubMed Central

    Cid, Melissa; Pedersen, Henriette Lodberg; Kaneko, Satoshi; Coutinho, Pedro M.; Henrissat, Bernard; Willats, William G. T.; Boraston, Alisdair B.

    2010-01-01

    The microbial enzymes that depolymerize plant cell wall polysaccharides, ultimately promoting energy liberation and carbon recycling, are typically complex in their modularity and often contain carbohydrate-binding modules (CBMs). Here, through analysis of an unknown module from a Thermotoga maritima endo-β-1,4-galactanase, we identify a new family of CBMs that are most frequently found appended to proteins with β-1,4-galactanase activity. Polysaccharide microarray screening, immunofluorescence microscopy, and biochemical analysis of the isolated module demonstrate the specificity of the module, here called TmCBM61, for β-1,4-linked galactose-containing ligands, making it the founding member of family CBM61. The ultra-high resolution x-ray crystal structures of TmCBM61 (0.95 and 1.4 Å resolution) in complex with β-1,4-galactotriose reveal the molecular basis of the specificity of the CBM for β-1,4-galactan. Analysis of these structures provides insight into the recognition of an unexpected helical galactan conformation through a mode of binding that resembles the recognition of starch. PMID:20826814

  19. The Structural Basis of Sirtuin Substrate Affinity

    SciTech Connect

    Cosgrove,M.; Bever, K.; Avalos, J.; Muhammad, S.; Zhang, X.; Wolberger, C.

    2006-01-01

    Sirtuins comprise a family of enzymes that catalyze the deacetylation of acetyllysine side chains in a reaction that consumes NAD+. Although several crystal structures of sirtuins bound to non-native acetyl peptides have been determined, relatively little about how sirtuins discriminate among different substrates is understood. We have carried out a systematic structural and thermodynamic analysis of several peptides bound to a single sirtuin, the Sir2 homologue from Thermatoga maritima (Sir2Tm). We report structures of five different forms of Sir2Tm: two forms bound to the p53 C-terminal tail in the acetylated and unacetylated states, two forms bound to putative acetyl peptide substrates derived from the structured domains of histones H3 and H4, and one form bound to polypropylene glycol (PPG), which resembles the apoenzyme. The structures reveal previously unobserved complementary side chain interactions between Sir2Tm and the first residue N-terminal to the acetyllysine (position -1) and the second residue C-terminal to the acetyllysine (position +2). Isothermal titration calorimetry was used to compare binding constants between wild-type and mutant forms of Sir2Tm and between additional acetyl peptide substrates with substitutions at positions -1 and +2. The results are consistent with a model in which peptide positions -1 and +2 play a significant role in sirtuin substrate binding. This model provides a framework for identifying sirtuin substrates.

  20. Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages.

    PubMed Central

    Arnaud, J-F; Viard, F; Delescluse, M; Cuguen, J

    2003-01-01

    Gene flow and introgression from cultivated to wild plant populations have important evolutionary and ecological consequences and require detailed investigations for risk assessments of transgene escape into natural ecosystems. Sugar beets (Beta vulgaris ssp. vulgaris) are of particular concern because: (i) they are cross-compatible with their wild relatives (the sea beet, B. vulgaris ssp. maritima); (ii) crop-to-wild gene flow is likely to occur via weedy lineages resulting from hybridization events and locally infesting fields. Using a chloroplastic marker and a set of nuclear microsatellite loci, the occurrence of crop-to-wild gene flow was investigated in the French sugar beet production area within a 'contact-zone' in between coastal wild populations and sugar beet fields. The results did not reveal large pollen dispersal from weed to wild beets. However, several pieces of evidence clearly show an escape of weedy lineages from fields via seed flow. Since most studies involving the assessment of transgene escape from crops to wild outcrossing relatives generally focused only on pollen dispersal, this last result was unexpected: it points out the key role of a long-lived seed bank and highlights support for transgene escape via man-mediated long-distance dispersal events. PMID:12908976

  1. Effects of Posidonia Oceanica Beach-Cast on Germination, Growth and Nutrient Uptake of Coastal Dune Plants

    PubMed Central

    Del Vecchio, Silvia; Marbà, Núria; Acosta, Alicia; Vignolo, Clara; Traveset, Anna

    2013-01-01

    Seagrass meadows play an important role in marine ecosystems. A part of seagrass production is also exported to adjacent coastal terrestrial systems, possibly influencing their functioning. In this work we experimentally analyzed the effect of Posidonia oceanica beach-cast on plant germination, growth, and nutrient uptake of two plant species (Cakile maritima and Elymus farctus) that grow on upper beaches and fore dunes along the Mediterranean coasts. We compared plants growing in simple sand (control) with those growing in a substrate enriched with P. oceanica wrack (treatment) in laboratory. P. oceanica wrack doubled the N substrate pool and kept the substrate humid. Plants growing in the treated substrate grew faster, were twice as large as those growing in the control substrate, while tissues were enriched in N and P (Cakile by the 1.3 fold in N and 2.5 fold in P; Elymus by 1.5 fold in N and 2 fold in P). Our results suggest a positive effect of seagrass litter for the enhancing of dune species, highlighting its role for the conservation of coastal dune ecosystems. PMID:23894678

  2. Crystal structure of the RNA component of bacterial ribonuclease P

    SciTech Connect

    Torres-Larios, Alfredo; Swinger, Kerren K.; Krasilnikov, Andrey S.; Pan, Tao; Mondragon, Alfonso

    2010-03-08

    Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 {angstrom} resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

  3. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.

    SciTech Connect

    Korolev, S.; Ikeguchi, Y.; Skarina, T.; Beasley, S.; Arrowsmith, C.; Edwards, A.; Joachimiak, A.; Pegg, A. E.; Savchenko, A.; Pennsylvania State Univ. Coll. of Medicine; Milton S. Hershey Medical Center; Banting and Best Department of Medical Research; Univ. of Health Network

    2002-01-01

    Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 Angstroms resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an aminopropyltransferase, reveals deep cavities for binding substrate and cofactor, and a loop that envelops the active site. The AdoDATO binding site is lined with residues conserved in PAPT enzymes from bacteria to humans, suggesting a universal catalytic mechanism. Other conserved residues act sterically to provide a structural basis for polyamine specificity. The enzyme is tetrameric; each monomer consists of a C-terminal domain with a Rossmann-like fold and an N-terminal {beta}-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.

  4. The structure of putative N-acetyl glutamate kinase from Thermus thermophilus reveals an intermediate active site conformation of the enzyme.

    PubMed

    Sundaresan, Ramya; Ragunathan, Preethi; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kumarevel, Thirumananseri; Ponnuraj, Karthe

    2012-04-13

    The de novo biosynthesis of arginine in microorganisms and plants is accomplished via several enzymatic steps. The enzyme N-acetyl glutamate kinase (NAGK) catalyzes the phosphorylation of the γ-COO(-) group of N-acetyl-L-glutamate (NAG) by adenosine triphosphate (ATP) which is the second rate limiting step in arginine biosynthesis pathway. Here we report the crystal structure of putative N-acetyl glutamate kinase (NAGK) from Thermus thermophilus HB8 (TtNAGK) determined at 1.92Å resolution. The structural analysis of TtNAGK suggests that the dimeric quaternary state of the enzyme and arginine insensitive nature are similar to mesophilic Escherichia coli NAGK. These features are significantly different from its thermophilic homolog Thermatoga maritima NAGK which is hexameric and arginine-sensitive. TtNAGK is devoid of its substrates but contains two sulfates at the active site. Very interestingly the active site of the enzyme adopts a conformation which is not completely open or closed and likely represents an intermediate stage in the catalytic cycle unlike its structural homologs, which all exist either in the open or closed conformation. Engineering arginine biosynthesis pathway enzymes for the production of l-arginine is an important industrial application. The structural comparison of TtNAGK with EcNAGK revealed the structural basis of thermostability of TtNAGK and this information could be very useful to generate mutants of NAGK with increased overall stability. PMID:22452987

  5. A new approach to assess and predict the functional roles of proteins across all known structures.

    PubMed

    Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping; McLaughlin, William A

    2011-03-01

    The three dimensional atomic structures of proteins provide information regarding their function; and codified relationships between structure and function enable the assessment of function from structure. In the current study, a new data mining tool was implemented that checks current gene ontology (GO) annotations and predicts new ones across all the protein structures available in the Protein Data Bank (PDB). The tool overcomes some of the challenges of utilizing large amounts of protein annotation and measurement information to form correspondences between protein structure and function. Protein attributes were extracted from the Structural Biology Knowledgebase and open source biological databases. Based on the presence or absence of a given set of attributes, a given protein's functional annotations were inferred. The results show that attributes derived from the three dimensional structures of proteins enhanced predictions over that using attributes only derived from primary amino acid sequence. Some predictions reflected known but not completely documented GO annotations. For example, predictions for the GO term for copper ion binding reflected used information a copper ion was known to interact with the protein based on information in a ligand interaction database. Other predictions were novel and require further experimental validation. These include predictions for proteins labeled as unknown function in the PDB. Two examples are a role in the regulation of transcription for the protein AF1396 from Archaeoglobus fulgidus and a role in RNA metabolism for the protein psuG from Thermotoga maritima. PMID:21445639

  6. Castanea sativa Mill. leaves as new sources of natural antioxidant: an electronic spin resonance study.

    PubMed

    Calliste, Claude-Alain; Trouillas, Patrick; Allais, Daovy-Paulette; Duroux, Jean-Luc

    2005-01-26

    The antioxidant potential of Castanea sativa Mill. leaf (sweet chestnut) was explored as a new source of active extracts. The capacity of the different fractions issued from aqueous, methanol, and ethyl acetate extracts to inhibit the stable free radical 2,2-diphenyl-1-pycryl-hydrazyl, superoxide anion, and hydroxyl radical was measured by electronic spin resonance. Their scavenging potential was analyzed versus their amount of phenolic compounds. Among the active fractions, the most effective one was A6, an ethyl acetate fraction, which contained a high level of total phenolic compounds (29.1 g/100 g). Thus, a different extraction procedure was performed to concentrate the active compounds of A6 in the new C. sativa leaf extract (CSLE). Compared to reference antioxidants (quercetin and vitamin E) and standard extracts (Pycnogenol, from French Pinus maritima bark, and grape marc extract), it was observed that A6 and CSLE have high antioxidant potentials, equivalent to at least those of reference compounds. PMID:15656662

  7. Cloning of the Gene Encoding a Novel Thermostable α-Galactosidase from Thermus brockianus ITI360

    PubMed Central

    Fridjonsson, Olafur; Watzlawick, Hildegard; Gehweiler, Axel; Rohrhirsch, Thilo; Mattes, Ralf

    1999-01-01

    An α-galactosidase gene from Thermus brockianus ITI360 was cloned, sequenced, and expressed in Escherichia coli, and the recombinant protein was purified. The gene, designated agaT, codes for a 476-residue polypeptide with a calculated molecular mass of 53,810 Da. The native structure of the recombinant enzyme (AgaT) was estimated to be a tetramer. AgaT displays amino acid sequence similarity to the α-galactosidases of Thermotoga neapolitana and Thermotoga maritima and a low-level sequence similarity to α-galactosidases of family 36 in the classification of glycosyl hydrolases. The enzyme is thermostable, with a temperature optimum of activity at 93°C with para-nitrophenyl-α-galactopyranoside as a substrate. Half-lives of inactivation at 92 and 80°C are 100 min and 17 h, respectively. The pH optimum is between 5.5 and 6.5. The enzyme displayed high affinity for oligomeric substrates. The Kms for melibiose and raffinose at 80°C were determined as 4.1 and 11.0 mM, respectively. The α-galactosidase gene in T. brockianus ITI360 was inactivated by integrational mutagenesis. Consequently, no α-galactosidase activity was detectable in crude extracts of the mutant strain, and it was unable to use melibiose or raffinose as a single carbohydrate source. PMID:10473401

