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1

Family-group Names for Earwigs (Dermaptera)  

Microsoft Academic Search

Family-group names for all taxa of earwigs (living and extinct) are listed with dates and sources indicated; in total 85 entries are recorded along with a single entry of dubious taxonomic identity (i.e., Ocelliidae, nomen dubium, a name apparently applied to a fossil earwig nymph of uncertain status and identity). This survey revealed two instances in which currently accepted names

MICHAEL S. ENGEL; FABIAN HAAS

2007-01-01

2

Multifunctional weaponry: the chemical defenses of earwigs.  

PubMed

Earwigs protect themselves against predators using pincer-like cerci and/or malodorous exudates secreted from abdominal glands. Little is known about the chemistry of these secretions and their potential functions. However, because earwigs live in aggregations and overwinter in soil, they are exposed to high microbial loads throughout their lifecycle, and we therefore hypothesized that the secretions are used not only to deter predators but also to combat pathogens and parasites in their environment. We analyzed the defensive secretions of the European earwig Forficula auricularia, the short-winged earwig Apterygida media and the woodland earwig Chelidurella guentheri by gas chromatography-mass spectrometry. The secretions of all three species contained 2-methyl-1,4-benzoquinone and 2-ethyl-1,4-benzoquinone, whereas A. media also produced 2,3-dimethyl-1,4-benzoquinone and 2-ethyl-3-methyl-1,4-benzoquinone. The latter has not been identified in the exudates of insects before. The composition and/or quantity of these components were species-specific and partially sex-specific. All secretions showed antimicrobial activity against Gram-positive and Gram-negative bacteria as well as two entomopathogenic fungi. Furthermore, the secretion of F. auricularia displayed nematicidal activity against Caenorhabditis elegans. Our data support the hypothesis that earwig secretions are multifunctional, serving both to deter predators and sanitize the microenvironment. PMID:24090659

Gasch, Tina; Schott, Matthias; Wehrenfennig, Christoph; Düring, Rolf-Alexander; Vilcinskas, Andreas

2013-12-01

3

Dihydrodipicolinate synthase from Thermotoga maritima  

PubMed Central

DHDPS (dihydrodipicolinate synthase) catalyses the branch point in lysine biosynthesis in bacteria and plants and is feedback inhibited by lysine. DHDPS from the thermophilic bacterium Thermotoga maritima shows a high level of heat and chemical stability. When incubated at 90 °C or in 8 M urea, the enzyme showed little or no loss of activity, unlike the Escherichia coli enzyme. The active site is very similar to that of the E. coli enzyme, and at mesophilic temperatures the two enzymes have similar kinetic constants. Like other forms of the enzyme, T. maritima DHDPS is a tetramer in solution, with a sedimentation coefficient of 7.2 S and molar mass of 133 kDa. However, the residues involved in the interface between different subunits in the tetramer differ from those of E. coli and include two cysteine residues poised to form a disulfide bond. Thus the increased heat and chemical stability of the T. maritima DHDPS enzyme is, at least in part, explained by an increased number of inter-subunit contacts. Unlike the plant or E. coli enzyme, the thermophilic DHDPS enzyme is not inhibited by (S)-lysine, suggesting that feedback control of the lysine biosynthetic pathway evolved later in the bacterial lineage.

Pearce, F. Grant; Perugini, Matthew A.; Mckerchar, Hannah J.; Gerrard, Juliet A.

2006-01-01

4

Tissue distribution, characterization and in vitro inhibition of B-esterases in the earwig Forficula auricularia.  

PubMed

Earwigs are important natural enemies of numerous pests in pome fruit orchards worldwide. Studying the effects of agricultural practices on these biological control agents is important for understanding its vulnerability in the field. The aim of this study was to characterize the B-esterase activities in the European earwig Forficula auricularia and to evaluate in vitro its sensitivity to organophosphate and carbamate pesticides. Acetylcholinesterase (AChE) activity was mainly measured with 1.5mM acetylthiocholine as the substrate in the microsomal fraction of earwig heads (70% of total AChE activity). Carboxylesterase (CbE) activities were measured with three substrates [5mM 4-nitrophenyl acetate (4-NPA), 1mM 4-nitrophenyl valerate (4-NPV), and 2mM ?-naphtyl acetate (?-NA)] to examine different isoenzymes, which were present mainly in the cytosolic fraction (about 70-88% of total activities) of all earwig tissues. CbE activity was higher than AChE activity, especially with ?-NA, then 4-NPA and lastly 4-NPV. Chlorpyrifos-oxon an organophosphate, and carbaryl a carbamate pesticide, inhibited AChE and CbE activities in a concentration-dependent manner. Earwig CbE activities showed a stronger sensitivity to organophosphate than AChE, with the strongest effect for chlorpyrifos-oxon on male carboxylesterase activities. CbE and AChE showed about the same sensitivity to carbamate pesticides regardless of sex. These results suggest that B-type esterases in the European earwig F.auricularia are suitable biomarkers of pesticide exposure. PMID:25048940

Malagnoux, Laure; Capowiez, Yvan; Rault, Magali

2014-10-01

5

Transitional fossil earwigs - a missing link in Dermaptera evolution  

PubMed Central

Background The Dermaptera belongs to a group of winged insects of uncertain relationship within Polyneoptera, which has expanded anal region and adds numerous anal veins in the hind wing. Evolutional history and origin of Dermaptera have been in contention. Results In this paper, we report two new fossil earwigs in a new family of Bellodermatidae fam. nov. The fossils were collected from the Jiulongshan Formation (Middle Jurassic) in Inner Mongolia, northeast China. This new family, characterized by an unexpected combination of primitive and derived characters, is bridging the missing link between suborders of Archidermaptera and Eodermaptera. Phylogenetic analyses support the new family to be a new clade at the base of previously defined Eodermaptera and to be a stem group of (Eodermaptera+Neodermaptera). Conclusion Evolutional history and origin of Dermaptera have been in contention, with dramatically different viewpoints by contemporary authors. It is suggested that the oldest Dermaptera might possibly be traced back to the Late Triassic-Early Jurassic and they had divided into Archidermaptera and (Eodermaptera+Neodermaptera) in the Middle Jurassic.

2010-01-01

6

Wigeongrass ('Ruppia maritima'): A Literature Review.  

National Technical Information Service (NTIS)

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 plan...

H. A. Kantrud

1991-01-01

7

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

NASA Astrophysics Data System (ADS)

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.

Kamimura, Yoshitaka; Matsuo, Yoh

2001-11-01

8

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

PubMed Central

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.

Kocarek, Petr; John, Vaclav; Hulva, Pavel

2013-01-01

9

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

PubMed Central

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.

Pichon, Samuel; Arbore, Roberto; Kuhn-Buhlmann, Simone; Kolliker, Mathias; Walser, Jean-Claude

2014-01-01

10

Cloning and characterization of Thermotoga maritima ?-glucuronidase  

Microsoft Academic Search

The putative ?-glucuronidase from Thermotoga maritima, comprising 563 amino acid residues conjugated with a Hisx6 tag, was cloned and expressed in Escherichia coli. The enzyme has a moderately broad specificity, hydrolysing a range of p-nitrophenyl glycoside substrates, but has greatest activity on p-nitrophenyl ?-d-glucosiduronic acid (kcat=68s?1, kcat\\/KM= 4.5×105M?1s?1). The enzyme also shows a relatively broad pH-dependence with activity from pH4.5

Hamzah M. Salleh; Johannes Müllegger; Stephen P. Reid; Wing Y. Chan; Jiyoung Hwang; R. Antony J. Warren; Stephen G. Withers

2006-01-01

11

Environmental and genetic determinants of the male forceps length dimorphism in the European earwig Forficula auricularia L  

Microsoft Academic Search

Male dimorphisms are particularly conspicuous examples of alternative reproductive strategies. The male forceps length dimorphism\\u000a in the European earwig Forficula auricularia has long been considered an example of a status- (body size) dependent male dimorphism. In this paper, I test three hypotheses\\u000a relating to the dimorphism of F. auricularia. First, that the dimorphism is status dependent and determined by nutrition.

Joseph L. Tomkins

1999-01-01

12

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...

13

Wigeongrass (Ruppia maritima L.): a literature review  

USGS Publications Warehouse

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.

Kantrud, H. A.

1991-01-01

14

When it is costly to have a caring mother: food limitation erases the benefits of parental care in earwigs.  

PubMed

The aggregation of parents with offspring is generally associated with different forms of care that improve offspring survival at potential costs to parents. Under poor environments, the limited amount of resources available can increase the level of competition among family members and consequently lead to adaptive changes in parental investment. However, it remains unclear as to what extent such changes modify offspring fitness, particularly when offspring can survive without parents such as in the European earwig, Forficula auricularia. Here, we show that under food restriction, earwig maternal presence decreased offspring survival until adulthood by 43 per cent. This effect was independent of sibling competition and was expressed after separation from the female, indicating lasting detrimental effects. The reduced benefits of maternal presence on offspring survival were not associated with higher investment in future reproduction, suggesting a condition-dependent effect of food restriction on mothers and local mother-offspring competition for food. Overall, these findings demonstrate for the first time a long-term negative effect of maternal presence on offspring survival in a species with maternal care, and highlight the importance of food availability in the early evolution of family life. PMID:22535642

Meunier, Joël; Kölliker, Mathias

2012-08-23

15

Humic substances in estuarine soils colonized by Spartina maritima  

NASA Astrophysics Data System (ADS)

This study characterizes humic substances (HS) from two soils colonized by Spartina maritima at different physiographical positions in estuarine environments on the north-western coast of the Iberian Peninsula: the Villaviciosa site, a stand close to the main tidal channel, and the Ortigueira site, located in the low salt marsh. Humic and fulvic acids were extracted from the soils and characterized qualitatively by the following spectroscopic techniques: Fourier transform infrared spectroscopy, fluorescence spectroscopy and solid-state 13C nuclear magnetic resonance. The characterized HS showed a predominance of low humified compounds with a high proportion of aliphatic components and a low degree of aromaticity. The HS composition differed substantially between sites. In the Villaviciosa soil, the large amount of nonpolar aliphatic components and the very low degree of aromaticity may indicate a significant contribution of marine organic matter and/or microbial material to the HS. However, in the HS from the Ortigueira soil, the higher proportion of polysaccharides together with the presence of lignin-derived compounds may indicate greater inputs of vascular plant material. The ?13C isotopic composition of the bulk soils highlights the large input of Spartina maritima debris to the Ortigueira site, whereas in the Villaviciosa site, organic contributions from this C4 vascular plant were not so evident. The results indicate that in these soils colonized by Spartina maritima, physiographical position has an important effect on the composition of soil HS and, therefore, must be considered in the study of organic matter characteristics in such estuarine environments.

Santín, Cristina; González-Pérez, Martha; Otero, Xosé Luis; Ángel Álvarez, Miguel; Macías, Felipe

2009-03-01

16

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

PubMed Central

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.

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

2010-01-01

17

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...

18

Synergistic TRAIL sensitizers from Barleria alluaudii and Diospyros maritima#  

PubMed Central

Barleria alluaudii and Diospyros maritima were both investigated as part of an ongoing search for synergistic TRAIL (tumor necrosis factor-?-related apoptosis-inducing ligand) sensitizers. As a result of this study, two naphthoquinone epoxides, 2,3-epoxy-2,3-dihydrolapachol (1) and 2,3-epoxy-2,3-dihydro-8-hydroxylapachol (2), both not previously isolated from natural sources, and the known 2-methyl anthraquinone (3) were identified from B. alluaudii. Time-dependent density functional theory (TD-DFT) calculations of electronic circular dichroism (ECD) spectra were utilized to establish the absolute configuration of 1 and 2. Additionally, five known naphthoquinone derivatives, maritinone (4), elliptinone (5), plumbagin (6), (+)-cis-isoshinanolone (7), and ethylidene-6,6?-biplumbagin (8) were isolated from D. maritima. Compounds 1, 2, and 4–6 showed varying levels of synergy with TRAIL. Maritinone (4) and elliptinone (5) showed the highest synergistic effect, with more than a three-fold increase in activity observed with TRAIL than with compound alone.

Whitson, Emily L.; Sun, Han; Thomas, Cheryl L.; Henrich, Curtis J.; Sayers, Thomas J.; McMahon, James B.; Griesinger, Christian; McKee, Tawnya C.

2012-01-01

19

Synergistic TRAIL sensitizers from Barleria alluaudii and Diospyros maritima.  

PubMed

Barleria alluaudii and Diospyros maritima were both investigated as part of an ongoing search for synergistic TRAIL (tumor necrosis factor-?-related apoptosis-inducing ligand) sensitizers. As a result of this study, two naphthoquinone epoxides, 2,3-epoxy-2,3-dihydrolapachol (1) and 2,3-epoxy-2,3-dihydro-8-hydroxylapachol (2), both not previously isolated from natural sources, and the known 2-methylanthraquinone (3) were identified from B. alluaudii. Time-dependent density functional theory (TD-DFT) calculations of electronic circular dichroism (ECD) spectra were utilized to establish the absolute configuration of 1 and 2. Additionally, five known naphthoquinone derivatives, maritinone (4), elliptinone (5), plumbagin (6), (+)-cis-isoshinanolone (7), and ethylidene-6,6'-biplumbagin (8), were isolated from D. maritima. Compounds 1, 2, and 4-6 showed varying levels of synergy with TRAIL. Maritinone (4) and elliptinone (5) showed the highest synergistic effect, with more than a 3-fold increase in activity observed with TRAIL than with compound alone. PMID:22313254

Whitson, Emily L; Sun, Han; Thomas, Cheryl L; Henrich, Curtis J; Sayers, Thomas J; McMahon, James B; Griesinger, Christian; McKee, Tawnya C

2012-03-23

20

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

PubMed Central

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.

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

2012-01-01

21

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

PubMed Central

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.

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

2010-01-01

22

The structure of the fructan sinistrin from Urginea maritima.  

PubMed

The structure of sinistrin from red squill (Urginea maritima) was determined by methylation analysis and 13C NMR spectroscopy, using the fructans from Pucinella peisonis and quack-grass (Agropyron repens) as reference substances. Application of the reductive cleavage method showed that, of the beta-D-fructofuranosyl residues in sinistrin, 33% were 1-linked, 19% were 6-linked, 25% were terminal, and 19% were 1,6-linked. The average dp was 31 and, of the 3.24% of alpha-D-glucopyranosyl residues, 0.54% were terminal and 2.70% were 6-substituted. The fructan of quack grass was also highly branched with a (2-->6)-linked backbone, terminal alpha-D-glucopyranosyl residues, and a dp of approximately 45. The fructan from Pucinella peisonis was slightly branched, with a dp of approximately 10 and a (2-->6)-linked backbone. PMID:1473105

Spies, T; Praznik, W; Hofinger, A; Altmann, F; Nitsch, E; Wutka, R

1992-11-01

23

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

PubMed

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

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

2012-11-28

24

Unusual fatty acid compositions of the hyperthermophilic archaeon Pyrococcus furiosus and the bacterium Thermotoga maritima.  

PubMed Central

The fatty acid compositions of the hyperthermophilic microorganisms Thermotoga maritima and Pyrococcus furiosus were studied and compared. A total of 37 different fatty acids were identified in T. maritima, including the novel 13,14-dimethyloctacosanedioic acid. In contrast, a total of 18 different fatty acids were characterized, as minor components, in P. furiosus, and these included saturated, monounsaturated, and dicarboxylic acids. This is the first report of fatty acids from an archaeon.

Carballeira, N M; Reyes, M; Sostre, A; Huang, H; Verhagen, M F; Adams, M W

1997-01-01

25

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle  

PubMed Central

The generation of genome-scale data is becoming more routine, yet the subsequent analysis of omics data remains a significant challenge. Here, an approach that integrates multiple omics datasets with bioinformatics tools was developed that produces a detailed annotation of several microbial genomic features. This methodology was used to characterize the genome of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data were generated for whole-genome resequencing, transcription start site (TSS) determination, transcriptome profiling, and proteome profiling. These datasets, analyzed in combination with bioinformatics tools, served as a basis for the improvement of gene annotation, the elucidation of transcription units (TUs), the identification of putative non-coding RNAs (ncRNAs), and the determination of promoters and ribosome binding sites. This revealed many distinctive properties of the T. maritima genome organization relative to other bacteria. This genome has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and ribosome binding sites showed increased sequence conservation relative to other bacteria. The 5?UTRs follow an atypical bimodal length distribution comprised of “Short” 5?UTRs (11–17 nt) and “Common” 5?UTRs (26–32 nt). Transcriptional regulation is limited by a lack of intergenic space for the majority of TUs. Lastly, a high fraction of annotated genes are expressed independent of growth state and a linear correlation of mRNA/protein is observed (Pearson r?=?0.63, p<2.2×10?16 t-test). These distinctive properties are hypothesized to be a reflection of this organism's hyperthermophilic lifestyle and could yield novel insights into the evolutionary trajectory of microbial life on earth.

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

2013-01-01

26

A seascape genetic analysis reveals strong biogeographical structuring driven by contrasting processes in the polyploid saltmarsh species Puccinellia maritima and Triglochin maritima.  

PubMed

Little is known about the processes shaping population structure in saltmarshes. It is expected that the sea should act as a powerful agent of dispersal. Yet, in contrast, import of external propagules into a saltmarsh is thought to be small. To determine the level of connectivity between saltmarsh ecosystems at a macro-geographical scale, we characterized and compared the population structure of two polyploid saltmarsh species, Puccinellia maritima and Triglochin maritima based on a seascape genetics approach. A discriminant analysis of principal components highlighted a genetic structure for both species arranged according to a regional pattern. Subsequent analysis based on isolation-by-distance and isolation-by-resistance frameworks indicated a strong role of coastal sediment transport processes in delimiting regional structure in P. maritima, while additional overland propagule dispersal was indicated for T. maritima. The identification and comparison of regional genetic structure and likely determining factors presented here allows us to understand the biogeographical units along the UK coast, between which barriers to connectivity occur not only at the species level but at the ecosystem scale. This information is valuable in plant conservation and community ecology and in the management and restoration of saltmarsh ecosystems. PMID:24862943

Rouger, R; Jump, A S

2014-07-01

27

Diversity and Versatility of the Thermotoga maritima Sugar Kinome  

PubMed Central

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.

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

2012-01-01

28

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

Microsoft Academic Search

The methionine biosynthetic pathway found in bacteria is controlled at the first step, acylation of the ?-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

Maryam Goudarzi; Timothy L. Born

2006-01-01

29

Characterization of a Tetrameric Inositol Monophosphatase from the Hyperthermophilic Bacterium Thermotoga maritima  

PubMed Central

Inositol monophosphatase (I-1-Pase) catalyzes the dephosphorylation step in the de novo biosynthetic pathway of inositol and is crucial for all inositol-dependent processes. An extremely heat-stable tetrameric form of I-1-Pase from the hyperthermophilic bacterium Thermotoga maritima was overexpressed in Escherichia coli. In addition to its different quaternary structure (all other known I-1-Pases are dimers), this enzyme displayed a 20-fold higher rate of hydrolysis of d-inositol 1-phosphate than of the l isomer. The homogeneous recombinant T. maritima I-1-Pase (containing 256 amino acids with a subunit molecular mass of 28 kDa) possessed an unusually high Vmax (442 ?mol min?1 mg?1) that was much higher than the Vmax of the same enzyme from another hyperthermophile, Methanococcus jannaschii. Although T. maritima is a eubacterium, its I-1-Pase is more similar to archaeal I-1-Pases than to the other known bacterial or mammalian I-1-Pases with respect to substrate specificity, Li+ inhibition, inhibition by high Mg2+ concentrations, metal ion activation, heat stability, and activation energy. Possible reasons for the observed kinetic differences are discussed based on an active site sequence alignment of the human and T. maritima I-1-Pases.

Chen, Liangjing; Roberts, Mary F.

1999-01-01

30

Micromonospora maritima sp. nov., isolated from mangrove soil.  