  8. X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.

    PubMed

    Nicolet, Yvain; Rohac, Roman; Martin, Lydie; Fontecilla-Camps, Juan C

    2013-04-30

    Fe4S4 clusters are very common versatile prosthetic groups in proteins. Their redox property of being sensitive to O2-induced oxidative damage is, for instance, used by the cell to sense oxygen levels and switch between aerobic and anaerobic metabolisms, as exemplified by the fumarate, nitrate reduction regulator (FNR). Using the hydrogenase maturase HydE from Thermotoga maritima as a template, we obtained several unusual forms of FeS clusters, some of which are associated with important structural changes. These structures represent intermediate states relevant to both FeS cluster assembly and degradation. We observe one Fe2S2 cluster bound by two cysteine persulfide residues. This observation lends structural support to a very recent Raman study, which reported that Fe4S4-to-Fe2S2 cluster conversion upon oxygen exposure in FNR resulted in concomitant production of cysteine persulfide as cluster ligands. Similar persulfide ligands have been observed in vitro for several other Fe4S4 cluster-containing proteins. We have also monitored FeS cluster conversion directly in our protein crystals. Our structures indicate that the Fe4S4-to-Fe2S2 change requires large structural modifications, which are most likely responsible for the dimer-monomer transition in FNR. PMID:23596207

  9. Supporting adaptation decisions to address climate related impacts and hazards in the Caribbean (the CARIWIG project)

    NASA Astrophysics Data System (ADS)

    Burton, Aidan

    2015-04-01

    Managers and policy makers from regional and national institutions in the Caribbean require knowledge of the likely impacts and hazards arising from the present and future climate that are specific to their responsibility and geographical range, and relevant to their planning time-horizons. Knowledge, experience and the political support to develop appropriate adaptation strategies are also required. However, the climate information available for the region is of limited use as: observational records are intermittent and typically of short duration; climate model projections of the weather suffer from scale and bias issues; and statistical downscaling to provide locally relevant unbiased climate change information remains sporadic. Tropical cyclone activity is a considerable sporadic hazard in the region and yet related weather information is limited to historic events. Further, there is a lack of guidance for managers and policy makers operating with very limited resources to utilize such information within their remit. The CARIWIG project (June 2012 - May 2015) will be presented, reflecting on stakeholder impact, best practice and lessons learned. This project seeks to address the climate service needs of the Caribbean region through a combination of capacity building and improved provision of climate information services. An initial workshop with regional-scale stakeholders initiated a dialogue to develop a realistic shared vision of the needed information services which could be provided by the project. Capacity building is then achieved on a number of levels: knowledge and expertise sharing between project partners; raising understanding and knowledge of resources that support national and regional institutions' adaptation decisions; developing case studies in key sectors to test and demonstrate the information services; training for stakeholder technical staff in the use of the provided services; the development of a support network within and out-of-region between stakeholders and research institutes concerned with environmental hazards and impacts. The project seeks to provide locally relevant present and future-scenario climatic data through an intuitive web service. Present climate summary data, based on meteorological station observations, is provided for locations across the region. Relatively high resolution (25km) PRECIS regional climate projections (1961-2100) are available for the region conditioned with the HadCM3Q0 and ECHAM5 GCM using the A1B SRES emissions scenario. Bias corrected control and future climate scenarios (for 30-year time slices centred on the 2020s, 2050s and 2080s) comprising timeseries of daily meteorological variables are then simulated using the EARWIG and UKCP09 statistical downscaling approach adapted for the Caribbean. A novel modelling tool provides a basis for testing vulnerability to tailored scenarios of tropical cyclone hazard. The CARIWIG project seeks to provide a lasting impact through an emphasis on building regional stakeholder capacity and through technological design that allows the flexibility to include additional meteorological records and new climate projections as they become available.

  10. Masterplan to safeguard Venice and to restore the lagoon and conterminous areas

    NASA Astrophysics Data System (ADS)

    Bini, Claudio; Gallo, Alba; Nadimi-Goki, Mandana; Wahsha, Mohammad

    2015-04-01

    Venice and its lagoon constitute a complex system, well known all over the world for the peculiarity of the town and for the fragility of the lagoon ecosystem with its delicate equilibrium. The whole system has been, and is currently, affected by human activities (industry, agriculture, settlements, tourism) that impact severely the ecosystem. Discharge from the agricultural drainage basin affects particularly the area North of the city of Venice; the central and southern areas, instead, receive important pollutant inputs from the industrial zone of Porto Marghera since the early'50s. Additional sources of pollution are domestic sewage and waste disposal from the urban area, that is visited by more than 10M people every year. As a consequence of the increasing land contamination, significant amounts of contaminants (both organic and inorganic) are accumulated in soils of the borderline, in water and in lagoon sediments, which constitute a potential source of secondary pollution. Results of surveys carried out in recent years in the whole area show that contaminants concentration increased from the beginning of the industrial activities until the '90s, when Porto Marghera declined. Most of contaminants have concentrations above the background levels. The highest metal levels were found in an area between Porto Marghera and the city of Venice, where both industrial and urban sewage are discharged, provoking environmental and human health hazard. In order to safeguard the city of Venice, and to restore its lagoon and conterminous areas, a Master Plan of intervention has been developed since the early 2000s. The land currently interested by environmental analysis and/or restoration covers approximately 1350ha; 78% of these (1100ha) proved variously contaminated, with 85% of sites overcoming the National Reference Values. Contamination, besides being diffused, is quite complex, involving the co-existence of several contaminant families (PAH, PCB, dioxin, heavy metals). PAH and metals, in particular, present wide diffusion, both horizontal and vertical (until 5 m below the sea level), with As, Zn, Cd and Hg being the elements more represented in all the soil strata considered. The lagoon sediments inside industrial channels is higher than the other parts of the lagoon; major contaminants are metals (As, Cd, Hg, Pb) and organic micro-pollutants (PCB, PAH); ammonia and phosphate too are present with conspicuous concentrations, contributing to lagoon eutrophication. Groundwater contamination is diffused and complex, with As prevailing over Pb and Cr(VI). The primary objective of the Master Plan was to reduce/eliminate the risk associated to the contamination sources of past activities, and the consequent environmental and human health hazard. Restoration is still in progress, and concerns different intervention strategies: • Channel overbank containment to prevent contaminant migration to water; • Excavation, physical removal and re-distribution of channel sediments (A and B classes); • Landfilling of heavily contaminated sediments (C class); • Soil containment to impede contact with people and the environment; • Restoration of contaminated agricultural land with phytoremediation techniques. Concerning in particular the last item, restoration has been carried out with native or exotic vegetation (e.g. Fragmites australis, Juncus lacustris, Pterix vittata, Spartina maritima), or cultivated plants (e.g. Heliantus annuus, Zea mays, Brassica napus), with contrasting results. The exotic fern (Pterix vittata) proved highly effective to accumulate As, consistently with data from literature; Spartina maritima proved more effective than Fragmites australis to uptake metals, while cultivated plants could not survive to high heavy metal concentrations. At some sites, soil has been stored, selected and finally (the most contaminated part) delivered to landfill, while groundwater was remediated by bioremediation techniques.

  11. Structural Insights Into Amino Acid Binding and Gene Control by a Lysine Riboswitch

    SciTech Connect

    Serganov, A.; Huang, L; Patel, D

    2008-01-01

    In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches1, 2, 3, 4. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 A) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues5, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

  12. Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model.

    PubMed

    Su, Ji-Guo; Han, Xiao-Ming; Zhao, Shu-Xin; Hou, Yan-Xue; Li, Xing-Yuan; Qi, Li-Sheng; Wang, Ji-Hua

    2016-04-01

    The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its thermostability. In the present work, the favorable charged residues in Tm-Csp were grafted into Bc-Csp by a double point mutation of S48E/N62H, and the impacts of the mutation on the thermostability and unfolding/folding behavior of Bc-Csp were then investigated by using a modified Gō model, in which the electrostatic interactions between charged residues were considered in the model. Our simulation results show that this Tm-Csp-like charged residue mutation can effectively improve the thermostability of Bc-Csp without changing its two-state folding mechanism. Besides that, we also studied the unfolding kinetics and unfolding/folding pathway of the wild-type Bc-Csp and its mutant. It is found that this charged residue mutation obviously enhanced the stability of the C-terminal region of Bc-Csp, which decreases the unfolding rate and changes the unfolding/folding pathway of the protein. Our studies indicate that the thermostability, unfolding kinetics and unfolding/folding pathway of Bc-Csp can be artificially changed by introducing Tm-Csp-like favorable electrostatic interactions into Bc-Csp. Graphical abstract Tertiary structure of wild-type cold shock protein from the thermophile Bacillus caldolyticus. PMID:27021210

  13. Ethnopharmacological survey of wild medicinal plants in Showbak, Jordan.

    PubMed

    Al-Qura'n, S

    2009-05-01

    Two main research questions are framing this investigation: (1) the main taxa of the medicinal importance value altered the Showbak forest stand and species composition? (2) The most safe species and what are the toxic ones (unsafe). These two research questions are the vital ones to draw a clear image about the wild medicinal plants of this investigated area of Showbak region in Jordan. 79 wild medicinal plant species were investigated in this study which are used in traditional medication for the treatment of various diseases. Most of the locals interviewed dealt with well-known safe medicinal plants such as Aaronsohnia factorovskyi Warb. et Eig., Achillea santolina L., Adiantum capillus-veneris L., Artemisia herba-alba L., Ceratonia siliqua L., Clematis recta L., Herniaria hirsuta L., Malva neglecta Wallr., Rosmarinus officinalis L., Ruta chalepensis L., Salvia triloba L., Sarcopoterium spinosa (L.) Spach., Thymbra capitata (L.) Hof, and Urginea maritima Barker. Many of the wild medicinal plants investigated were toxic and needed to be practiced by practitioners and herbalists rather than the local healers. These plants include Calotropis procera Willd R.Br., Citrullus colocynthis (L.) Sch., Datura stramonium L., Digitalis purpurea L., Ecballium elaterium (L.) A.Rich., Euphorbia helioscopia L., Euphorbia tinctoria Boiss., Glaucium corniculatum (L.) Curt., Hyoscyamus aureus L., Mandragora officinarum L., Nerium oleander L., Ricinus communis L., Solanum nigrum L., Withania somnifera (L.) Dunel. The conservation of medicinal plants and natural resources is becoming increasingly important, so this research is trying to collect information from local population concerning the use of medicinal plants in Showbak; identify the most important specie; determine the relative importance value of the species and calculate the informant consensus factor (ICF) for the medicinal plants. Obtaining results is relied on the interviewee's personal information and the medicinal use of specific plants. PMID:19429338

  14. Taxonomic revision of the spider genera Agyneta and Tennesseellum (Araneae, Linyphiidae) of North America north of Mexico with a study of the embolic division within Micronetinae sensu Saaristo & Tanasevitch 1996.