PubMed

Strain D10-9-5(T) was isolated from mangrove soil in Samut Sakhon province, Thailand. A polyphasic approach was used to determine the taxonomic position of the strain. The strain presented single rough spores on substrate mycelium and no aerial mycelium. Chemotaxonomic data supported the assignment of strain D10-9-5(T) to the genus Micromonospora based on the presence of meso-diaminopimelic acid and glycolyl muramic acid in the peptidoglycan, ribose, mannose, galactose, xylose and glucose as whole-cell sugars, MK-10(H(4)) (14.8?%), MK-10(H(6)) (46.7?%) and MK-10(H(8)) (27.5?%) as the predominant isoprenoid quinones, iso-C(15?:?0) (17.9?%), anteiso-C(17?:?0) (14.6?%), iso-C(17?:?0) (9.6?%), C(17?:?0) (8.0?%), iso-C(16?:?0) (7.7?%) and C(17?:?1)?8c (7.0?%) as the major cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylethanolamine as the predominant phospholipids in the cell wall. The 16S rRNA gene sequence and phylogenetic analysis showed that strain D10-9-5 was closely related to Micromonospora marina JCM 12870(T) (99.6?%), Micromonospora coxensis JCM 13248 (T) (99.4?%), Micromonospora aurantiaca JCM 10878(T) (99.3?%), Micromonospora humi JCM15292(T) (99.3?%), Micromonospora halophytica JCM 3125(T) (99.1%) and Micromonospora chalcea JCM 3031(T) (99.1?%). Strain D10-9-5(T) could be clearly distinguished from related members of the genus Micromonospora by its physiological and biochemical characteristics as well as its phylogenetic position and level of DNA-DNA relatedness. Therefore, the strain represents a novel species for which the name Micromonospora maritima sp. nov. is proposed; the type strain is D10-9-5(T) (?=?JCM 17013(T)?=?NBRC 108767(T)?=?PCU 322(T)?=?TISTR 2000(T)). PMID:22523171

Songsumanus, Apakorn; Tanasupawat, Somboon; Igarashi, Yasuhiro; Kudo, Takuji

2013-02-01

31

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

PubMed Central

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 ?-specific glycosyl hydrolases; the latter were presumably involved in hydrolysis of ?-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.

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

2006-01-01

32

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

PubMed Central

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 ?-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 ?-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.

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

2004-01-01

33

Transcriptional analysis of dynamic heat-shock response by the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

The thermal stress response of the hyperthermophilic bacterium Thermotoga maritima was characterized using a 407-open reading frame-targeted cDNA microarray. Transient gene expression was followed for 90 min, following a shift from 80 degrees C to 90 degrees C. While some aspects of mesophilic heat-shock response were conserved in T. maritima, genome content suggested differentiating features that were borne out by transcriptional analysis. Early induction of predicted heat-shock operons hrcA-grpE-dnaJ (TM0851-TM0850-TM0849), groES-groEL (TM0505-TM0506), and dnaK-sHSP (TM0373-TM0374) was consistent with conserved CIRCE elements upstream of hrcA and groES. Induction of the T. maritima rpoE/ sigW and rpoD/ sigA homologs suggests a mechanism for global heat-shock response in the absence of an identifiable ortholog to a major heat-shock sigma factor. In contrast to heat-shock response in Escherichia coli, the majority of genes encoding ATP-dependent proteases were downregulated, including clpP (TM0695), clpQ (TM0521), clpY (TM0522), lonA (TM1633), and lonB (TM1869). Notably, T. maritima showed indications of a late heat-shock response with the induction of a marR homolog (TM0816), several other putative transcriptional regulators (TM1023, TM1069), and two alpha-glucosidases (TM0434 and TM1068). Taken together, the results reported here indicate that, while T. maritima shares core elements of the bacterial heat-shock response with mesophiles, the thermal stress regulatory strategies of this organism differ significantly. However, it remains to be elucidated whether these differences are related to thermophilicity or phylogenetic placement. PMID:14991425

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

2004-06-01

34

Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)).  

PubMed

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 MH(2) (T) 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

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

2011-07-01

35

Complete genome sequence of Hippea maritima type strain (MH2T)  

SciTech Connect

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.

Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Lu, Megan [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute

2011-01-01

36

Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269.  

PubMed

The crystal structure of the Thermotoga maritima gene product TM0269, determined as part of genome-wide structural coverage of T. maritima by the Joint Center for Structural Genomics, revealed structural homology with the fourth module of the cobalamin-dependent methionine synthase (MetH) from Escherichia coli, despite the lack of significant sequence homology. The gene specifying TM0269 lies in close proximity to another gene, TM0268, which shows sequence homology with the first three modules of E. coli MetH. The fourth module of E. coli MetH is required for reductive remethylation of the cob(II)alamin form of the cofactor and binds the methyl donor for this reactivation, S-adenosylmethionine (AdoMet). Measurements of the rates of methionine formation in the presence and absence of TM0269 and AdoMet demonstrate that both TM0269 and AdoMet are required for reactivation of the inactive cob(II)alamin form of TM0268. These activity measurements confirm the structure-based assignment of the function of the TM0269 gene product. In the presence of TM0269, AdoMet, and reductants, the measured activity of T. maritima MetH is maximal near 80 degrees C, where the specific activity of the purified protein is approximately 15% of that of E. coli methionine synthase (MetH) at 37 degrees C. Comparisons of the structures and sequences of TM0269 and the reactivation domain of E. coli MetH suggest that AdoMet may be bound somewhat differently by the homologous proteins. However, the conformation of a hairpin that is critical for cobalamin binding in E. coli MetH, which constitutes an essential structural element, is retained in the T. maritima reactivation protein despite striking divergence of the sequences. PMID:17656578

Huang, Sha; Romanchuk, Gail; Pattridge, Katherine; Lesley, Scott A; Wilson, Ian A; Matthews, Rowena G; Ludwig, Martha

2007-08-01

37

Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269  

PubMed Central

The crystal structure of the Thermotoga maritima gene product TM0269, determined as part of genome-wide structural coverage of T. maritima by the Joint Center for Structural Genomics, revealed structural homology with the fourth module of the cobalamin-dependent methionine synthase (MetH) from Escherichia coli, despite the lack of significant sequence homology. The gene specifying TM0269 lies in close proximity to another gene, TM0268, which shows sequence homology with the first three modules of E. coli MetH. The fourth module of E. coli MetH is required for reductive remethylation of the cob(II)alamin form of the cofactor and binds the methyl donor for this reactivation, S-adenosylmethionine (AdoMet). Measurements of the rates of methionine formation in the presence and absence of TM0269 and AdoMet demonstrate that both TM0269 and AdoMet are required for reactivation of the inactive cob(II)alamin form of TM0268. These activity measurements confirm the structure-based assignment of the function of the TM0269 gene product. In the presence of TM0269, AdoMet, and reductants, the measured activity of T. maritima MetH is maximal near 80°C, where the specific activity of the purified protein is ?15% of that of E. coli methionine synthase (MetH) at 37°C. Comparisons of the structures and sequences of TM0269 and the reactivation domain of E. coli MetH suggest that AdoMet may be bound somewhat differently by the homologous proteins. However, the conformation of a hairpin that is critical for cobalamin binding in E. coli MetH, which constitutes an essential structural element, is retained in the T. maritima reactivation protein despite striking divergence of the sequences.

Huang, Sha; Romanchuk, Gail; Pattridge, Katherine; Lesley, Scott A.; Wilson, Ian A.; Matthews, Rowena G.; Ludwig, Martha

2007-01-01

38

Native crystal structure of a nitric oxide-releasing lectin from the seeds of Canavalia maritima  

Microsoft Academic Search

Here, we report the crystallographic study of a lectin from Canavalia maritima seeds (ConM) and its relaxant activity on vascular smooth muscle, to provide new insights into the understanding of structure\\/function relationships of this class of proteins. ConM was crystallized and its structure determined by standard molecular replacement techniques. The amino acid residues, previously suggested incorrectly by manual sequencing, have

Carlos Alberto de Almeida Gadelha; Frederico Bruno Mendes Batista Moreno; Tatiane Santi-Gadelha; João Batista Cajazeiras; Bruno Anderson Matias da Rocha; Ana Maria Sampaio Assreuy; Mário Rogério Lima Mota; Nilson Vieira Pinto; Ana Vaneska Passos Meireles; Júlio César Borges; Beatriz Tupinamba Freitas; Fernanda Canduri; Emmanuel Prata Souza; Plínio Delatorre; David Neil Criddle; Walter Filgueira de Azevedo; Benildo Sousa Cavada

2005-01-01

39

Factors associated with determination of root ²²Na (+) influx in the salt accumulation halophyte Suaeda maritima.  

PubMed

Salinity is an increasing problem for agricultural production worldwide. The result of low-affinity Na(+) uptake is toxic to the cytoplasm of most crop plants. Nevertheless, the pathways for this low-affinity Na(+) uptake are still uncertain. In this work we used ²²Na(+) isotope tracing technology to investigate factors associated with determination of root ²²Na(+) influx in the salt accumulation halophyte Suaeda maritima. We found that a 2 min of exposure to the ²²Na(+) labeled uptake solution was optimal for determining ²²Na(+) influx into excised roots of S. maritima and that 7 min of blotting is suitable in ²²Na(+) influx experiments. ²²Na(+) influx did not increase linearly with the increasing external Na(+) concentration, in the range tested, of 2 to 300 mM NaCl. But root ²²Na(+) influx and root Na(+) concentration were well correlated. ²²Na(+) influx into excised roots of S. maritima was not, however, well correlated with the plant size. All the above results indicated further that this ²²Na(+) isotope influx procedure is a good method for quantify Na(+) uptake rate by the roots of the salt accumulation halophyte. PMID:20217274

Zhang, Jin-Lin; Wetson, Anne M; Wang, Suo-Min; Gurmani, Ali R; Bao, Ai-Ke; Wang, Chun-Mei

2011-01-01

40

Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways? †  

PubMed Central

Members of a novel glycerate-2-kinase (GK-II) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the GarK (GK-I) family. The recently reported three-dimensional structure of GK-II from Thermotoga maritima (TM1585; PDB code 2b8n) revealed a new fold distinct from other known kinase families. Here, we verified the enzymatic activity of TM1585, assessed its kinetic characteristics, and used directed mutagenesis to confirm the essential role of the two active-site residues Lys-47 and Arg-325. The main objective of this study was to apply comparative genomics for the reconstruction of metabolic pathways associated with GK-II in all bacteria and, in particular, in T. maritima. Comparative analyses of ?400 bacterial genomes revealed a remarkable variety of pathways that lead to GK-II-driven utilization of glycerate via a glycolysis/gluconeogenesis route. In the case of T. maritima, a three-step serine degradation pathway was inferred based on the tentative identification of two additional enzymes, serine-pyruvate aminotransferase and hydroxypyruvate reductase (TM1400 and TM1401, respectively), that convert serine to glycerate via hydroxypyruvate. Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution.

Yang, Chen; Rodionov, Dmitry A.; Rodionova, Irina A.; Li, Xiaoqing; Osterman, Andrei L.

2008-01-01

41

Sequence, assembly and evolution of a primordial ferredoxin from Thermotoga maritima.  

PubMed Central

A gene coding for the ferredoxin of the primordial, strictly anaerobic and hyperthermophilic bacterium Thermotoga maritima was cloned, sequenced and expressed in Escherichia coli. The ferredoxin gene encodes a polypeptide of 60 amino acids that incorporates a single 4Fe-4S cluster. T. maritima ferredoxin expressed in E. coli is a heat-stable, monomeric protein, the spectroscopic properties of which show that its 4Fe-4S cluster is correctly assembled within the mesophilic host, and that it remains stable during purification under aerobic conditions. Removal of the iron-sulfur cluster results in an apo-ferredoxin that has no detectable secondary structure. This observation indicates that in vivo formation of the ferredoxin structure is coupled to the insertion of the iron-sulfur cluster into the polypeptide chain. Sequence comparison of T. maritima ferredoxin with other 4Fe-4S ferredoxins revealed high sequence identities (75% and 50% respectively) to the ferredoxins from the hyperthermophilic members of the Archaea, Thermococcus litoralis and Pyrococcus furiosus. The high sequence similarity supports a close relationship between these extreme thermophilic organisms from different phylogenetic domains and suggests that ferredoxins with a single 4Fe-4S cluster are the primordial representatives of the whole protein family. This observation suggests a new model for the evolution of ferredoxins. Images

Darimont, B; Sterner, R

1994-01-01

42

Phosphoribosyl anthranilate isomerase from Thermotoga maritima is an extremely stable and active homodimer.  

PubMed Central

The metabolism of hyperthermophilic microorganisms can function properly at temperatures close to 100 degrees C. It follows that they are equipped with both thermostable enzymes and mechanisms that handle labile metabolites. We wanted to understand how stable and active phosphoribosyl anthranilate isomerase (tPRAI) from the hyperthermophile Thermotoga maritima is at its optimum growth temperature of 80 degrees C, and how its thermolabile substrate, N-(5'-phosphoribosyl)-anthranilate (PRA), is protected from rapid decomposition. To this end, the trpF gene of T. maritima was expressed heterologously in Escherichia coli and tPRAI was purified. In contrast to most PRAIs from mesophiles, which are monomers with the eightfold beta alpha (or TIM) barrel fold, tPRAI is a homodimer. It is strongly resistant toward inactivation by temperatures up to 95 degrees C, by acidification to pH 3.2, and by proteases in the presence and absence of detergents. tPRAI is about 35-fold more active at its physiologic temperature than is the enzyme from E. coli (ePRAI) at 37 degrees C. This high catalytic efficiency of tPRAI is likely to complete successfully with the rapid spontaneous hydrolysis of PRA at 80 degrees C. Thus, with respect to both stability and function, tPRAI appears well adapted to the extreme habitat of T. maritima. Single crystals of tPRAI have been obtained that are suitable for X-ray analysis at high resolution.

Sterner, R.; Kleemann, G. R.; Szadkowski, H.; Lustig, A.; Hennig, M.; Kirschner, K.

1996-01-01

43

Growth and photosynthetic responses of the cordgrass Spartina maritima to CO2 enrichment and salinity.  

PubMed

Future climatic scenarios combine increasing concentrations of atmospheric CO(2) and rising sea levels. Spartina maritima is a C(4) halophyte that is an important pioneer and ecosystem engineer in salt marshes of the Atlantic coast of southern Europe. A glasshouse experiment investigated the combined effects on its growth and photosynthetic apparatus of approximately doubling CO(2) concentration (from 380 to 700 ?mol mol(-1)) at a range of salinity (0, 171 and 510 mM NaCl). We measured relative growth rates, gas exchange, chlorophyll fluorescence parameters, photosynthetic pigment concentrations, and total ash, Na(+), K(2+), Ca(2+) and N concentrations. Elevated CO(2) stimulated growth of S. maritima by c. 65% at all external salinities; this growth enhancement was associated with greater net photosynthetic rate (A) and improved leaf water relations. A increased despite a drop in stomatal conductance in response to 700 ?mol mol(-1) CO(2). CO(2) and salinity had a marked overall effect on the photochemical (PSII) apparatus and the synthesis of photosynthetic pigments. ?(PSII) values at midday decreased significantly with external salinity in plants grown at 380 ?mol mol(-1) CO(2); and F(v)/F(m) and ?(PSII) values were higher at 700 ?mol mol(-1) CO(2) in presence of NaCl. Plant nutrient concentrations declined under elevated CO(2), which can be ascribed to the dilution effect caused by an increase in biomass. The results suggest that the productivity S. maritima and the ecosystem services it provides will increase in likely future climatic scenarios. PMID:20719357

Mateos-Naranjo, E; Redondo-Gómez, S; Andrades-Moreno, L; Davy, A J

2010-10-01

44

Membrane-bound pyrophosphatase of Thermotoga maritima requires sodium for activity.  

PubMed

Membrane-bound pyrophosphatase of the hyperthermophilic bacterium Thermotoga maritima(Tm-PPase), a homologue of H(+)-translocating pyrophosphatase, was expressed in Escherichia coli and isolated as inner membrane vesicles. In contrast to all previously studied H(+)-PPases, both native and recombinant Tm-PPases exhibited an absolute requirement for Na(+) but displayed the highest activity in the presence of millimolar levels of both Na(+) and K(+). Detergent-solubilized recombinant Tm-PPase was thermostable and retained the monovalent cation requirements of the membrane-embedded enzyme. Steady-state kinetic analysis of pyrophosphate hydrolysis by the wild-type enzyme suggested that two Na(+) binding sites and one K(+) binding site are involved in enzyme activation. The affinity of the site that binds Na(+) first is increased with increasing K(+) concentration. In contrast, only one Na(+) binding site (K(+)-dependent) and one K(+) binding site were involved in activation of the Asp(703) --> Asn variant. Thus, Asp(703) may form part of the K(+)-independent Na(+) binding site. Unlike all other membrane and soluble PPases, Tm-PPase did not catalyze oxygen exchange between phosphate and water. However, solubilized Tm-PPase exhibited low but measurable PP(i)-synthesizing activity, which also required Na(+) but was inhibited by K(+). These results demonstrate that T. maritima PPase belongs to a previously unknown subfamily of Na(+)-dependent H(+)-PPase homologues and may be an analogue of Na(+),K(+)-ATPase. PMID:15697234

Belogurov, Georgiy A; Malinen, Anssi M; Turkina, Maria V; Jalonen, Ulla; Rytkönen, Kalle; Baykov, Alexander A; Lahti, Reijo

2005-02-15

45

Purification, crystallization and preliminary crystallographic analysis of a thermostable endonuclease IV from Thermotoga maritima.  

PubMed

The DNA-repair enzyme endonuclease IV from the thermophilic bacterium Thermotoga maritima MSB8 (reference sequence NC_000853) has been expressed in Escherichia coli and crystallized for X-ray analysis. T. maritima endonuclease IV is a 287-amino-acid protein with 32% sequence identity to E. coli endonuclease IV. The protein was purified to homogeneity and was crystallized using the sitting-drop vapor-diffusion method. The protein crystallized in space group P6(1), with one biological molecule in the asymmetric unit, corresponding to a Matthews coefficient of 2.39 A(3) Da(-1) and 47% solvent content. The unit-cell parameters of the crystals were a = b = 123.2, c = 35.6 A. Microseeding and further optimization yielded crystals with an X-ray diffraction limit of 2.36 A. A single 70 degrees data set was collected and processed, resulting in an overall R(merge) and a completeness of 9.5% and 99.3%, respectively. PMID:20054139

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

2009-12-01

46

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

PubMed Central

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.

Ni, Xinhai; Hager, Lowell P.

1998-01-01

47

Structural investigations of the highly flexible recombinant ribosomal protein L12 from Thermotoga maritima.  

PubMed

Ribosomal protein L7/L12, the only multicopy component of the ribosome, is involved in translation factor binding and in the ribosomal GTPase center. The gene for L7/L12 from Thermotoga maritima was cloned and the protein expressed at high levels in Escherichia coli. Purification of L7/L12 was achieved under non-denaturing conditions via heat treatment and two chromatographic steps. Circular dichroism melting profiles were monitored at 222 nm, showing the melting temperature of the protein at pH 7.5 around 110 degrees C, compared to approximately 60 degrees C for the highly homologous Escherichia coli protein. The unfolding was reversible and renaturation closely followed the path of the thermal melting. Dynamic light scattering, gel filtration chromatography, and crosslinking experiments suggested that under physiological buffer conditions Thermotoga maritima L7/L12 exists as a tetramer. The protein was crystallized under two conditions, yielding an orthorhombic (C222(1)) and a cubic (12(1)3) space group with an estimated two and three to four L7/L12 molecules per asymmetric unit, respectively. The crystals contained the full-length protein, and cryogenic buffers were developed which improved the mosaic spreads and the resolution limits. For the structure solution isoleucine was mutated to methionine at two separate positions, the mutant forms expressed as selenomethionine variants and crystallized. PMID:10782993

Wahl, M C; Huber, R; Marinkoviç, S; Weyher-Stingl, E; Ehlert, S

2000-03-01

48

Different CMS sources found in Beta vulgaris ssp maritima : mitochondrial variability in wild populations revealed by a rapid screening procedure  

Microsoft Academic Search

Mitochondrial DNA (mtDNA) variation in natural Beta maritima populations has been characterized by way of Southern blot hybridizations of total DNA using non-radioactive probes and chemiluminescent detection. It was found that the previously described N (“normal”) mitochondrial type could be subdivided into three subtypes. A new mitochondrial genotype (type R) was distinguished in addition to the previously described type S.

P. Saumitou-Laprade; G. J. A. Rouwendal; J. Cuguen; F. A. Krens; G. Michaelis

1993-01-01

49

Antioxidant activity and biologic properties of a procyanidin-rich extract from pine ( pinus maritima) bark, pycnogenol  

Microsoft Academic Search

There is growing interest in the biologic activities of plant extracts such as that obtained from the bark of the French maritime pine Pinus maritima, Pycnogenol. Pycnogenol (PYC) is a standardized extract composed of a mixture of flavonoids, mainly procyandins and phenolic acids. Studies indicate that PYC components are highly bioavailable. Uniquely PYC displays greater biologic effects as a mixture

L Packer; G Rimbach; F Virgili

1999-01-01

50

Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis.  

PubMed

Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family. PMID:23877482

Ferreira de Carvalho, J; Chelaifa, H; Boutte, J; Poulain, J; Couloux, A; Wincker, P; Bellec, A; Fourment, J; Bergès, H; Salmon, A; Ainouche, M

2013-12-01

51

Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools.  