    PubMed

    Duprr, Nadine

    2013-01-01

    The genera Agyneta Hull 1911 and Tennesseellum Petrunkevitch 1925 are revised for North America north of Mexico. The synonymy of Meioneta Hull 1920 with Agyneta Hull 1911 proposed by Saaristo 1973 is corroborated. The North American fauna north of Mexico of Agyneta now includes a total of 69 species, of which 31 are new species: A. watertoni n. sp., A. perspicua n. sp., A. aquila n. sp., A. yukona n. sp., A. darrelli n. sp., A. bucklei n. sp., A. erinacea n. sp., A. crawfordi n. sp., A. vinki n. sp., A. panthera n. sp., A. miniata n. sp., A. danielbelangeri n. sp., A. pistrix n. sp., A. flax n. sp., A. barfoot n. sp., A. sandia n. sp., A. spicula n. sp., A. grandcanyon n. sp., A. chiricahua n. sp., A. crista n. sp., A. tuberculata n. sp., A. catalina n. sp., A. ledfordi n. sp., A. platnicki n. sp., A. bronx n. sp., A. paquini n. sp., A. girardi n. sp., A. flibuscrocus n. sp., A. delphina n. sp., A. okefenokee n. sp. and A. issaqueena n. sp. The genus Tennesseellum includes two spe-cies, with one new species, T. gollum n. sp. Ten new synonyms are recognized: Meioneta grayi Barnes 1953 = Anibontes mimus Chamberlin 1924; Meioneta dactylata Chamberlin & Ivie 1944, Meioneta officiosa (Barrows 1940) = Meioneta micaria (Emerton 1882); Meioneta imitata Chamberlin & Ivie 1944 = Meioneta leucophora Chamberlin & Ivie 1944; Meioneta ferosa (Chamberlin & Ivie 1943) = Meioneta fillmorana (Chamberlin 1919); Meioneta fuscipes Chamberlin & Ivie 1944 = Meioneta floridana (Banks 1896); Meioneta alaskensis Holm 1960 = Meioneta maritima (Emerton 1919); Meioneta meridionalis (Crosby & Bishop 1936), Meioneta zebrina Chamberlin & Ivie, 1944 = Meioneta parva (Banks 1896); Meioneta zygia (Keyserling 1886) = Meioneta fabra (Keyserling 1886). Ten informal species groups are proposed based on the study on the male palpal conformation of the embolus and radical division; these groups are not intened to be phylogenetic hypotheses. The limits and composition of the subfamily Micronetinae sensu Saaristo & Tanasevitch 1996 are discussed. PMID:26146700

  15. Surface display of the thermophilic lipase Tm1350 on the spore of Bacillus subtilis by the CotB anchor protein.

    PubMed

    Chen, Huayou; Tian, Rui; Ni, Zhong; Zhang, Qing; Zhang, Tianxi; Chen, Zhi; Chen, Keping; Yang, Shengli

    2015-07-01

    Lipases expressed in microbial hosts have great commercial value, but their applications are restricted by the high costs of production and harsh conditions used in industrial processes, such as high temperature and alkaline environment. In this study, an Escherichia coli-Bacillus subtilis shuttle vector (pHS-cotB-Tm1350) was constructed for the spore surface display of the lipase Tm1350 from hyperthermophilic bacterium Thermotoga maritima MSB8. Successful display of the CotB-Tm1350 fusion protein on spore surface was confirmed by Western blot analysis and activity measurements. The optimal catalytic temperature and pH of the spore surface-displayed Tm1350 were 80 °C and 9, respectively, which were higher than non-immobilized Tm1350 (70 °C and pH 7.5). Analysis of thermal and pH stability showed that spore surface-displayed Tm1350 retained 81 or 70 % of its original activity after 8 h of incubation at pH 8 or pH 9 (70 °C), which were 18 % higher than the retained activity of the non-immobilized Tm1350 under the same conditions. Meanwhile, recycling experiments showed that the recombinant spores could be used for up to three reaction cycles without a significant decrease in the catalytic rate (84 %). These results suggested that enzyme display on the surface of the B. subtilis spore could serve as an effective approach for enzyme immobilization, which has potential applications in the harsh biochemical industry. PMID:26026992

  16. Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli.

    PubMed

    Pek, Han Bin; Klement, Maximilian; Ang, Kok Siong; Chung, Bevan Kai-Sheng; Ow, Dave Siak-Wei; Lee, Dong-Yup

    2015-01-01

    Various isoforms of invertases from prokaryotes, fungi, and higher plants has been expressed in Escherichia coli, and codon optimisation is a widely-adopted strategy for improvement of heterologous enzyme expression. Successful synthetic gene design for recombinant protein expression can be done by matching its translational elongation rate against heterologous host organisms via codon optimization. Amongst the various design parameters considered for the gene synthesis, codon context bias has been relatively overlooked compared to individual codon usage which is commonly adopted in most of codon optimization tools. In addition, matching the rates of transcription and translation based on secondary structure may lead to enhanced protein folding. In this study, we evaluated codon context fitness as design criterion for improving the expression of thermostable invertase from Thermotoga maritima in Escherichia coli and explored the relevance of secondary structure regions for folding and expression. We designed three coding sequences by using (1) a commercial vendor optimized gene algorithm, (2) codon context for the whole gene, and (3) codon context based on the secondary structure regions. Then, the codon optimized sequences were transformed and expressed in E. coli. From the resultant enzyme activities and protein yield data, codon context fitness proved to have the highest activity as compared to the wild-type control and other criteria while secondary structure-based strategy is comparable to the control. Codon context bias was shown to be a relevant parameter for enhancing enzyme production in Escherichia coli by codon optimization. Thus, we can effectively design synthetic genes within heterologous host organisms using this criterion. PMID:26047917

  17. Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene.

    PubMed Central

    Opperman, T; Richardson, J P

    1994-01-01

    Genes from Pseudomonas fluorescens, Chromatium vinosum, Micrococcus luteus, Deinococcus radiodurans, and Thermotoga maritima with homology to the Escherichia coli rho gene were cloned and sequenced, and their sequences were compared with other available sequences. The species for all of the compared sequences are members of five bacterial phyla, including Thermotogales, the most deeply diverged phylum. This suggests that a rho-like gene is ubiquitous in the Bacteria and was present in their common ancestor. The comparative analysis revealed that the Rho homologs are highly conserved, exhibiting a minimum identity of 50% of their amino acid residues in pairwise comparisons. The ATP-binding domain had a particularly high degree of conservation, consisting of some blocks with sequences of residues that are very similar to segments of the alpha and beta subunits of F1-ATPase and of other blocks with sequences that are unique to Rho. The RNA-binding domain is more diverged than the ATP-binding domain. However, one of its most highly conserved segments includes a RNP1-like sequence, which is known to be involved in RNA binding. Overall, the degree of similarity is lowest in the first 50 residues (the first half of the RNA-binding domain), in the putative connector region between the RNA-binding and the ATP-binding domains, and in the last 50 residues of the polypeptide. Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution. PMID:8051015

  18. Evolution of the pair rule gene network: Insights from a centipede☆

    PubMed Central

    Green, Jack; Akam, Michael

    2013-01-01

    Comparative studies have examined the expression and function of homologues of the Drosophila melanogaster pair rule and segment polarity genes in a range of arthropods. The segment polarity gene homologues have a conserved role in the specification of the parasegment boundary, but the degree of conservation of the upstream patterning genes has proved more variable. Using genomic resources we identify a complete set of pair rule gene homologues from the centipede Strigamia maritima, and document a detailed time series of expression during trunk segmentation. We find supportive evidence for a conserved hierarchical organisation of the pair rule genes, with a division into early- and late-activated genes which parallels the functional division into primary and secondary pair rule genes described in insects. We confirm that the relative expression of sloppy-paired and paired with respect to wingless and engrailed at the parasegment boundary is conserved between myriapods and insects; suggesting that functional interactions between these genes might be an ancient feature of arthropod segment patterning. However, we find that the relative expression of a number of the primary pair rule genes is divergent between myriapods and insects. This corroborates suggestions that the evolution of upper tiers in the segmentation gene network is more flexible. Finally, we find that the expression of the Strigamia pair rule genes in periodic patterns is restricted to the ectoderm. This suggests that any direct role of these genes in segmentation is restricted to this germ layer, and that mesoderm segmentation is either dependent on the ectoderm, or occurs through an independent mechanism. PMID:23810931

  19. Expression of myriapod pair rule gene orthologs

    PubMed Central

    2011-01-01

    Background Segmentation is a hallmark of the arthropods; most knowledge about the molecular basis of arthropod segmentation comes from work on the fly Drosophila melanogaster. In this species a hierarchic cascade of segmentation genes subdivides the blastoderm stepwise into single segment wide regions. However, segmentation in the fly is a derived feature since all segments form virtually simultaneously. Conversely, in the vast majority of arthropods the posterior segments form one at a time from a posterior pre-segmental zone. The pair rule genes (PRGs) comprise an important level of the Drosophila segmentation gene cascade and are indeed the first genes that are expressed in typical transverse stripes in the early embryo. Information on expression and function of PRGs outside the insects, however, is scarce. Results Here we present the expression of the pair rule gene orthologs in the pill millipede Glomeris marginata (Myriapoda: Diplopoda). We find evidence that these genes are involved in segmentation and that components of the hierarchic interaction of the gene network as found in insects may be conserved. We further provide evidence that segments are formed in a single-segment periodicity rather than in pairs of two like in another myriapod, the centipede Strigamia maritima. Finally we show that decoupling of dorsal and ventral segmentation in Glomeris appears already at the level of the PRGs. Conclusions Although the pair rule gene network is partially conserved among insects and myriapods, some aspects of PRG interaction are, as suggested by expression pattern analysis, convergent, even within the Myriapoda. Conserved expression patterns of PRGs in insects and myriapods, however, may represent ancestral features involved in segmenting the arthropod ancestor. PMID:21352542

  20. An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability.

    PubMed

    Singh, Mrityunjay K; Manoj, Narayanan

    2016-06-01

    The carbohydrate esterase family 7 (CE7) belonging to the α/β hydrolase superfamily contains a structurally conserved loop extension element relative to the canonical α/β hydrolase fold. This element called the β-interface loop contributes 20-30% of the total buried surface area at intersubunit interfaces of the functional hexameric state. To test whether this loop is an enabling region for the structure and function of the oligomeric assembly, we designed a truncation variant of the thermostable CE7 acetyl esterase from Thermotoga maritima (TmAcE). Although deletion of 26 out of 40 residues in the loop had little impact on the hexamer formation, the variant exhibited altered dynamics of the oligomeric assembly and a loss of thermal stability. Furthermore, the mutant lacked catalytic activity. Crystal structures of the variant and a new crystal form of the wild type protein determined at 2.75Å and 1.76Å, respectively, provide a rationale for the properties of the variant. The hexameric assembly in the variant is identical to that of the wild type and differed only in the lack of buried surface area interactions at the original intersubunit interfaces. This is accompanied by disorder in an extended region of the truncated loop that consequently induces disorder in the neighboring oxyanion hole loop. Overall, the results suggest that the β-interface loop in CE7 enzymes is dispensable for the oligomeric assembly. Rather, the loop extension event was evolutionarily selected to regulate activity, conformational flexibility and thermal stability. PMID:27085421

  1. Conformational Changes of the Clamp of the Protein Translocation ATPase SecA.

    PubMed

    Chen, Yu; Bauer, Benedikt W; Rapoport, Tom A; Gumbart, James C

    2015-07-17

    Post-translational protein translocation across the bacterial plasma membrane is mediated by the interplay of the SecA ATPase and the protein-conducting SecY channel. SecA consists of several domains, including two nucleotide-binding domains (NBD1 and NBD2), a polypeptide cross-linking domain (PPXD), a helical scaffold domain (HSD), and a helical wing domain (HWD). PPXD, HSD, and NBD2 form a clamp that positions the polypeptide substrate above the channel so that it can be pushed into the channel by a two-helix finger of the HSD. How the substrate is accommodated in the clamp during translocation is unclear. Here, we report a crystal structure of Thermotoga maritima SecA at 1.9 Å resolution. Structural analysis and free-energy calculations indicate that the new structure represents an intermediate state during the transition of the clamp from an open to a closed conformation. Molecular dynamics simulations show that closure of the clamp occurs in two phases, an initial movement of PPXD, HSD, and HWD as a unit, followed by a movement of PPXD alone toward NBD2. Simulations in the presence of a polypeptide chain show that the substrate associates with the back of the clamp by dynamic hydrogen bonding and that the clamp is laterally closed by a conserved loop of the PPXD. Mutational disruption of clamp opening or closure abolishes protein translocation. These results suggest how conformational changes of SecA allow substrate binding and movement during protein translocation. PMID:25982945

  2. Ocean Acidification and the Loss of Phenolic Substances in Marine Plants

    PubMed Central

    Arnold, Thomas; Mealey, Christopher; Leahey, Hannah; Miller, A. Whitman; Hall-Spencer, Jason M.; Milazzo, Marco; Maers, Kelly

    2012-01-01

    Rising atmospheric CO2 often triggers the production of plant phenolics, including many that serve as herbivore deterrents, digestion reducers, antimicrobials, or ultraviolet sunscreens. Such responses are predicted by popular models of plant defense, especially resource availability models which link carbon availability to phenolic biosynthesis. CO2 availability is also increasing in the oceans, where anthropogenic emissions cause ocean acidification, decreasing seawater pH and shifting the carbonate system towards further CO2 enrichment. Such conditions tend to increase seagrass productivity but may also increase rates of grazing on these marine plants. Here we show that high CO2 / low pH conditions of OA decrease, rather than increase, concentrations of phenolic protective substances in seagrasses and eurysaline marine plants. We observed a loss of simple and polymeric phenolics in the seagrass Cymodocea nodosa near a volcanic CO2 vent on the Island of Vulcano, Italy, where pH values decreased from 8.1 to 7.3 and pCO2 concentrations increased ten-fold. We observed similar responses in two estuarine species, Ruppia maritima and Potamogeton perfoliatus, in in situ Free-Ocean-Carbon-Enrichment experiments conducted in tributaries of the Chesapeake Bay, USA. These responses are strikingly different than those exhibited by terrestrial plants. The loss of phenolic substances may explain the higher-than-usual rates of grazing observed near undersea CO2 vents and suggests that ocean acidification may alter coastal carbon fluxes by affecting rates of decomposition, grazing, and disease. Our observations temper recent predictions that seagrasses would necessarily be “winners” in a high CO2 world. PMID:22558120

  3. On the distribution and evaluation of Na, Mg and Cl in leaves of selected halophytes

    NASA Astrophysics Data System (ADS)

    Pongrac, Paula; Vogel-Mikuš, Katarina; Regvar, Marjana; Kaligarič, Mitja; Vavpetič, Primož; Kelemen, Mitja; Grlj, Nataša; Shelef, Oren; Golan-Goldhirsh, Avi; Rachmilevitch, Shimon; Pelicon, Primož

    2013-07-01

    Diverse physiological, biochemical and morphological adaptations enable plants to survive in extreme saline environments where osmotic and ionic stresses limit growth and development. Halophytes are salt-tolerant plants that can withstand extraordinarily high levels of Na and Cl in their leaves. The tissue and cellular distribution patterns of salt ions can be linked to the underlying mechanisms of salt tolerance. Application of fast, reliable, multi-elemental and quantitative techniques such as micro-proton-induced X-ray emission (micro-PIXE) will significantly contribute to and accelerate studies of plant salt tolerance, especially as micro-PIXE also provides spatially resolved quantitative data for light elements, such as Na and Mg. The spatial concentration distributions of Na, Mg, Cl, K, P and S in leaves of four halophytes (Bassia indica, Atriplex prostrata, Spartina maritima and Limonium angustifolium) were determined using micro-PIXE, to study the salt-tolerance strategies of the selected halophytes. Different distribution patterns of the studied elements were seen in the leaves; however, in all four of these plant species, Na was excluded from photosynthetically active chlorophyl tissues. With the exception of L. angustifolium, Cl, P and S contents (representing chloride, phosphate and sulphate ionic forms, respectively) did not ensure charge balance in the leaves, which suggests other anionic compounds, such as nitrate and organic anions, have crucial roles in maintaining electroneutrality in these halophytes. By increasing soil salinisation worldwide, the possibility to reliably complement spatial distributions of Na, Mg, Cl, K, P and S with plant structural morphology will contribute significantly to our understanding of plant tolerance mechanisms at the tissue and cell levels. In addition, these kinds of studies are of particular value for designing crop plants with high salt tolerance and for the development of phytoremediation technologies.

  4. Radionuclides transfer into halophytes growing in tidal salt marshes from the Southwest of Spain.

    PubMed

    Luque, Carlos J; Vaca, Federico; García-Trapote, Ana; Hierro, Almudena; Bolívar, Juan P; Castellanos, Eloy M

    2015-12-01

    Estuaries are sinks of materials and substances which are released directly into them or transported from rivers that drain the basin. It is usual to find high organic matter loads and fine particles in the sediments. We analyzed radionuclide concentrations ((210)Po, (230)Th, (232)Th, (234)U, (238)U, (226)Ra, (228)Th, (228)Ra, (40)K) in sediments and three different organs (roots, stems and leaves) of three species of halophytes plants (Spartina maritima, Spartina densiflora and Sarcocornia perennis). The study was carried out in two tidal salt marshes, one polluted by U-series radionuclides and another nearby that was unpolluted and was used as a control (or reference) area. The Tinto River salt marsh shows high levels of U-series radionuclides coming from mining and industrial discharges. On the contrary, the unperturbed Piedras River salt marsh is located about 25 km from the Tinto marsh, and shows little presence of contaminants and radionuclides. The results of this work have shown that natural radionuclide concentrations (specially the U-isotopes) in the Tinto salt marsh sediments are one order of magnitude higher than those in the Piedras marsh. These radionuclide enhancements are reflected in the different organs of the plants, which have similar concentration increases as the sediments where they have grown. Finally, the transfer factor (TF) of the most polluted radionuclides (U-isotopes and (210)Po) in the Tinto area are one order of magnitude higher than in the Piedras area, indicating that the fraction of each radionuclide in the sediment originating from the pollution is more available for the plants than the indigenous fraction. This means that the plants of the salt marshes are unhelpful as bioindicators or for the phytoremediation of radionuclides. PMID:26334596

  5. Nursery fidelity, food web interactions and primary sources of nutrition of the juveniles of Solea solea and S. senegalensis in the Tagus estuary (Portugal): A stable isotope approach

    NASA Astrophysics Data System (ADS)

    Vinagre, C.; Salgado, J.; Costa, M. J.; Cabral, H. N.

    2008-01-01

    Stable carbon and nitrogen isotopes were used to assess site fidelity of Solea solea and Solea senegalensis juveniles, to investigate food web interactions and to determine the dominant nutrient pathways in two nursery areas in the Tagus estuary, Portugal. Samples of water from the main sources and from the nursery areas and respective saltmarsh creeks were collected for isotope analysis, as well as sediment, benthic microalgae, saltmarsh halophytes, S. solea, S. senegalensis and its main prey, Nereis diversicolor, Scrobicularia plana and Corophium spp. While site fidelity was high in 0-group juveniles, it was lower for 1-group juveniles, possibly due to an increase in mobility and energy demands with increasing size. Analysis of the food web revealed a complex net of relations. Particulate organic matter from the freshwater sources, from each nursery's waters and saltmarsh creeks presented similar isotopic composition. Sediment isotopic composition and saltmarsh halophytes also did not differentiate the two areas. All components of the food web from the benthic microalgae upwards were isotopically different between the nursery areas. These components were always more enriched in δ13C and δ15N at the lower nursery area than at the nursery located upstream, appearing as if there were two parallel trophic chains with little trophic interaction between each other. A mixture of carbon and nitrogen sources is probably being incorporated into the food web. The lower nursery area is more dependent upon an isotopically enriched energy pathway, composed of marine particulate organic matter, marine benthic microalgae and detritus of the C 4 saltmarsh halophyte Spartina maritima. The two nursery areas present a different level of dependence upon the freshwater and marine energy pathways, due to hydrological features, which should be taken into account for S. solea and S. senegalensis fisheries and habitat management.

  6. Tuning protein mechanics through an ionic cluster graft from an extremophilic protein.

    PubMed

    Tych, Katarzyna M; Batchelor, Matthew; Hoffmann, Toni; Wilson, Michael C; Paci, Emanuele; Brockwell, David J; Dougan, Lorna

    2016-03-14

    Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins. PMID:26809452

  7. Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea.

    PubMed

    Poddar, Abhijit; Lepcha, Rinchen T; Mukherjee, Debasish; Bhattacharyya, Dhananjay; Das, Subrata K

    2014-09-01

    A Gram-negative, short rod, aerobic bacterium, designated W11(T), was isolated from seawater. Heterotrophic growth was observed at 10-45 °C and pH 6-10. Optimal growth was observed at 30-37 °C and pH 7-9. It can grow in the presence of 0.5-12% NaCl (w/v), and the optimal NaCl required for growth was 5-6%. 16S rRNA gene sequence similarity revealed that strain W11(T) clustered within the radiation of the genus Idiomarina and showed 99.24% similarity with Idiomarina donghaiensis JCM 15533(T), 97.64% with Idiomarina marina JCM 15083(T), 97.37% with Idiomarina tainanensis JCM 15084(T) and 97.16% with Idiomarina maritima JCM 15534(T). DNA-DNA similarities between strains W11(T) with other closely related strains were below 70%. Polar lipids included a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethanolamine, an unidentified phosopholipid, two unidentified aminolipids and two unidentified lipids. DNA G + C content was 41.2 ± 0.1 mol%. Major fatty acids were iso-C15:0, iso-C17:0, iso-C17:1ω9c, C16:0, iso-C11:0 3OH and C16:1ω7c/C16:1ω7c. The isoprenoid ubiquinone was Q8. On the basis of the present polyphasic taxonomic study, strain W11(T) is considered to represent a novel species of the genus Idiomarina, for which the name Idiomarina woesei sp. nov. is proposed. The type strain is W11(T) (= DSM 27808(T) = JCM 19499(T) = LMG 27903(T)). PMID:25078320

  8. Evolution of the pair rule gene network: Insights from a centipede.

    PubMed

    Green, Jack; Akam, Michael

    2013-10-01

    Comparative studies have examined the expression and function of homologues of the Drosophila melanogaster pair rule and segment polarity genes in a range of arthropods. The segment polarity gene homologues have a conserved role in the specification of the parasegment boundary, but the degree of conservation of the upstream patterning genes has proved more variable. Using genomic resources we identify a complete set of pair rule gene homologues from the centipede Strigamia maritima, and document a detailed time series of expression during trunk segmentation. We find supportive evidence for a conserved hierarchical organisation of the pair rule genes, with a division into early- and late-activated genes which parallels the functional division into primary and secondary pair rule genes described in insects. We confirm that the relative expression of sloppy-paired and paired with respect to wingless and engrailed at the parasegment boundary is conserved between myriapods and insects; suggesting that functional interactions between these genes might be an ancient feature of arthropod segment patterning. However, we find that the relative expression of a number of the primary pair rule genes is divergent between myriapods and insects. This corroborates suggestions that the evolution of upper tiers in the segmentation gene network is more flexible. Finally, we find that the expression of the Strigamia pair rule genes in periodic patterns is restricted to the ectoderm. This suggests that any direct role of these genes in segmentation is restricted to this germ layer, and that mesoderm segmentation is either dependent on the ectoderm, or occurs through an independent mechanism. PMID:23810931

  9. Aquatic insects of New York salt marsh associated with mosquito larval habitat and their potential utility as bioindicators.

    PubMed

    Rochlin, Ilia; Dempsey, Mary E; Iwanejko, Tom; Ninivaggi, Dominick V

    2011-01-01

    The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insect-based index of biological integrity for salt marsh health assessment. PMID:22957707

  10. Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel that Evolved by Gene Duplication

    SciTech Connect

    Pejcha, Robert; Ludwig, Martha L.

    2010-03-08

    Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two ({beta}{alpha}){sub 8} barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys){sub 3}Zn site in the related enzymes, MetH and betaine-homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E {center_dot} Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

  11. Impacts of summer ozone exposure on the growth and overwintering of UK upland vegetation

    NASA Astrophysics Data System (ADS)

    Hayes, Felicity; Mills, Gina; Williams, Philip; Harmens, Harry; Bker, Patrick

    The effects of ozone exposure on species of an upland grassland were assessed. Thirty-three species from Snowdonia, North Wales, UK, were exposed for 10 weeks to a weekly episodic ozone regime in solardomes representing predicted future concentrations. Two solardomes were used as controls, with ozone added to charcoal-filtered air to give a continuous ozone concentration of 30 ppb (O 3(30)). A weekly episodic ozone regime was applied to two other solardomes, with concentrations rising for 8 h per day to 80 ppb on day 1, 100 ppb on days 2 and 3, and 80 ppb on day 4; ozone concentrations remained at 30 ppb at all other times (O 3(30+peaks)). The control and background ozone concentrations of 30 ppb were maintained throughout the night as well as during the daytime. During exposure to the episodic ozone regime, some species were sensitive to ozone and showed ozone-specific leaf injury symptoms (e.g . Carex echinata) and/or premature senescence (e.g. Festuca rubra) and/or changes in above-ground biomass (e.g. Armeria maritima), whereas other species (e.g Holcus lanatus and Carex demissa) showed no effects. Some species, although showing no effects during the 10-week ozone exposure, showed carry-over effects on biomass the following spring, after a winter period of ambient ozone exposure (e.g. Galium saxatile, Nardus stricta and Saxifraga stellaris). The carry-over effects shown in this study indicate the potential ecological impact of ozone on semi-natural vegetation species and indicate the importance of longer-term studies on the effects of ozone on plants.