PubMed

The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif patterns, membership of the query sequences in family databases, metabolic pathway involvement and gene proximity. We re-examined the completely sequenced genome of Thermotoga maritima by employing the combined use of the above methods. By analyzing all 1877 proteins encoded in this genome, we identified 193 cases of conflicting annotations (10%), of which 164 are new function predictions and 29 are amendments of previously proposed assignments. These results suggest that the combined use of existing computational tools can resolve inconclusive sequence similarities and significantly improve the prediction of protein function from genome sequence. PMID:11071948

Kyrpides, N C; Ouzounis, C A; Iliopoulos, I; Vonstein, V; Overbeek, R

2000-11-15

52

Solvent effects on environmentally coupled hydrogen tunnelling during catalysis by dihydrofolate reductase from Thermotoga maritima.  

PubMed

Protein motions may be perturbed by altering the properties of the reaction medium. Here we show that dielectric constant, but not viscosity, affects the rate of the hydride-transfer reaction catalysed by dihydrofolate reductase from Thermotoga maritima (TmDHFR), in which quantum-mechanical tunnelling has previously been shown to be driven by protein motions. Neither dielectric constant nor viscosity directly alters the kinetic isotope effect of the reaction or the mechanism of coupling of protein motions to tunnelling. Glycerol and sucrose cause a significant increase in the rate of hydride transfer, but lead to a reduction in the magnitude of the kinetic isotope effect as well as an extension of the temperature range over which "passive" protein dynamics (rather than "active" gating motions) dominate the reaction. Our results are in agreement with the proposal that non-equilibrium dynamical processes (promoting motions) drive the hydride-transfer reaction in TmDHFR. PMID:18924193

Loveridge, E Joel; Evans, Rhiannon M; Allemann, Rudolf K

2008-01-01

53

Structure of a periplasmic glucose-binding protein from Thermotoga maritima  

PubMed Central

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 ?/? domains connected by a three-stranded hinge region. In the current structure, a ligand (?-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.

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

2012-01-01

54

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

PubMed

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

Goudarzi, Maryam; Born, Timothy L

2006-10-01

55

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

PubMed Central

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.

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

2012-01-01

56

Structure of Thermotoga maritima Stationary Phase Survival Protein SurE: A Novel Acid Phosphatase  

PubMed Central

Summary Background The rpoS, nlpD, pcm, and surE genes are among many whose expression is induced during the stationary phase of bacterial growth. rpoS codes for the stationary-phase RNA polymerase ? subunit, and nlpD codes for a lipoprotein. The pcm gene product repairs damaged proteins by converting the atypical isoaspartyl residues back to L-aspartyls. The physiological and biochemical functions of surE are unknown, but its importance in stress is supported by the duplication of the surE gene in E. coli subjected to high-temperature growth. The pcm and surE genes are highly conserved in bacteria, archaea, and plants. Results The structure of SurE from Thermotoga maritima was determined at 2.0 Å. The SurE monomer is composed of two domains; a conserved N-terminal domain, a Rossman fold, and a C-terminal oligomerization domain, a new fold. Monomers form a dimer that assembles into a tetramer. Biochemical analysis suggests that SurE is an acid phosphatase, with an optimum pH of 5.5–6.2. The active site was identified in the N-terminal domain through analysis of conserved residues. Structure-based site-directed point mutations abolished phosphatase activity. T. maritima SurE intra- and inter-subunit salt bridges were identified that may explain the SurE thermostability. Conclusions The structure of SurE provided information about the protein’s fold, oligomeric state, and active site. The protein possessed magnesium-dependent acid phosphatase activity, but the physiologically relevant substrate(s) remains to be identified. The importance of three of the assigned active site residues in catalysis was confirmed by site-directed mutagenesis.

Zhang, R.-G.; Skarina, T.; Katz, J.E.; Beasley, S.; Khachatryan, A.; Vyas, S.; Arrowsmith, C.H.; Clarke, S.; Edwards, A.; Joachimiak, A.; Savchenko, A.

2009-01-01

57

Electron spin resonance study of free radicals formed from a procyanidin-rich pine ( Pinus maritima) bark extract, pycnogenol  

Microsoft Academic Search

The free radical generated from the oxidation of a French maritima pine bark extract Pycnogenol (PYC), by the horseradish peroxidase (HRP)–hydrogen peroxide (H2O2) system at pH 7.4–10.0 was studied using electron spin resonance (ESR) spectrometer. The formation rate of the PYC radical (aH = 0.92G; g = 2.0055) was dependent on the PYC and HRP concentrations and pH; the lifetime

Qiong Guo; Baolu Zhao; Lester Packer

1999-01-01

58

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

Microsoft Academic Search

Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bac- terium 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

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

2005-01-01

59

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

PubMed

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

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

2013-10-01

60

Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 A resolution.  

PubMed

The extremely thermostable glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima has been crystallized and the three-dimensional structure has been determined by X-ray diffraction methods. Crystals up to a maximum size of 1.2 mm have been grown in 3% polyethylene glycol, 120 mM ammonium acetate and 50 mM bis-tris propane (pH 6.5). The enzyme crystallized in the trigonal space group P3(1)21 with the cell dimensions a = b = 147.3 A, c = 273.6 A. The diffraction limit of these crystals is 3.0 A. Measured diffraction data have a completeness of 94% up to a resolution of 3.0 A and contain 75% of all possible data in the last resolution shell between 3.1 and 3.0 A. The crystal structure of T. maritima glutamate dehydrogenase has been solved by Patterson search methods using the hexameric Pyrococcus furiosus glutamate dehydrogenase as a search model. The crystallographic refinement has been carried out to a maximum resolution of 3.1 A and an crystallographic R-value of 22.5% (Rfree = 29.5%). The three-dimensional structure of the T. maritima enzyme shows typical features of hexameric glutamate dehydrogenases: six subunits are arranged in 32 symmetry. Each subunit consists of two domains connected by a flexible hinge region. Secondary structure elements as well as residues important for the catalytic activity of the enzyme are highly conserved. A structural comparison of the two glutamate dehydrogenases from the hyperthermophiles T. maritima and P. furiosus with the enzyme from the mesophilic bacterium Clostridium symbiosum has revealed that common as well as distinct mechanisms contribute to the thermal stability of these enzymes. The number of intrasubunit ion pairs is increased and the volume of intrasubunit cavities decreased in both thermostable enzymes, whereas striking differences have been observed in the subunit interfaces. In P. furiosus glutamate dehydrogenase the subunit interactions are dominated by ionic interactions realized by large saltbridge networks. However, in T. maritima glutamate dehydrogenase the number of intersubunit ion pairs is reduced and the hydrophobic interactions are increased. PMID:9135121

Knapp, S; de Vos, W M; Rice, D; Ladenstein, R

1997-04-11

61

Improvement of the efficiency of transglycosylation catalyzed by ?-galactosidase from Thermotoga maritima by protein engineering.  

PubMed

At high concentrations of p-nitrophenyl-?-D-galactopyranoside (pNPGal) as a substrate, its hydrolysis catalyzed by ?-galactosidase from Thermotoga maritima (TmGalA) is accompanied by transglycosylation resulting in production of a mixture of (?1,2)-, (?1,3)-, and (?1,6)-p-nitrophenyl (pNP)-digalactosides. Molecular modeling of the reaction stage preceding the formation of the pNP-digalactosides within the active site of the enzyme revealed amino acid residues which modification was expected to increase the efficiency of transglycosylation. Upon the site-directed mutagenesis to the predicted substitutions of the amino acid residues, genes encoding the wild type TmGalA and its mutants were expressed in E. coli, and the corresponding enzymes were isolated and tested for the presence of the transglycosylating activity in synthesis of different pNP-digalactosides. Three mutants, F328A, P402D, and G385L, were shown to markedly increase the total transglycosylation as compared to the wild type enzyme. Moreover, the F328A mutant displayed an ability to produce a regio-isomer with the (?1,2)-bond at yield 16-times higher than the wild type TmGalA. PMID:24237145

Bobrov, K S; Borisova, A S; Eneyskaya, E V; Ivanen, D R; Shabalin, K A; Kulminskaya, A A; Rychkov, G N

2013-10-01

62

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

PubMed

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

Hayden, Luke; Arthur, Wallace

2014-05-01

63

In the Absence of Thioredoxins, What Are the Reductants for Peroxiredoxins in Thermotoga maritima?  

PubMed Central

Abstract Three peroxiredoxins (Prxs) were identified in Thermotoga maritima, which possesses neither glutathione nor typical thioredoxins: one of the Prx6 class; one 2-Cys PrxBCP; and a unique hybrid protein containing an N-terminal 1-Cys PrxBCP domain fused to a flavin mononucleotide-containing nitroreductase (Ntr) domain. No peroxidase activity was detected for Prx6, whereas both bacterioferritin comigratory proteins (BCPs) were regenerated by a NADH/thioredoxin reductase/glutaredoxin (Grx)-like system, constituting a unique peroxide removal system. Only two of the three Grx-like proteins were able to support peroxidase activity. The inability of TmGrx1 to regenerate oxidized 2-Cys PrxBCP probably results from the thermodynamically unfavorable difference in their disulfide/dithiol Em values, ?150 and ?315?mV, respectively. Mutagenesis of the Prx-Ntr fusion, combined with kinetic and structural analyses, indicated that electrons are not transferred between its two domains. However, their separate activities could function in a complementary manner, with peroxide originating from the chromate reductase activity of the Ntr domain reduced by the Prx domain. Antioxid. Redox Signal. 18, 1613–1622.

Couturier, Jeremy; Prosper, Pascalita; Winger, Alison M.; Hecker, Arnaud; Hirasawa, Masakazu; Knaff, David B.; Gans, Pierre; Jacquot, Jean-Pierre; Navaza, Alda

2013-01-01

64

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

PubMed

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

Green, Jack E; Akam, Michael

2014-08-15

65

Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima  

PubMed Central

Protein crystallization continues to be a major bottleneck in X-ray crystallography. Previous studies suggest that symmetric proteins, such as homodimers, might crystallize more readily than monomeric proteins or asymmetric complexes. Proteins that are naturally monomeric can be made homodimeric artificially. Our approach is to create homodimeric proteins by introducing single cysteines into the protein of interest, which are then oxidized to form a disulfide bond between the two monomers. By introducing the single cysteine at different sequence positions, one can produce a variety of synthetically dimerized versions of a protein, with each construct expected to exhibit its own crystallization behavior. In earlier work, we demonstrated the potential utility of the approach using T4 lysozyme as a model system. Here we report the successful application of the method to Thermotoga maritima CelA, a thermophilic endoglucanase enzyme with low sequence identity to proteins with structures previously reported in the Protein Data Bank. This protein had resisted crystallization in its natural monomeric form, despite a broad survey of crystallization conditions. The synthetic dimerization of the CelA mutant D188C yielded well-diffracting crystals with molecules in a packing arrangement that would not have occurred with native, monomeric CelA. A 2.4 Å crystal structure was determined by single anomalous dispersion using a seleno-methionine derivatized protein. The results support the notion that synthetic symmetrization can be a useful approach for enlarging the search space for crystallizing monomeric proteins or asymmetric complexes.