  12. MULCHES AND OTHER COVER MATERIALS TO REDUCE WEED GROWTH IN CONTAINER-GROWN NURSERY STOCK.

    PubMed

    Rys, F; Van Wesemael, D; Van Haecke, D; Mechant, E; Gobin, B

    2014-01-01

    Due to the recent EU-wide implementation of Integrated Pest Management (IPM), alternative methods to reduce weed growth in container-grown nursery stock are needed to cut back the use of herbicides. Covering the upper layer of the substrate is known as a potential method to prevent or reduce weed growth in plant containers. As a high variety of mulches and other cover materials are on the market, however, it is no longer clear for growers which cover material is most efficient for use in containers. Therefore, we examined the effect on weed growth of different mulches and other cover materials, including Pinus maritima, P. sylvestris, Bio-Top Basic, Bio-Top Excellent, coco chips fine, hemp fibres, straw pellets, coco disk 180LD and jute disk. Cover materials were applied immediately after repotting of Ligustrum ovalifolium or planting of Fagus sylvatica. At regular times, both weed growth and side effects (e.g., plant growth, water status of the substrate, occurrence of mushrooms, foraging of birds, complete cover of the substrate and fixation) were assessed. All examined mulches or other cover materials were able to reduce weed growth on the containers during the whole growing season. Weed suppression was even better than that of a chemical treated control. Although all materials showed some side effects, the impact on plant growth is most important to the grower and depends not only on material characteristics (e.g., biodegradation, nutrient leaching and N-immobilisation) but also on container size and climatic conditions. In conclusion, mulches and other cover materials can be a valuable tool within IPM to lower herbicide use. To enable a deliberate choice of which cover material is best used in a specific situation more research is needed on lifespan and stability as well as on economic characteristics of the materials. PMID:26084081

  13. A Diferrous-Dinitrosyl Intermediate in the N2O-Generating Pathway of a Deflavinated Flavo-Diiron Protein

    PubMed Central

    2015-01-01

    Flavo-diiron proteins (FDPs) function as anaerobic nitric oxide scavengers in some microorganisms, catalyzing reduction of nitric to nitrous oxide. The FDP from Thermotoga maritima can be prepared in a deflavinated form with an intact diferric site (deflavo-FDP). Hayashi et al. [(2010) Biochemistry 49, 7040–7049] reported that reaction of NO with reduced deflavo-FDP produced substoichiometric N2O. Here we report a multispectroscopic approach to identify the iron species in the reactions of deflavo-FDP with NO. Mössbauer spectroscopy identified two distinct ferrous species after reduction of the antiferromagnetically coupled diferric site. Approximately 60% of the total ferrous iron was assigned to a diferrous species associated with the N2O-generating pathway. This pathway proceeds through successive diferrous-mononitrosyl (S = 1/2 FeII{FeNO}7) and diferrous-dinitrosyl (S = 0 [{FeNO}7]2) species that form within ∼100 ms of mixing of the reduced protein with NO. The diferrous-dinitrosyl intermediate converted to an antiferromagnetically coupled diferric species that was spectroscopically indistinguishable from that in the starting deflavinated protein. These diiron species closely resembled those reported for the flavinated FDP [Caranto et al. (2014) J. Am. Chem. Soc. 136, 7981–7992], and the time scales of their formation and decay were consistent with the steady state turnover of the flavinated protein. The remaining ∼40% of ferrous iron was inactive in N2O generation but reversibly bound NO to give an S = 3/2 {FeNO}7 species. The results demonstrate that N2O formation in FDPs can occur via conversion of S = 0 [{FeNO}7]2 to a diferric form without participation of the flavin cofactor. PMID:25144650

  14. Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain

    SciTech Connect

    Miller, D.J.; Ouellette, N.; Evodokimova, E.; Savchenko, A.; Edwards, A.; Anderson, W.F.

    2010-03-08

    S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S{sup +}-CH{sub 3} bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

  15. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets

    PubMed Central

    Zachow, Christin; Müller, Henry; Tilcher, Ralf; Berg, Gabriele

    2014-01-01

    The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8%) than for sugar beet (≤57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes. PMID:25206350

  16. Primary production dynamics in a pristine groundwater influenced coastal lagoon of the Yucatan Peninsula

    NASA Astrophysics Data System (ADS)

    Medina-Gómez, Israel; Herrera-Silveira, Jorge A.

    2006-06-01

    Dzilam lagoon is a shallow (0.6 m mean depth) ecosystem with 9.4 km 2 surface area, located in the north coast of the Yucatan Peninsula, and connected to the Gulf of Mexico through a permanent inlet. Freshwater input is possible through numerous sinkholes distributed throughout the lagoon, which also represent a continuous source of nitrate and silicate. The low anthropogenic influence has maintained a pristine condition in Dzilam lagoon, manifested in a spatial heterogeneity of water quality and primary production strongly related to the environmental fluctuations. To determine the annual variability of primary production and identify the factors controlling it, 12 monthly samplings were undertaken at six stations, from September 1998 to August 1999. Thus, physical-chemical parameters, inorganic nutrients concentrations, chlorophyll- a, phytoplankton production and seagrass biomass were measured. The water residence time in Dzilam lagoon is higher during dry season due to the significant evaporation rate, and shorter in rainy season because of increase in precipitation and volume of groundwater discharge. The multivariate analysis results suggest that the salinity gradient, changes in aquatic vegetation biomass, and the remineralized nutrients in sediments constitute key processes depicting the water quality and net primary production in Dzilam lagoon. Furthermore, the biogeochemical benthic processes, combined with a longer stay of phytoplankton cells within the lagoon, enhanced primary production in the water column during dry season, as opposite as rainy period, when the inferior water residence time yielded lower production values. The seagrasses ( Halodule wrightii and Ruppia maritima) showed the highest biomass (110.5 g dw/m 2/d) in dry season, while the lowest recordings were observed during cold fronts, with a salient belowground contribution (rhizomes and roots). Seagrasses and phytoplankton participation to the total primary production in Dzilam lagoon were seasonally alternated, yielding a high primary productivity along the annual cycle. Despite of this complementary arrangement, the submerged aquatic vegetation displayed an overall higher contribution during the year (65%) relate to phytoplankton.

  17. Pullulanase type I from Fervidobacterium pennavorans Ven5: cloning, sequencing, and expression of the gene and biochemical characterization of the recombinant enzyme.

    PubMed

    Bertoldo, C; Duffner, F; Jorgensen, P L; Antranikian, G

    1999-05-01

    The gene encoding the type I pullulanase from the extremely thermophilic anaerobic bacterium Fervidobacterium pennavorans Ven5 was cloned and sequenced in Escherichia coli. The pulA gene from F. pennavorans Ven5 had 50.1% pairwise amino acid identity with pulA from the anaerobic hyperthermophile Thermotoga maritima and contained the four regions conserved among all amylolytic enzymes. The pullulanase gene (pulA) encodes a protein of 849 amino acids with a 28-residue signal peptide. The pulA gene was subcloned without its signal sequence and overexpressed in E. coli under the control of the trc promoter. This clone, E. coli FD748, produced two proteins (93 and 83 kDa) with pullulanase activity. A second start site, identified 118 amino acids downstream from the ATG start site, with a Shine-Dalgarno-like sequence (GGAGG) and TTG translation initiation codon was mutated to produce only the 93-kDa protein. The recombinant purified pullulanases (rPulAs) were optimally active at pH 6 and 80 degrees C and had a half-life of 2 h at 80 degrees C. The rPulAs hydrolyzed alpha-1,6 glycosidic linkages of pullulan, starch, amylopectin, glycogen, alpha-beta-limited dextrin. Interestingly, amylose, which contains only alpha-1,4 glycosidic linkages, was not hydrolyzed by rPulAs. According to these results, the enzyme is classified as a debranching enzyme, pullulanase type I. The extraordinary high substrate specificity of rPulA together with its thermal stability makes this enzyme a good candidate for biotechnological applications in the starch-processing industry. PMID:10224005

  18. Breeding productivity of Smith Island black ducks

    USGS Publications Warehouse

    Haramis, G.M.; Jorde, D.G.; Olsen, G.H.; Stotts, D.B.; Harrison, M.K.

    2002-01-01

    We investigated the breeding performance of American black ducks (Anas rubripes) on Smith Island, Chesapeake Bay, to improve our understanding of island black duck breeding ecology and to make management recommendations to enhance productivity. During 1995-96, we implanted 56 female black ducks with 20-g radio transmitters and tracked 35 of the individuals through the breeding season to locate nests, determine nest fate, and identify brood habitat. We also increased preseason banding efforts and compared capture characteristics over 12 years with those from the Deal Island Wildlife Management Area, a banding site on the mainland of Tangier Sound. A low rate of nesting (37%), lack of renesting, and poor hatching success (31%) indicated that island salt marsh habitats present a harsh environment for breeding black ducks. Black ducks located 11 of 13 nests (85%) in black needlerush (Juncus roemerianus) marsh where they were vulnerable to flooding from extreme tides and to egg predators. No nests were found on forested tree hammocks, a feature that distinguishes Smith Island from nearby South Marsh and Bloodsworth Islands. Nest predators included red foxes (Vulpes vulpes), herring gulls (Larus argentams), fish crows (Corvus ossifragus), and, potentially, Norway rats (Rattus norvegicus). Unlike mainland red foxes, foxes radio tracked on Smith Island were found to be capable swimmers and effective low marsh predators. We found shoreline meadows of widgeon grass (Ruppia maritima) to be important foraging sites for black ducks and suspected that the virtual absence of fresh water in this high salinity environment (1217+ ppt) to incur some cost in terms of growth and survival of ducklings. Preseason bandings revealed a high proportion of banded adults and a strong positive correlation in age ratios with the Deal Island banding site. This latter finding strongly suggests a negative universal effect of storm tides on nest success for Tangier Sound black ducks. Management to reduce nest predators, especially gulls and foxes, likely will have the greatest immediate benefit for island breeding black ducks.

  19. Diversity and Plant Growth Promoting Capacity of Endophytic Fungi Associated with Halophytic Plants from the West Coast of Korea.

    PubMed

    Khalmuratova, Irina; Kim, Hyun; Nam, Yoon-Jong; Oh, Yoosun; Jeong, Min-Ji; Choi, Hye-Rim; You, Young-Hyun; Choo, Yeon-Sik; Lee, In-Jung; Shin, Jae-Ho; Yoon, Hyeokjun; Kim, Jong-Guk

    2015-12-01

    Five halophytic plant species, Suaeda maritima, Limonium tetragonum, Suaeda australis, Phragmites australis, and Suaeda glauca Bunge, which are native to the Muan salt marsh of South Korea, were examined for fungal endophytes by sequencing the internal transcribed spacer (ITS) region containing ITS1, 5.8S rRNA, and ITS2. In total, 160 endophytic fungal strains were isolated and identified from the roots of the 5 plant species. Taxonomically, all 160 strains belonged to the phyla Ascomycota, Basidiomycota, and Zygomycota. The most dominant genus was Fusarium, followed by the genera Penicillium and Alternaria. Subsequently, using 5 statistical methods, the diversity indices of the endophytes were determined at genus level. Among these halophytic plants, P. australis was found to host the greatest diversity of endophytic fungi. Culture filtrates of endophytic fungi were treated to Waito-C rice seedlings for plant growth-promoting effects. The fungal strain Su-3-4-3 isolated from S. glauca Bunge provide the maximum plant length (20.1 cm) in comparison with wild-type Gibberella fujikuroi (19.6 cm). Consequently, chromatographic analysis of the culture filtrate of Su-3-4-3 showed the presence of physiologically active gibberellins, GA1 (0.465 ng/mL), GA3 (1.808 ng/mL) along with other physiologically inactive GA9 (0.054 ng/mL) and GA24 (0.044 ng/mL). The fungal isolate Su-3-4-3 was identified as Talaromyces pinophilus. PMID:26839496

  20. Vegetation change on a northeast tidal marsh: Interaction of sea-level rise and marsh accretion

    SciTech Connect

    Warren, R.S.; Niering, W.A. )

    1993-01-01

    Increasing rates of relative sea-level rise (RSL) have been linked to coastal wetland losses along the Gulf of Mexico and elsewhere. Rapidly rising RSL may be affecting New England tidal marshes. Studies of the Wequetequock-Pawcatuck tidal marshes over four decades have documented dramatic changes in vegetation apparently related primarily to differential rates of marsh accretion and sea-level rise though sediment supply and anthropogenic modifications of the system may also be involved. When initially studied in 1947-1948 the high marsh supported a Juncus gerardi-Spartina patens belting pattern typical of many New England salt marshes. On most of the marsh complex the former Juncus belt has now been replaced by forbs, primarily Triglochin maritima, while the former S. patens high marsh is now a complex of vegetation types-stunted Spartina alterniflora, Distichlis spicata, forbs, and relic stands of S. patens. The mean surface elevation of areas where the vegetation has changed is significantly lower than that of areas still supporting the earlier pattern (4.6 vs. 13.9 cm above mean tide level). The differences in surface elevation reflect differences in accretion of marsh peat. Stable areas have been accreting at the rate of local sea-level rise, 2.0-2.5 mm/yr at least since 1938; changed areas have accreted at about one half that rate. Lower surface elevations result in greater frequency and duration of tidal flooding, and thus in increased peat saturation, salinity, and sulfide concentrations, and in decreased redox potential, as directly measured over the growing season at both changed and stable sites. These edaphic changes may have combined to favor establishment of a wetter, more open vegetation type. Similar changes have been observed on other Long Island Sound marshes and may be a model for the potential effects of sea-level rise on New England tidal salt marshes. 39 refs., 4 figs., 1 tab.

  1. Aquatic Insects of New York Salt Marsh Associated with Mosquito Larval Habitat and their Potential Utility as Bioindicators

    PubMed Central

    Rochlin, Ilia; Dempsey, Mary E.; Iwanejko, Tom; Ninivaggi, Dominick V.

    2011-01-01

    The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insectbased index of biological integrity for salt marsh health assessment. PMID:22957707

  2. Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme

    PubMed Central

    Hayashi, Takahiro; Caranto, Jonathan D.; Wampler, David A.; Kurtz, Donald M.; Monne-Loccoz, Pierre

    2010-01-01

    Flavodiiron proteins (FDPs) catalyze reductive scavenging of dioxygen and nitric oxide in air sensitive microorganisms. FDPs contain a distinctive non-heme diiron/flavin mononucleotide (FMN) active site. Alternative mechanisms for the nitric oxide reductase (NOR) activity have been proposed consisting of either protonation of a diiron-bridging hyponitrite or super-reduction of a diferrous-dinitrosyl by the proximal FMNH2 in the rate-determining step. In order to test these alternative mechanisms, we examined a deflavinated FDP (deflavo-FDP) from Thermotoga maritima. The deflavo-FDP retains an intact diiron site but does not show multi-turnover NOR or O2 reductase (O2R) activity. Reactions of the reduced (diferrous) deflavo-FDP with nitric oxide were examined by UV-vis absorption, EPR, resonance Raman, and FTIR spectroscopies. Anaerobic addition of nitric oxide up to 1 NO:diferrous deflavo-FDP results in formation of a diiron-mononitrosyl complex characterized by a broad S = 1/2 EPR signal arising from antiferromagnetic coupling of an S = 3/2 {FeNO}7 with an S = 2 Fe(II). Further addition of NO results in two reaction pathways, one of which produces N2O and the diferric site and the other of which produces a stable diiron-dinitrosyl complex. Both NO-treated and as-isolated deflavo-FDPs regain full NOR and O2R activities upon simple addition of FMN. The production of N2O upon addition of NO to the mononitrosyl deflavo-FDP supports the hyponitrite mechanism, but the concomitant formation of a stable diiron-dinitrosyl complex in the deflavo-FDP is consistent with a super-reduction pathway in the flavinated enzyme. We conclude that a diiron-mononitrosyl complex is an intermediate in the NOR catalytic cycle of FDPs. PMID:20669924

  3. Starch biosynthetic genes and enzymes are expressed and active in the absence of starch accumulation in sugar beet tap-root

    PubMed Central

    2014-01-01

    Background Starch is the predominant storage compound in underground plant tissues like roots and tubers. An exception is sugar beet tap-root (Beta vulgaris ssp altissima) which exclusively stores sucrose. The underlying mechanism behind this divergent storage accumulation in sugar beet is currently not fully known. From the general presence of starch in roots and tubers it could be speculated that the lack in sugar beet tap-roots would originate from deficiency in pathways leading to starch. Therefore with emphasis on starch accumulation, we studied tap-roots of sugar beet using parsnip (Pastinaca sativa) as a comparator. Results Metabolic and structural analyses of sugar beet tap-root confirmed sucrose as the exclusive storage component. No starch granules could be detected in tap-roots of sugar beet or the wild ancestor sea beet (Beta vulgaris ssp. maritima). Analyses of parsnip showed that the main storage component was starch but tap-root tissue was also found to contain significant levels of sugars. Surprisingly, activities of four main starch biosynthetic enzymes, phosphoglucomutase, ADP-glucose pyrophosphorylase, starch synthase and starch branching enzyme, were similar in sugar beet and parsnip tap-roots. Transcriptional analysis confirmed expression of corresponding genes. Additionally, expression of genes involved in starch accumulation such as for plastidial hexose transportation and starch tuning functions could be determined in tap-roots of both plant species. Conclusion Considering underground storage organs, sugar beet tap-root upholds a unique property in exclusively storing sucrose. Lack of starch also in the ancestor sea beet indicates an evolved trait of biological importance. Our findings in this study show that gene expression and enzymatic activity of main starch biosynthetic functions are present in sugar beet tap-root during storage accumulation. In view of this, the complete lack of starch in sugar beet tap-roots is enigmatic. PMID:24758347

  4. Novel α-L-Fucosidases from a Soil Metagenome for Production of Fucosylated Human Milk Oligosaccharides

    PubMed Central

    Lezyk, Mateusz; Jers, Carsten; Kjaerulff, Louise; Gotfredsen, Charlotte H.; Mikkelsen, Maria D.; Mikkelsen, Jørn D.

    2016-01-01

    This paper describes the discovery of novel α-L-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. Seven novel α-L-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in E. coli as recombinant 6xHis-tagged proteins. All seven fucosidases belong to glycosyl hydrolase family 29 (GH 29). Six of the seven α-L-fucosidases were substrate-inhibited, moderately thermostable and most hydrolytically active in the pH range 6–7, when tested with para-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as the substrate. In contrast, one fucosidase (Mfuc6) exhibited a high pH optimum and an unusual sigmoidal kinetics towards pNP-Fuc substrate. When tested for trans-fucosylation activity using pNP-Fuc as donor, most of the enzymes were able to transfer fucose to pNP-Fuc (self-condensation) or to lactose. With the α-L-fucosidase from Thermotoga maritima and the metagenome-derived Mfuc5, different fucosyllactose variants including the principal fucosylated HMO 2’-fucosyllactose were synthesised in yields of up to ~6.4%. Mfuc5 was able to release fucose from xyloglucan and could also use it as a fucosyl-donor for synthesis of fucosyllactose. This is the first study describing the use of glycosyl hydrolases for the synthesis of genuine fucosylated human milk oligosaccharides. PMID:26800369

  5. Maltose Metabolism in the Hyperthermophilic Archaeon Thermococcus litoralis: Purification and Characterization of Key Enzymes

    PubMed Central

    Xavier, Karina B.; Peist, Ralf; Kossmann, Marina; Boos, Winfried; Santos, Helena

    1999-01-01

    Maltose metabolism was investigated in the hyperthermophilic archaeon Thermococcus litoralis. Maltose was degraded by the concerted action of 4-α-glucanotransferase and maltodextrin phosphorylase (MalP). The first enzyme produced glucose and a series of maltodextrins that could be acted upon by MalP when the chain length of glucose residues was equal or higher than four, to produce glucose-1-phosphate. Phosphoglucomutase activity was also detected in T. litoralis cell extracts. Glucose derived from the action of 4-α-glucanotransferase was subsequently metabolized via an Embden-Meyerhof pathway. The closely related organism Pyrococcus furiosus used a different metabolic strategy in which maltose was cleaved primarily by the action of an α-glucosidase, a p-nitrophenyl-α-d-glucopyranoside (PNPG)-hydrolyzing enzyme, producing glucose from maltose. A PNPG-hydrolyzing activity was also detected in T. litoralis, but maltose was not a substrate for this enzyme. The two key enzymes in the pathway for maltose catabolism in T. litoralis were purified to homogeneity and characterized; they were constitutively synthesized, although phosphorylase expression was twofold induced by maltodextrins or maltose. The gene encoding MalP was obtained by complementation in Escherichia coli and sequenced (calculated molecular mass, 96,622 Da). The enzyme purified from the organism had a specific activity for maltoheptaose, at the temperature for maximal activity (98°C), of 66 U/mg. A Km of 0.46 mM was determined with heptaose as the substrate at 60°C. The deduced amino acid sequence had a high degree of identity with that of the putative enzyme from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 (66%) and with sequences of the enzymes from the hyperthermophilic bacterium Thermotoga maritima (60%) and Mycobacterium tuberculosis (31%) but not with that of the enzyme from E. coli (13%). The consensus binding site for pyridoxal 5′-phosphate is conserved in the T. litoralis enzyme. PMID:10348846

  6. Design of an α-l-transfucosidase for the synthesis of fucosylated HMOs.

    PubMed

    Saumonneau, Amélie; Champion, Elise; Peltier-Pain, Pauline; Molnar-Gabor, Dora; Hendrickx, Johann; Tran, Vinh; Hederos, Markus; Dekany, Gyula; Tellier, Charles

    2016-03-01

    Human milk oligosaccharides (HMOs) are recognized as benefiting breast-fed infants in multiple ways. As a result, there is growing interest in the synthesis of HMOs mimicking their natural diversity. Most HMOs are fucosylated oligosaccharides. α-l-Fucosidases catalyze the hydrolysis of α-l-fucose from the non-reducing end of a glucan. They fall into the glycoside hydrolase GH29 and GH95 families. The GH29 family fucosidases display a classic retaining mechanism and are good candidates for transfucosidase activity. We recently demonstrated that the α-l-fucosidase from Thermotoga maritima (TmαFuc) from the GH29 family can be evolved into an efficient transfucosidase by directed evolution ( Osanjo et al. 2007). In this work, we developed semi-rational approaches to design an α-l-transfucosidase starting with the α-l-fucosidase from commensal bacteria Bifidobacterium longum subsp. infantis (BiAfcB, Blon_2336). Efficient fucosylation was obtained with enzyme mutants (L321P-BiAfcB and F34I/L321P-BiAfcB) enabling in vitro synthesis of lactodifucotetraose, lacto-N-fucopentaose II, lacto-N-fucopentaose III and lacto-N-difucohexaose I. The enzymes also generated more complex HMOs like fucosylated para-lacto-N-neohexaose (F-p-LNnH) and mono- or difucosylated lacto-N-neohexaose (F-LNnH-I, F-LNnH-II and DF-LNnH). It is worth noting that mutation at these two positions did not result in a strong decrease in the overall activity of the enzyme, which makes these variants interesting candidates for large-scale transfucosylation reactions. For the first time, this work provides an efficient enzymatic method to synthesize the majority of fucosylated HMOs. PMID:26582607

  7. Toward a Molecular Understanding of Metal Transport by P1B-Type ATPases

    PubMed Central

    Rosenzweig, Amy C.; Argüello, José M.

    2012-01-01

    The P1B family of P-type ATPases couples the transport of cytoplasmic transition metals across biological membranes to the hydrolysis of ATP. These ubiquitous transporters function in maintaining cytoplasmic metal quotas and in the assembly of metalloproteins, and have been classified into subfamilies (P1B-1–P1B-5) on the basis of their transported substrates (Cu+, Zn2+, Cu2+, and Co2+) and signature sequences in their transmembrane segments. In addition, each subgroup presents a characteristic membrane topology and specific regulatory cytoplasmic metal-binding domains. In recent years, significant major aspects of their transport mechanism have been described, including the stoichiometry of transport and the delivery of substrates to transport sites by metallochaperones. Toward understanding their structure, the metal coordination by transport sites has been characterized for Cu+ and Zn2+-ATPases. In addition, atomic resolution structures have been determined, providing key insight into the elements that enable transition metal transport. Because the Cu+-transporting ATPases are found in humans and are linked to disease, this subfamily has been the focus of intense study. As a result, significant progress has been made toward understanding Cu+-ATPase function on the molecular level, using both the human proteins and the bacterial homologs, most notably the CopA proteins from Archaeoglobus fulgidus, Bacillus subtilis, and Thermotoga maritima. This chapter thus focuses on the mechanistic and structural information obtained by studying these latter Cu+-ATPases, with some consideration of how these aspects might differ for the other subfamilies of P1B-ATPases. PMID:23046649

  8. Metagenomic cellulases highly tolerant towards the presence of ionic liquids--linking thermostability and halotolerance.