Forse, G Jason; Ram, Nina; Banatao, D Rey; Cascio, Duilio; Sawaya, Michael R; Klock, Heath E; Lesley, Scott A; Yeates, Todd O

2011-01-01

66

Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.  

PubMed

Members of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target. PMID:11877432

Zhang, Rong-Guang; Kim, Youngchang; Skarina, Tatiana; Beasley, Steven; Laskowski, Roman; Arrowsmith, Cheryl; Edwards, Aled; Joachimiak, Andrzej; Savchenko, Alexei

2002-05-24

67

Population size, female fecundity, and sex ratio variation in gynodioecious Plantago maritima.  

PubMed

Theory predicts that the sex ratio of gynodioecious populations (in which hermaphrodites and females coexist) will be affected by the relative female fitness of females and hermaphrodites, and by founder events and genetic drift in small populations. We documented the sex ratio and size of 104 populations of the gynodioecious, perennial herb Plantago maritima in four archipelagos in eastern Sweden and western Finland (from latitude 53 to 64 degrees N). The sex ratio varied significantly both among and within archipelagos (range 0-70% females, median 6.3% females). The frequency of females was highest in the northernmost archipelago and lowest in the southernmost archipelago. As predicted, females were more frequently missing from small than from large populations, and the variance in sex ratio increased with decreasing population size. The relative fecundity of female plants (mean seed output per female/mean seed output per hermaphrodite) ranged from 0.43 to 2.16 (median 1.01, n = 12 populations). Among the 12 populations sampled for seed production (four in each of three archipelagos), the frequency of females was positively related to relative fecundity of females and negatively related to population size. The results suggest that the local sex ratio is influenced both by the relative fecundity of females and hermaphrodites and by stochastic processes in small populations. PMID:16674579

Nilsson, Emil; Agren, Jon

2006-05-01

68

In vitro transcription close to the melting point of DNA: analysis of Thermotoga maritima RNA polymerase-promoter complexes at 75 degrees C using chemical probes.  

PubMed

The interaction of DNA dependent RNA polymerase of the extreme thermophile bacteria Thermotoga maritima with a promoter bearing DNA fragment was investigated in the temperature range from 20 to 85 degrees C. We show that the T. maritima RNA polymerase recognizes and utilizes the Escherichia coli T7 A1 promoter with an efficiency similar to that of the E. coli polymerase. We have investigated the interaction of both polymerases with the same promoter over a wide range of temperatures using hydroxyl radical foot-printing and osmium tetroxide probing. This study revealed that the T. maritima polymerase goes through a series of isomerisation events very similar to the E. coli polymerase, i.e. the closed, intermediate and open complexes, but the transitions themselves occur at radically different temperatures. This indicates that conformational changes in the DNA that accompany initiation of transcription such as promoter melting are determined by the polymerase rather than the DNA sequence. PMID:7731814

Meier, T; Schickor, P; Wedel, A; Cellai, L; Heumann, H

1995-03-25

69

In vitro transcription close to the melting point of DNA: analysis of Thermotoga maritima RNA polymerase-promoter complexes at 75 degrees C using chemical probes.  

PubMed Central

The interaction of DNA dependent RNA polymerase of the extreme thermophile bacteria Thermotoga maritima with a promoter bearing DNA fragment was investigated in the temperature range from 20 to 85 degrees C. We show that the T. maritima RNA polymerase recognizes and utilizes the Escherichia coli T7 A1 promoter with an efficiency similar to that of the E. coli polymerase. We have investigated the interaction of both polymerases with the same promoter over a wide range of temperatures using hydroxyl radical foot-printing and osmium tetroxide probing. This study revealed that the T. maritima polymerase goes through a series of isomerisation events very similar to the E. coli polymerase, i.e. the closed, intermediate and open complexes, but the transitions themselves occur at radically different temperatures. This indicates that conformational changes in the DNA that accompany initiation of transcription such as promoter melting are determined by the polymerase rather than the DNA sequence. Images

Meier, T; Schickor, P; Wedel, A; Cellai, L; Heumann, H

1995-01-01

70

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

PubMed Central

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.

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

2010-01-01

71

Flowering time in wild beet ( Beta vulgaris ssp. maritima) along a latitudinal cline  

NASA Astrophysics Data System (ADS)

The wild beet ( Beta vulgaris ssp. maritima, a perennial species from the Mediterranean and the European Atlantic coasts) shows marked variation in flowering time in terms of both the year of first flowering and flowering date in a given year. Much of this variability is related to latitude. Beta vulgaris plants flower either in the same year as they germinate or in their second year. This is mainly due to differences in their requirement for vernalization, which is determined by a single gene B/b and by quantitative trait loci. The more southern the origin of the plants, the less vernalization is required. Also the B allele, which cancels vernalization requirement completely, has a high frequency in the Mediterranean region, but is completely absent in the northern part of the distribution of this species. We found that flowering date variation in relation to the latitude of origin is maintained under greenhouse conditions but does not follow a simple clinal relationship. From the Mediterranean northwards to the west coast of Brittany, flowering occurs progressively earlier, but from Brittany northwards to south-east England and The Netherlands it is progressively later. A possible explanation for this difference is that in the southern part of the range sensitivity to daylength and warmth control flowering time, whereas further north vernalization requirement is also a key factor. A substantial part of all differences in flowering time was heritable: heritability within populations was measured as 0.33 under greenhouse conditions. The high heritability implies evolutionary change may occur in this character.

Dijk, Henk Van; Boudry, Pierre; McCombre, Helen; Vernet, Philippe

72

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

PubMed Central

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-?-D-xylopyranoside monoacetates as substrates in a ?-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 ?/?-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.

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-Andre; Kengen, Serve W. M.; Wilson, Ian A.

2012-01-01

73

Hepatoprotective and antioxidant properties of Suaeda maritima (L.) dumort ethanolic extract on concanavalin-A induced hepatotoxicity in rats.  

PubMed

Hepatoprotective and antioxidant properties of Suaeda maritima (L.) Dumort on concanavalin-A induced stress in Wistar albino rats have been reported. Rats were administered with ethanolic extract of Suaeda maritimna at the concentration of 75, 150 and 300 mg/kg of body wt. for 9 days and concanavalin-A was administrated (iv) 12 mg/kg on 9th day. Rats in concanavalin-A administered group showed elevated levels of AST, ALT, ALP and bilurubin. Pretreatment of rats with ethanolic extract (300 mg/kg) significantly reduced these serum parameters compared to concavalin-A administered group. Histopathological examination of liver sections showed that, normal liver architecture was disturbed by hepatotoxin intoxication. The extract treated group and silymarin treated group retained the normal cell architecture, although less visible changes were observed. Preliminary phytochemical analysis showed the presence of triterpenioids and may be responsible for the hepatoprotective activity. The LD50 was calculated as 3 g/kg of the body weight. IC50 values of hydroxyl (52.21+/-1.32 microg/ml) and nitric oxide radicals (09.14+/-0.94 microg/ml) scavenging results showed comparable activity with vitamin-C. Results of this study may be useful for the development of herbal medicine from Suaeda maritima for the treatment of hepatitis. PMID:21702225

Ravikumar, S; Gnanadesigan, M; Inbaneson, S Jacob; Kalaiarasi, A

2011-06-01

74

A novel amylolytic enzyme from Thermotoga maritima, resembling cyclodextrinase and ?-glucosidase, that liberates glucose from the reducing end of the substrates  

Microsoft Academic Search

The gene previously designated as putative cyclodextrinase from Thermotoga maritima (TMG) was cloned and overexpressed in Escherichia coli. The recombinant TMG was partially purified and its enzymatic characteristics on various substrates were examined. The enzyme hydrolyzes various maltodextrins including maltotriose to maltoheptaose and cyclomaltodextrins (CDs) to mainly glucose and maltose. Although TMG could not degrade pullulan, it rapidly hydrolyzes acarbose,

Myoung-Hee Lee; Young-Wan Kim; Tae-Jip Kim; Cheon-Seok Park; Jung-Wan Kim; Tae-Wha Moon; Kwan-Hwa Park

2002-01-01

75

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

PubMed Central

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 ?mol/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.

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

2013-01-01

76

The effect of macrofauna, meiofauna and microfauna on the degradation of Spartina maritima detritus from a salt marsh area  

NASA Astrophysics Data System (ADS)

Decomposition of salt marsh plants results from physical, chemical and biological processes including abiotic and biotic fragmentation, microbial decay and chemical transformation. According to literature data, only a few species have the ability to feed directly on living plant material, so fungi and bacteria seem to be the principal competitors for the organic substrates. Nevertheless, by consuming bacteria, protists and fungi associated to the detritus, macrofauna and meiofauna recycle the incorporated nutrients. Moreover, this nutrient regeneration may be seen as an effective factor in maintaining and stimulating bacterial production. In fact, it is well known that many detritus feeding species have very low assimilation efficiencies. The objective of the present study was to compare the nutrient mass balance of carbon; nitrogen and phosphorus in Spartina maritima covered areas and bare bottom sediment, with and without contribution of macrofauna, meiofauna and microbial populations. Nutrients mass balance was studied taking into account the initial and final nutrient concentrations in the sediment, water and plant material. Faunal activity was measured as a function of remineralised carbon, nitrogen and phosphorus. The experimental set-up included sixteen sub-experiments, which varied with respect to type of fauna, plant biomass and oxic status. Each sub-experiment was performed in small glass containers (3 L) containing about 900 g wwt sediment and 2.5 L estuarine water. Plant material, cut from intact plants, sediment cores and estuarine water were brought from the southern arm of the Mondego estuary (Portugal). The results showed that although the bacterial activity was responsible for the Spartina maritima degradation, the presence of meiofauna and macrofauna significantly enhanced the process. Moreover, the presence of Spartina maritima positively affected the mineralisation of the sediment carbon and nitrogen, especially when the three faunal components were present, and denitrification rates were highest in the presence of the macrofauna and meiofauna. The present study suggests that macrofauna and meiofauna have an important role on the ecosystem nutrient flux and that fauna might function as a sink for excess nutrients, that otherwise could be exported to the coastal waters.

Lillebø, Ana Isabel; Flindt, Mogens R.; Pardal, Miguel Ângelo; Marques, João Carlos

1999-07-01

77

Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.  

PubMed

As a part of a structural genomics program, the 2.2 angstroms resolution crystal structure of the PurC gene product from Thermotoga maritima has been solved. This 26.2 kDa protein belongs to the phophoribosylaminoimidazole-succinocarboxamide or SAICAR synthase family of enzymes, the members of which are involved in de novo purine biosynthesis. SAICAR synthase can be divided into three subdomains: two alpha+beta regions exhibiting structural homology with ATP-binding proteins and a carboxy-terminal subdomain of two alpha-helices. The asymmetric unit contains two copies of the protein which are covalently linked by a disulfide bond between Cys126(A) and Cys126(B). This 230-amino-acid protein exhibits high structural homology with SAICAR synthase from baker's yeast. The protein structure is described and compared with that of the ATP-SAICAR synthase complex from yeast. PMID:16582479

Zhang, Rongguang; Skarina, Tatiana; Evdokimova, Elena; Edwards, Aled; Savchenko, Alexei; Laskowski, Roman; Cuff, Marianne E; Joachimiak, Andrzej

2006-04-01

78

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

SciTech Connect

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.

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

79

The conformational flexibility of the helicase-like domain from Thermotoga maritima reverse gyrase is restricted by the topoisomerase domain.  

PubMed

Reverse gyrase is the only enzyme known to introduce positive supercoils into DNA. Positive supercoiling is achieved by the functional cooperation of a helicase-like and a topoisomerase domain. The isolated helicase-like domain is a DNA-stimulated ATPase, and the isolated topoisomerase domain can relax supercoiled DNA. In the context of reverse gyrase, these individual activities are suppressed or attenuated. The helicase-like domain of Thermotoga maritima reverse gyrase is a nucleotide-dependent conformational switch that binds DNA and ATP cooperatively. It provides a nucleotide-dependent DNA-binding site to reverse gyrase and thus serves as a valuable model for the investigation of the effect of nucleotides on DNA processing by reverse gyrase that is key to its supercoiling activity. To improve our understanding of the structural basis for the functional cooperation of a helicase domain with a DNA topoisomerase, we have determined the structures of the isolated helicase-like domain of T. maritima reverse gyrase in five different conformations. Comparison of these structures reveals extensive domain flexibility in the absence of conformational restrictions by the topoisomerase that is consistent with single-molecule Fo?rster resonance energy transfer experiments presented here. The structure of the first ADP-bound form provides novel details about nucleotide binding to reverse gyrase. It demonstrates that reverse gyrases use the canonical nucleotide binding mode common to superfamily 2 helicases despite large deviations in the conserved motifs. A characteristic insert region adopts drastically different structures in different reverse gyrases. Counterparts of this insert region are located at very different positions in other DNA-processing enzymes but may point toward a general role in DNA strand separation. PMID:21627332

del Toro Duany, Yoandris; Klostermeier, Dagmar; Rudolph, Markus G

2011-07-01

80

Crystal structures of the antitermination factor NusB from Thermotoga maritima and implications for RNA binding.  

PubMed

NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. We have determined five crystal structures of NusB from Thermotoga maritima. In three crystal forms the protein appeared monomeric, whereas the two other crystal forms contained assemblies, which resembled the M. tuberculosis dimers. In solution, T. maritima NusB could be cross-linked as dimers, but it migrated as a monomer in gel-filtration analyses, suggesting a monomer/dimer equilibrium with a preference for the monomer. Binding to boxA-like RNA sequences could be detected by gel-shift analyses and UV-induced cross-linking. An N-terminal arginine-rich sequence is a probable RNA binding site of the protein, exhibiting aromatic residues as potential stacking partners for the RNA bases. Anions located in various structures support the assignment of this RNA binding site. The proposed RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. Therefore, in certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes. PMID:15279620

Bonin, Irena; Robelek, Rudolf; Benecke, Heike; Urlaub, Henning; Bacher, Adelbert; Richter, Gerald; Wahl, Markus C

2004-11-01

81

Crystal structures of the antitermination factor NusB from Thermotoga maritima and implications for RNA binding  

PubMed Central

NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. We have determined five crystal structures of NusB from Thermotoga maritima. In three crystal forms the protein appeared monomeric, whereas the two other crystal forms contained assemblies, which resembled the M. tuberculosis dimers. In solution, T. maritima NusB could be cross-linked as dimers, but it migrated as a monomer in gel-filtration analyses, suggesting a monomer/dimer equilibrium with a preference for the monomer. Binding to boxA-like RNA sequences could be detected by gel-shift analyses and UV-induced cross-linking. An N-terminal arginine-rich sequence is a probable RNA binding site of the protein, exhibiting aromatic residues as potential stacking partners for the RNA bases. Anions located in various structures support the assignment of this RNA binding site. The proposed RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. Therefore, in certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes.

2004-01-01

82

Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration  

PubMed Central

Background Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. E. coli) remains challenging sometimes. Results An open reading frame TM0438 from a hyperthermophilic bacterium Thermotoga maritima putatively encoding 6-phosphogluconate dehydrogenase (6PGDH) was cloned and expressed in E. coli. The purified protein was confirmed to have 6PGDH activity with a molecular mass of 53 kDa. The kcat of this enzyme was 325 s-1 and the Km values for 6-phosphogluconate, NADP+, and NAD+ were 11, 10 and 380 ?M, respectively, at 80°C. This enzyme had half-life times of 48 and 140 h at 90 and 80°C, respectively. Through numerous approaches including expression vectors, hosts, cultivation conditions, inducers, and codon-optimization of the 6pgdh gene, the soluble 6PGDH expression levels were enhanced to ~250 mg per liter of culture by more than 500-fold. The recombinant 6PGDH accounted for >30% of total E. coli cellular proteins when lactose was used as a low-cost inducer. In addition, this enzyme coupled with glucose-6-phosphate dehydrogenase for the first time was demonstrated to generate two moles of NADPH per mole of glucose-6-phosphate. Conclusion We have achieved a more than 500-fold improvement in the expression of soluble T. maritima 6PGDH in E. coli, characterized its basic biochemical properties, and demonstrated its applicability for NADPH regeneration by a new enzyme cocktail. The methodology for over-expression and simple purification of this thermostable protein would be useful for the production of other thermostable proteins in E. coli.

Wang, Yiran; Zhang, Y-H Percival

2009-01-01

83

The Unique Chaperone Operon of Thermotoga maritima: Cloning and Initial Characterization of a Functional Hsp70 and Small Heat Shock Protein  

PubMed Central

The hyperthermophilic eubacterium Thermotoga maritima possesses an operon encoding an Hsp70 molecular chaperone protein and a protein with meaningful homology to the small heat shock protein family of chaperones. This represents the first demonstrated co-operon organization for these two important classes of molecular chaperones. We have cloned and initially characterized these proteins as functional chaperones in vitro: the Hsp70 is capable of ATP hydrolysis and substrate binding, and the small heat shock protein can suppress protein aggregation and stably bind a refolding-competent substrate. In addition, the primary sequence of the Hsp70 is used to infer the phylogenetic relationships of T. maritima, one of the deepest-branching eubacteria known.

Michelini, Edward T.; Flynn, Gregory C.

1999-01-01

84

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

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

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

2014-05-01

85

The effect of salt stress on lipid peroxidation and antioxidants in leaves of sugar beet Beta vulgaris L. and wild beet Beta maritima L  

Microsoft Academic Search

The changes in lipid peroxidation and the possible involvement of the antioxidant system in relation to the tolerance to salt stress was investigated in the cultivated beet Beta vulgaris L. cv. ansa and its wild salt-tolerant relative Beta maritima TR 51196. The 40 days old beet seedlings were subjected to 0, 150 and 500 mM NaCl for 12 days. In

M Bor; F Özdemir; I Türkan

2003-01-01

86

Crystal structure of a lectin from Canavalia maritima (ConM) in complex with trehalose and maltose reveals relevant mutation in ConA-like lectins  

Microsoft Academic Search

The crystal structure of Canavalia maritima lectin (ConM) complexed with trehalose and maltose revealed relevant point mutations in ConA-like lectins. ConM with the disaccharides and other ConA-like lectins complexed with carbohydrates demonstrated significant differences in the position of H-bonds. The main difference in the ConM structure is the replacement of Pro202 by Ser202, a residue that promotes the approximation of

Plínio Delatorre; Bruno A. M. Rocha; Carlos A. A. Gadelha; Tatiane Santi-Gadelha; João B. Cajazeiras; Emmanuel P. Souza; Kyria S. Nascimento; Valder N. Freire; Alexandre H. Sampaio; Walter F. Azevedo; Benildo S. Cavada

2006-01-01

87

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

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.

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

2014-01-01

88

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

Microsoft Academic Search

Sugar and sugar alcohol concentrations were analyzed in subcellular compartments of mesophyll cells, in the apoplast, and\\u000a 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,\\u000a whereas celery translocated mannitol as

Jan Nadwodnik; Gertrud Lohaus

2008-01-01

89

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

PubMed

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 ?M of selenite only (group II), or in DMEM containing 100 ?M of selenite and 300 ?g/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 ?M/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

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

2011-10-01

90

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

SciTech Connect

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.

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

2007-01-01

91

Evolutionary optimization of life-history traits in the sea beet Beta vulgaris subsp. maritima: Comparing model to data  

NASA Astrophysics Data System (ADS)

At evolutionary equilibrium, ecological factors will determine the optimal combination of life-history trait values of an organism. This optimum can be assessed by assuming that the species maximizes some criterion of fitness such as the Malthusian coefficient or lifetime reproductive success depending on the degree of density-dependence. We investigated the impact of the amount of resources and habitat stability on a plant's age at maturity and life span by using an evolutionary optimization model in combination with empirical data. We conducted this study on sea beet, Beta vulgaris subsp. maritima, because of its large variation in life span and age at first reproduction along a latitudinal gradient including considerable ecological variation. We also compared the consequence in our evolutionary model of maximizing either the Malthusian coefficient or the lifetime reproductive success. Both the data analysis and the results of evolutionary modeling pointed to habitat disturbance and resources like length of the growing season as factors negatively related to life span and age at maturity in sea beet. Resource availability had a negative theoretical influence with the Malthusian coefficient as the chosen optimality criterion, while there was no influence in the case of lifetime reproductive success. As suggested by previous theoretical work the final conclusion on what criterion is more adequate depends on the assumptions of how in reality density-dependence restrains population growth. In our case of sea beet data R0 seems to be less appropriate than ?.