    PubMed

    Ilmberger, Nele; Meske, Diana; Juergensen, Julia; Schulte, Michael; Barthen, Peter; Rabausch, Ulrich; Angelov, Angel; Mientus, Markus; Liebl, Wolfgang; Schmitz, Ruth A; Streit, Wolfgang R

    2012-07-01

    Cellulose is an important renewable resource for the production of bioethanol and other valuable compounds. Several ionic liquids (ILs) have been described to dissolve water-insoluble cellulose and/or wood. Therefore, ILs would provide a suitable reaction medium for the enzymatic hydrolysis of cellulose if cellulases were active and stable in the presence of high IL concentrations. For the discovery of novel bacterial enzymes with elevated stability in ILs, metagenomic libraries from three different hydrolytic communities (i.e. an enrichment culture inoculated with an extract of the shipworm Teredo navalis, a biogas plant sample and elephant faeces) were constructed and screened. Altogether, 14 cellulolytic clones were identified and subsequently assayed in the presence of six different ILs. The most promising enzymes, CelA2, CelA3 (both derived from the biogas plant) and CelA84 (derived from elephant faeces), showed high activities (up to 6.4 U/mg) in the presence of 30% (v/v) ILs. As these enzymes were moderately thermophilic and halotolerant, they retained 40% to 80% relative activity after 34 days in 4 M NaCl, and they were benchmarked with two thermostable enzymes, CelA from Thermotoga maritima and Cel5K from a metagenome library derived from Avachinsky crater in Kamchatka. These enzymes also exhibited high activity (up to 11.1 U/mg) in aqueous IL solutions (30% (v/v)). Some of the enzymes furthermore exhibited remarkable stability in 60% (v/v) IL. After 4 days, CelA3 and Cel5K retained up to 79% and 100% of their activity, respectively. Altogether, the obtained data suggest that IL tolerance appears to correlate with thermophilicity and halotolerance. PMID:22143172

  9. Depositional History of a Saline Blue Hole on Eleuthera Island, Bahamas: Implications for Sea Level History and Climate Change

    NASA Astrophysics Data System (ADS)

    Brady, K.; Bernard, M.; Bender, S.; Roy, Z.; Boush, L. E.; Myrbo, A.; Brown, E. T.; Buynevich, I. V.; Berman, M.; Gnivecki, P.

    2013-12-01

    Physical, chemical and biological properties of Duck Pond Blue Hole (DPBH), located on the southern portion of Eleuthera Island, Bahamas, were examined to analyze its depositional history and the record of climate and anthropogenic changes on the island. DPBH is a small (.001 km2), circular inland blue hole with average salinity ranging from 20-28 ppt and a maximum depth of ~8 m. Sediment cores were recovered using standard piston coring techniques along a transect consisting of three sites yielding cores of varying lengths--170, 155 and 151 cm, respectively. Radiocarbon dating, x-ray fluorescence (XRF), grain size analysis, loss on ignition (LOI), smear slide and mollusk processing and identification were performed on the cores. The sediment recovered is dominated by brown, tan and white carbonate sand with varying amounts of organic matter. Sedimentation rates vary between 0.1-0.5 mm/year. Mollusks are found throughout the cores but gastropods dominate in the upper portions, which date from 2000 years BP to present day. Bivalves are abundant in intervals dating between 5000 and 2500 years BP. The most common bivalve species were Polymesoda maritima, Anomalocardis auberiana and Ervilia concentrica. The most common gastropods were Cerithidea costata and Cerithium lutosum. Drill holes made by predaceous gastropods occur on some of the gastropods, but on most of the bivalves. Drilling frequency is highest between 5000 and 2500 years BP even though gastropods are rarely preserved in that interval. Through smear slide analysis, diatoms, forams and ostracodes were also found to occur throughout the core record. Peaks in Fe and Sr from XRF scans at 0.5 cm intervals may represent records of high atmospheric dust concentrations and sea level fluctuations, respectively. Plotting mollusk bed depths versus calibrated age reveals a sea level rise over the last 6000 years that includes a rapid rise and subsequent fall at ~2500 year BP.

  10. Structural Basis for Substrate Binding and the Catalytic Mechanism of Type III Pantothenate Kinase

    SciTech Connect

    Yang, Kun; Strauss, Erick; Huerta, Carlos; Zhang, Hong

    2008-07-15

    Pantothenate kinase (PanK) catalyzes the first step of the universal five-step coenzyme A (CoA) biosynthetic pathway. The recently characterized type III PanK (PanK-III, encoded by the coaX gene) is distinct in sequence, structure and enzymatic properties from both the long-known bacterial type I PanK (PanK-I, exemplified by the Escherichia coli CoaA protein) and the predominantly eukaryotic type II PanK (PanK-II). PanK-III enzymes have an unusually high K{sub m} for ATP, are resistant to feedback inhibition by CoA, and are unable to utilize the N-alkylpantothenamide family of pantothenate analogues as alternative substrates, thus making type III PanK ineffective in generating CoA analogues as antimetabolites in vivo. Previously, we reported the crystal structure of the PanK-III from Thermotoga maritima and identified it as a member of the 'acetate and sugar kinase/heat shock protein 70/actin' (ASKHA) superfamily. Here we report the crystal structures of the same PanK-III in complex with one of its substrates (pantothenate), its product (phosphopantothenate) as well as a ternary complex structure of PanK-III with pantothenate and ADP. These results are combined with isothermal titration calorimetry experiments to present a detailed structural and thermodynamic characterization of the interactions between PanK-III and its substrates ATP and pantothenate. Comparison of substrate binding and catalytic sites of PanK-III with that of eukaryotic PanK-II revealed drastic differences in the binding modes for both ATP and pantothenate substrates, and suggests that these differences may be exploited in the development of new inhibitors specifically targeting PanK-III.

  11. Structure of the invertebrate fauna in salt marshes of the Wadden Sea coast of Schleswig-Holstein influenced by sheep-grazing

    NASA Astrophysics Data System (ADS)

    Meyer, H.; Fock, H.; Haase, A.; Reinke, H. D.; Tulowitzki, I.

    1995-03-01

    Results of investigations on the influence of five different sheep grazing intensities on the invertebrate fauna of two mainland salt marsh sites of the German Wadden Sea coast are presented for the years 1990 and 1991. The investigation of the invertebrate fauna has been carried out since 1989 in the Puccinellia maritima zone, and the Festuca-Puccinellia as well as the Festuca-Armeria zones, with trapping transects arranged along an inundation gradient. Apart from specific biotic effects, grazing causes changes in environmental characteristics. Effects on microclimate comprise higher ranges of variance in soil-surface temperature on grazed sites. Decreasing food resources caused by grazing bring disadvantages to herbivores, the major part of the invertebrate fauna, due to merotope destruction (e. g. inflorescences of Aster tripolium) and the decline of host plant stands (e. g. A. tripolium, Plantago ssp.). Flower visitors and pollen feeding species that depend on A. tripolium have become extinct. Increasing food resources, caused by grazing, lead to higher population densities of a few specialized grass-feeding and surface-grazing invertebrates (e. g. Mayetiola ssp., Psammotettix putoni, Bledius tricornis). Soil characteristics in the lower salt marsh have not been altered significantly by grazing; hence, the direct effect of grazing and trampling leads to a decrease in population density of many species such as Assiminea grayana, Orchestia gammarellus and collembolans. The biomass and abundance of detritivores and many herbivores increased from 1990 to 1991 on the totally grazed fields, whereas predators diminished in numbers at the same time. A descriptive model is presented, involving grazing, winter temperature, and precipitation as basic factors.

  12. Domain-swapping of mesophilic xylanase with hyper-thermophilic glucanase

    PubMed Central

    2012-01-01

    Background Domain fusion is limited at enzyme one terminus. The issue was explored by swapping a mesophilic Aspergillus niger GH11 xylanase (Xyn) with a hyper-thermophilic Thermotoga maritima glucanase (Glu) to construct two chimeras, Xyn-Glu and Glu-Xyn, with an intention to create thermostable xylanase containing glucanase activity. Results When expressed in E. coli BL21(DE3), the two chimeras exhibited bi-functional activities of xylanase and glucanase. The Xyn-Glu Xyn moiety had optimal reaction temperature (Topt) at 50 °C and thermal in-activation half-life (t1/2) at 50 °C for 47.6 min, compared to 47 °C and 17.6 min for the Xyn. The Glu-Xyn Xyn moiety had equivalent Topt to and shorter t1/2 (5.2 min) than the Xyn. Both chimera Glu moieties were more thermostable than the Glu, and the three enzyme Topt values were higher than 96 °C. The Glu-Xyn Glu moiety optimal pH was 5.8, compared to 3.8 for the Xyn-Glu Glu moiety and the Glu. Both chimera two moieties cooperated with each other in degrading substrates. Conclusions Domain-swapping created different effects on each moiety properties. Fusing the Glu domain at C-terminus increased the xylanase thermostability, but fusing the Glu domain at N-terminus decreased the xylanase thermostability. Fusing the Xyn domain at either terminus increased the glucanase thermostability, and fusing the Xyn domain at C-terminus shifted the glucanase pH property 2 units higher towards alkaline environments. Fusing a domain at C-terminus contributes more to enzyme catalytic activity; whereas, fusing a bigger domain at N-terminus disturbs enzyme substrate binding affinity. PMID:22676349

  13. Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

    PubMed Central

    Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

    2010-01-01

    The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the millisecond time scale that appears to be frozen in the crystals. These observations suggest that a search for molecular regions showing increased structural disorder and slow dynamic processes in solution while being well ordered in the corresponding crystal structure might be a valid initial step in the challenge of identifying putative active sites in functionally unannotated proteins with known three-dimensional structure. PMID:20944236

  14. Ancestral Patterning of Tergite Formation in a Centipede Suggests Derived Mode of Trunk Segmentation in Trilobites

    PubMed Central

    Ortega-Hernández, Javier; Brena, Carlo

    2012-01-01

    Trilobites have a rich and abundant fossil record, but little is known about the intrinsic mechanisms that orchestrate their body organization. To date, there is disagreement regarding the correspondence, or lack thereof, of the segmental units that constitute the trilobite trunk and their associated exoskeletal elements. The phylogenetic position of trilobites within total-group Euarthropoda, however, allows inferences about the underlying organization in these extinct taxa to be made, as some of the fundamental genetic processes for constructing the trunk segments are remarkably conserved among living arthropods. One example is the expression of the segment polarity gene engrailed, which at embryonic and early postembryonic stages is expressed in extant panarthropods (i.e. tardigrades, onychophorans, euarthropods) as transverse stripes that define the posteriormost region of each trunk segment. Due to its conservative morphology and allegedly primitive trunk tagmosis, we have utilized the centipede Strigamia maritima to study the correspondence between the expression of engrailed during late embryonic to postembryonic stages, and the development of the dorsal exoskeletal plates (i.e. tergites). The results corroborate the close correlation between the formation of the tergite borders and the dorsal expression of engrailed, and suggest that this association represents a symplesiomorphy within Euarthropoda. This correspondence between the genetic and phenetic levels enables making accurate inferences about the dorsoventral expression domains of engrailed in the trunk of exceptionally preserved trilobites and their close relatives, and is suggestive of the widespread occurrence of a distinct type of genetic segmental mismatch in these extinct arthropods. The metameric organization of the digestive tract in trilobites provides further support to this new interpretation. The wider evolutionary implications of these findings suggest the presence of a derived morphogenetic patterning mechanism responsible for the reiterated occurrence of different types of trunk dorsoventral segmental mismatch in several phylogenetically distant, extinct and extant, arthropod groups. PMID:23285116

  15. A New Root-Knot Nematode Parasitizing Sea Rocket from Spanish Mediterranean Coastal Dunes: Meloidogyne dunensis n. sp. (Nematoda: Meloidogynidae)

    PubMed Central

    Palomares Rius, J. E.; Vovlas, N.; Troccoli, A.; Liébanas, G.; Landa, B. B.; Castillo, P.

    2007-01-01

    High infection rates of European sea rocket feeder roots by an unknown root-knot nematode were found in a coastal dune soil at Cullera (Valencia) in central eastern Spain. Morphometry, esterase and malate dehydrogenase electrophoretic phenotypes and phylogenetic trees demonstrated that this nematode species differs clearly from other previously described root-knot nematodes. Studies of host-parasite relationships showed a typical susceptible reaction in naturally infected European sea rocket plants and in artificially inoculated tomato (cv. Roma) and chickpea (cv. UC 27) plants. The species is herein described and illustrated and named as Meloidogyne dunensis n. sp. The new root-knot nematode can be distinguished from other Meloidogyne spp. by: (i) perineal pattern rounded-oval, formed of numerous fine dorsal and ventral cuticle striae and ridges, lateral fields clearly visible; (ii) female excretory pore at the level of stylet knobs, EP/ST ratio 1.6; (iii) second-stage juveniles with hemizonid located 1 to 2 annuli anteriorly to excretory pore and long, narrow, tapering tail; and (iv) males with lateral fields composed of four incisures anteriorly and posteriorly, while six distinct incisures are observed for large part at mid-body. Phylogenetic trees derived from distance and maximum parsimony analyses based on 18S, ITS1–5.8S-ITS2 and D2-D3 of 28S rDNA showed that M. dunensis n. sp. can be differentiated from all described root-knot nematode species, and it is clearly separated from other species with resemblance in morphology, such as M. duytsi, M. maritima, M. mayaguensis and M. minor. PMID:19259488

  16. The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects.

    PubMed

    Figiel, Małgorzata; Chon, Hyongi; Cerritelli, Susana M; Cybulska, Magdalena; Crouch, Robert J; Nowotny, Marcin

    2011-03-25

    RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoimmune disorder. The 3.1 Å crystal structure of human RNase H2 presented here allowed us to map the positions of all 29 mutations found in Aicardi-Goutières syndrome patients, several of which were not visible in the previously reported mouse RNase H2. We propose the possible effects of these mutations on the protein stability and function. Bacterial and eukaryotic RNases H2 differ in composition and substrate specificity. Bacterial RNases H2 are monomeric proteins and homologs of the eukaryotic RNases H2 catalytic subunit, which in addition possesses two accessory proteins. The eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and (5')RNA-DNA(3')/DNA junction hybrids as substrates with similar efficiency, whereas bacterial RNases H2 are highly specialized in the recognition of the (5')RNA-DNA(3') junction and very poorly cleave RNA/DNA hybrids in the presence of Mg(2+) ions. Using the crystal structure of the Thermotoga maritima RNase H2-substrate complex, we modeled the human RNase H2-substrate complex and verified the model by mutational analysis. Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition. PMID:21177858

  17. The Structural and Biochemical Characterization of Human RNase H2 Complex Reveals the Molecular Basis for Substrate Recognition and Aicardi-Goutières Syndrome Defects*

    PubMed Central

    Figiel, Małgorzata; Chon, Hyongi; Cerritelli, Susana M.; Cybulska, Magdalena; Crouch, Robert J.; Nowotny, Marcin

    2011-01-01

    RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoimmune disorder. The 3.1 Å crystal structure of human RNase H2 presented here allowed us to map the positions of all 29 mutations found in Aicardi-Goutières syndrome patients, several of which were not visible in the previously reported mouse RNase H2. We propose the possible effects of these mutations on the protein stability and function. Bacterial and eukaryotic RNases H2 differ in composition and substrate specificity. Bacterial RNases H2 are monomeric proteins and homologs of the eukaryotic RNases H2 catalytic subunit, which in addition possesses two accessory proteins. The eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and (5′)RNA-DNA(3′)/DNA junction hybrids as substrates with similar efficiency, whereas bacterial RNases H2 are highly specialized in the recognition of the (5′)RNA-DNA(3′) junction and very poorly cleave RNA/DNA hybrids in the presence of Mg2+ ions. Using the crystal structure of the Thermotoga maritima RNase H2-substrate complex, we modeled the human RNase H2-substrate complex and verified the model by mutational analysis. Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition. PMID:21177858

  18. Ocean acidification and the loss of phenolic substances in marine plants.

    PubMed

    Arnold, Thomas; Mealey, Christopher; Leahey, Hannah; Miller, A Whitman; Hall-Spencer, Jason M; Milazzo, Marco; Maers, Kelly

    2012-01-01

    Rising atmospheric CO(2) often triggers the production of plant phenolics, including many that serve as herbivore deterrents, digestion reducers, antimicrobials, or ultraviolet sunscreens. Such responses are predicted by popular models of plant defense, especially resource availability models which link carbon availability to phenolic biosynthesis. CO(2) availability is also increasing in the oceans, where anthropogenic emissions cause ocean acidification, decreasing seawater pH and shifting the carbonate system towards further CO(2) enrichment. Such conditions tend to increase seagrass productivity but may also increase rates of grazing on these marine plants. Here we show that high CO(2) / low pH conditions of OA decrease, rather than increase, concentrations of phenolic protective substances in seagrasses and eurysaline marine plants. We observed a loss of simple and polymeric phenolics in the seagrass Cymodocea nodosa near a volcanic CO(2) vent on the Island of Vulcano, Italy, where pH values decreased from 8.1 to 7.3 and pCO(2) concentrations increased ten-fold. We observed similar responses in two estuarine species, Ruppia maritima and Potamogeton perfoliatus, in in situ Free-Ocean-Carbon-Enrichment experiments conducted in tributaries of the Chesapeake Bay, USA. These responses are strikingly different than those exhibited by terrestrial plants. The loss of phenolic substances may explain the higher-than-usual rates of grazing observed near undersea CO(2) vents and suggests that ocean acidification may alter coastal carbon fluxes by affecting rates of decomposition, grazing, and disease. Our observations temper recent predictions that seagrasses would necessarily be "winners" in a high CO(2) world. PMID:22558120

  19. Contribution to the knowledge of the veterinary science and of the ethnobotany in Calabria region (Southern Italy)

    PubMed Central

    Passalacqua, Nicodemo G; De Fine, Giuseppe; Guarrera, Paolo Maria

    2006-01-01

    Background A series of preliminary research projects on plants used in Calabria (Southern Italy) in veterinary science and in other ethno-botanical fields (minor nourishment, domestic and handicraft sector) was carried out in the last twenty years. From the ethno-botanical point of view, Calabria is one of the most interesting region, since in the ancient times it was subject to the dominant cultures of several people (Greeks, Romans, Byzantines, Arabs, Normans etc.). Until some decades ago the road network was poorly developed and villages were isolated, so that the culture of the "subsistence" and some archaic customs were kept. Methods Data were collected by means of "open" interviews to farmers, shepherds and housewives in the last twenty years. More than 100 informants were interviewed, mostly over 50 years old. Plants were identified by local informants through gathering in the area or through examination of the fresh plants collected by the researchers. The collected data were compared with pharmacobotanical papers mainly of southern Italy and with other studies, in order to highlight novelties or concordances of uses. Results The use of 62 taxa distributed into 34 families are described. Among these, 8 are or were employed in veterinary science, 8 as anti-parasitic agents, 19 in minor nourishment, 5 as seasoning, 38 for other uses. Some toxic species for cattle are also mentioned. Conclusion Among the major findings: the use of Helleborus bocconei for bronchitis of bovines and of Scrophularia canina for lameness in veterinary science; Nerium oleander and Urginea maritima as anti-parasitic agents; Epilobium angustifolium, Centaurea napifolia L. and C. sphaerocephala L. in minor nourishment. PMID:17156472

  20. Two Alternative Pathways for the Synthesis of the Rare Compatible Solute Mannosylglucosylglycerate in Petrotoga mobilis▿

    PubMed Central

    Fernandes, Chantal; Mendes, Vitor; Costa, Joana; Empadinhas, Nuno; Jorge, Carla; Lamosa, Pedro; Santos, Helena; da Costa, Milton S.

    2010-01-01

    The compatible solute mannosylglucosylglycerate (MGG), recently identified in Petrotoga miotherma, also accumulates in Petrotoga mobilis in response to hyperosmotic conditions and supraoptimal growth temperatures. Two functionally connected genes encoding a glucosyl-3-phosphoglycerate synthase (GpgS) and an unknown glycosyltransferase (gene Pmob_1143), which we functionally characterized as a mannosylglucosyl-3-phosphoglycerate synthase and designated MggA, were identified in the genome of Ptg. mobilis. This enzyme used the product of GpgS, glucosyl-3-phosphoglycerate (GPG), as well as GDP-mannose to produce mannosylglucosyl-3-phosphoglycerate (MGPG), the phosphorylated precursor of MGG. The MGPG dephosphorylation was determined in cell extracts, and the native enzyme was partially purified and characterized. Surprisingly, a gene encoding a putative glucosylglycerate synthase (Ggs) was also identified in the genome of Ptg. mobilis, and an active Ggs capable of producing glucosylglycerate (GG) from ADP-glucose and d-glycerate was detected in cell extracts and the recombinant enzyme was characterized, as well. Since GG has never been identified in this organism nor was it a substrate for the MggA, we anticipated the existence of a nonphosphorylating pathway for MGG synthesis. We putatively identified the corresponding gene, whose product had some sequence homology with MggA, but it was not possible to recombinantly express a functional enzyme from Ptg. mobilis, which we named mannosylglucosylglycerate synthase (MggS). In turn, a homologous gene from Thermotoga maritima was successfully expressed, and the synthesis of MGG was confirmed from GDP-mannose and GG. Based on the measurements of the relevant enzyme activities in cell extracts and on the functional characterization of the key enzymes, we propose two alternative pathways for the synthesis of the rare compatible solute MGG in Ptg. mobilis. PMID:20061481

  1. Diversity and Plant Growth Promoting Capacity of Endophytic Fungi Associated with Halophytic Plants from the West Coast of Korea

    PubMed Central

    Khalmuratova, Irina; Kim, Hyun; Nam, Yoon-Jong; Oh, Yoosun; Jeong, Min-Ji; Choi, Hye-Rim; You, Young-Hyun; Choo, Yeon-Sik; Lee, In-Jung; Shin, Jae-Ho

    2015-01-01

    Five halophytic plant species, Suaeda maritima, Limonium tetragonum, Suaeda australis, Phragmites australis, and Suaeda glauca Bunge, which are native to the Muan salt marsh of South Korea, were examined for fungal endophytes by sequencing the internal transcribed spacer (ITS) region containing ITS1, 5.8S rRNA, and ITS2. In total, 160 endophytic fungal strains were isolated and identified from the roots of the 5 plant species. Taxonomically, all 160 strains belonged to the phyla Ascomycota, Basidiomycota, and Zygomycota. The most dominant genus was Fusarium, followed by the genera Penicillium and Alternaria. Subsequently, using 5 statistical methods, the diversity indices of the endophytes were determined at genus level. Among these halophytic plants, P. australis was found to host the greatest diversity of endophytic fungi. Culture filtrates of endophytic fungi were treated to Waito-C rice seedlings for plant growth-promoting effects. The fungal strain Su-3-4-3 isolated from S. glauca Bunge provide the maximum plant length (20.1 cm) in comparison with wild-type Gibberella fujikuroi (19.6 cm). Consequently, chromatographic analysis of the culture filtrate of Su-3-4-3 showed the presence of physiologically active gibberellins, GA1 (0.465 ng/mL), GA3 (1.808 ng/mL) along with other physiologically inactive GA9 (0.054 ng/mL) and GA24 (0.044 ng/mL). The fungal isolate Su-3-4-3 was identified as Talaromyces pinophilus. PMID:26839496

  2. Crystal structure of α-galactosidase from Lactobacillus acidophilus NCFM: insight into tetramer formation and substrate binding.

    PubMed

    Fredslund, Folmer; Hachem, Maher Abou; Larsen, René Jonsgaard; Sørensen, Pernille Gerd; Coutinho, Pedro M; Lo Leggio, Leila; Svensson, Birte

    2011-09-23

    Lactobacillus acidophilus NCFM is a probiotic bacterium known for its beneficial effects on human health. The importance of α-galactosidases (α-Gals) for growth of probiotic organisms on oligosaccharides of the raffinose family present in many foods is increasingly recognized. Here, the crystal structure of α-Gal from L. acidophilus NCFM (LaMel36A) of glycoside hydrolase (GH) family 36 (GH36) is determined by single-wavelength anomalous dispersion. In addition, a 1.5