Hautekèete, N.-C.; Van Dijk, H.; Piquot, Y.; Teriokhin, A.

2009-01-01

92

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

SciTech Connect

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.

van Bueren,A.; Boraston, A.

2006-01-01

93

Electron spin resonance study of free radicals formed from a procyanidin-rich pine (Pinus maritima) bark extract, pycnogenol.  

PubMed

The free radical generated from the oxidation of a French maritima pine bark extract Pycnogenol (PYC), by the horseradish peroxidase (HRP)-hydrogen peroxide (H2O2) system at pH 7.4-10.0 was studied using electron spin resonance (ESR) spectrometer. The formation rate of the PYC radical (aH = 0.92 G; g = 2.0055) was dependent on the PYC and HRP concentrations and pH; the lifetime of the radical was up to 90 min. Furthermore, it was found that the PYC radical was mainly composed of the secondary radical formed from procyanidin B3, one of major procyanidins in PYC. The primary radical signal of procyanidin B3 with hyperfine splitting constants aH = 3.67 G (1H), aH = 0.92 G (3H), and g = 2.0055 was transient and disappeared quickly, whereas its secondary radical signal appeared and increased with time. The secondary radical from dimer procyanidin B3 showed quite high stability, differing from the radical from monomer (+)-catechin that could not be observed possibly because of its instability. These results provide evidence to support the idea that the intramolecular hydrogen bond between the O* at the 4' position in one B ring and an OH group in the other B ring of procyanidin B3 is formed during its oxidation in the presence of HRP and H2O2. PMID:10641725

Guo, Q; Zhao, B; Packer, L

1999-12-01

94

Structural analysis of alpha-L-arabinofuranosidase from Thermotoga maritima reveals characteristics for thermostability and substrate specificity.  

PubMed

An alpha-L-arabinofuranosidase (TmAFase) from Thermotoga maritima MSB8 is a highly thermostable exo-acting hemicellulase that exhibits a relatively higher activity towards arabinan and arabinoxylan, compared with other glycoside hydrolase 51 family enzymes. In the present study, we carried out the enzymatic characterization and structural analysis of TmAFase. Tight domain associations found in TmAFase, such as an inter-domain disulfide bond (Cys306 and Cys476) in each monomer, a novel extended arm (amino acids 374-385) at the dimer interface, and total 12 salt bridges in the hexamer, may account for the thermostability of the enzyme. One of the xylan binding determinants (Trp96) was identified in the active site, and a region of amino acids (374-385) protrudes out forming an obvious wall at the substrate-binding groove to generate a cavity. The altered cavity shape with a strong negative electrostatic distribution is likely related to the unique substrate preference of TmAFase towards branched polymeric substrates. PMID:23221536

Dumbrepatil, Arti; Park, Jung-Mi; Jung, Tae Yang; Song, Hyung-Nam; Jang, Myoung-Uoon; Han, Nam Soo; Kim, Tae-Jip; Woo, Eui Jeon

2012-12-01

95

Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

The genome of the hyperthermophilic bacterium Thermotoga maritima encodes numerous putative peptides/proteins of 100 amino acids or less. While most of these open reading frames (ORFs) are transcribed during growth, their corresponding physiological roles are largely unknown. The onset of stationary phase in T. maritima was accompanied by significant morphological changes and upregulation of several ORFs located in the TM1298-TM1336 genome locus. This region contains putative HicAB toxin-antitoxin pairs, hypothetical proteins, radical S-adenosylmethionine (SAM) enzymes, and ABC transporters. Of particular note was the TM1315-TM1319 operon, which includes a putative 31-amino-acid peptide (TM1316) that was the most highly transcribed gene in the transcriptome during stationary phase. Antibodies directed against a synthetic version of TM1316 were used to track its production, which correlated closely with transcriptomic data. Immunofluorescence microscopy revealed that TM1316 was localized to the cell envelope and prominent in cell aggregates formed during stationary phase. The only functionally characterized locus with an organization similar to that of TM1315-TM1319 is in Bacillus subtilis, which contains subtilosin A, a cyclic peptide with Cys-to-?-carbon linkages that functions as an antilisterial bacteriocin. While the organization of TM1316 resembled that of the Bacillus peptide (e.g., in its number of amino acids and spacing of Cys residues), preparations containing high levels of TM1316 affected the growth of neither Thermotoga species nor Pyrococcus furiosus, a hyperthermophilic archaeon isolated from the same locale as T. maritima. Several other putative Cys-rich peptides could be identified in the TM1298-TM1336 locus, and while their roles are also unclear, they merit examination as potential antimicrobial agents in hyperthermophilic biotopes. PMID:23974142

Frock, Andrew D; Montero, Clemente I; Blumer-Schuette, Sara E; Kelly, Robert M

2013-11-01

96

Stationary Phase and Nutrient Levels Trigger Transcription of a Genomic Locus Containing a Novel Peptide (TM1316) in the Hyperthermophilic Bacterium Thermotoga maritima  

PubMed Central

The genome of the hyperthermophilic bacterium Thermotoga maritima encodes numerous putative peptides/proteins of 100 amino acids or less. While most of these open reading frames (ORFs) are transcribed during growth, their corresponding physiological roles are largely unknown. The onset of stationary phase in T. maritima was accompanied by significant morphological changes and upregulation of several ORFs located in the TM1298-TM1336 genome locus. This region contains putative HicAB toxin-antitoxin pairs, hypothetical proteins, radical S-adenosylmethionine (SAM) enzymes, and ABC transporters. Of particular note was the TM1315-TM1319 operon, which includes a putative 31-amino-acid peptide (TM1316) that was the most highly transcribed gene in the transcriptome during stationary phase. Antibodies directed against a synthetic version of TM1316 were used to track its production, which correlated closely with transcriptomic data. Immunofluorescence microscopy revealed that TM1316 was localized to the cell envelope and prominent in cell aggregates formed during stationary phase. The only functionally characterized locus with an organization similar to that of TM1315-TM1319 is in Bacillus subtilis, which contains subtilosin A, a cyclic peptide with Cys–to–?-carbon linkages that functions as an antilisterial bacteriocin. While the organization of TM1316 resembled that of the Bacillus peptide (e.g., in its number of amino acids and spacing of Cys residues), preparations containing high levels of TM1316 affected the growth of neither Thermotoga species nor Pyrococcus furiosus, a hyperthermophilic archaeon isolated from the same locale as T. maritima. Several other putative Cys-rich peptides could be identified in the TM1298-TM1336 locus, and while their roles are also unclear, they merit examination as potential antimicrobial agents in hyperthermophilic biotopes.

Frock, Andrew D.; Montero, Clemente I.; Blumer-Schuette, Sara E.

2013-01-01

97

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

SciTech Connect

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.

Diao, Jiasheng; Hasson, Miriam S.; (Purdue)

2009-04-01

98

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

PubMed

Enzymes for use in the sugar industry are preferred to be thermotolerant. In this study, a synthetic codon-optimized gene encoding a highly thermostable ?-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 ?-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

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

2013-02-01

99

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

PubMed Central

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-Å crystal structure of Buk2 complexed with (?,?-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.

Diao, Jiasheng; Hasson, Miriam S.

2009-01-01

100

Antioxidant activity and biologic properties of a procyanidin-rich extract from pine (Pinus maritima) bark, pycnogenol.  

PubMed

There is growing interest in the biologic activities of plant extracts such as that obtained from the bark of the French maritime pine Pinus maritima, Pycnogenol. Pycnogenol (PYC) is a standardized extract composed of a mixture of flavonoids, mainly procyandins and phenolic acids. Studies indicate that PYC components are highly bioavailable. Uniquely PYC displays greater biologic effects as a mixture than its purified components do individually indicating that the components interact synergistically. PYC has been reported to have cardiovascular benefits, such as a vasorelaxant activity, angiotensin-converting enzyme (ACE) inhibiting activity, and the ability to enhance the microcirculation by increasing capillary permeability. Investigations of the cellular mechanisms of these therapeutic effects have demonstrated that PYC has strong free radical-scavenging activity against reactive oxygen and nitrogen species. The oligomeric components of PYC contribute significantly to the ESR free radical signal. PYC also participates in the cellular antioxidant network as indicated by its ability to regenerate the ascorbyl radical and to protect endogenous vitamin E and glutathione from oxidative stress. PYC modulates NO metabolism in activated macrophages by quenching the NO radical and inhibiting both iNOS mRNA expression and iNOS activity. The spectrum of different effects of NO in the circulation and the nervous system suggest the potential applications of PYC in immune and circulatory disorders as well as in neurodegenerative disease. PYC can bind to proteins, altering their structure and thereby modulating the activity of key enzymes and proteins involved in metabolic pathways. PYC effects redox-sensitive signal transduction pathways and alters gene expression. Aspects of PYC's activity are presented and discussed together with possible future implications and directions in the field of flavonoid research. PMID:10490291

Packer, L; Rimbach, G; Virgili, F

1999-09-01

101

Ferulic acid excretion as a marker of consumption of a French maritime pine (Pinus maritima) bark extract.  

PubMed

French maritime pine (Pinus maritima) bark extract (PBE) is a polyphenol-rich food supplement patented under the name of Pycnogenol and known to have strong antioxidant activity and different beneficial effects on human health. Although its biological properties have begun to be extensively studied both in vitro, in laboratory animals and more recently in humans, little is known about its bioavailability. The present study investigated the urinary excretion of free and conjugated ferulic acid, present in quantitatively detectable amounts in PBE, after oral PBE administration to human subjects. Eleven healthy adult subjects (4 women and 7men) consumed either a single dose (200 mg PBE) or two doses of PBE (100 and 200 mg, respectively) within a 48-h interval. Two days before the oral administration of PBE and during the urine sample collection period volunteers adhered to a diet low in polyphenols. Aliquots of all urine production were collected over 24 h. Free and conjugated ferulic acid was assessed in urine by HPLC using diode array detection. A close association between the dietary intake of PBE and the urinary excretion of ferulic acid was detected. Moreover, the results indicate that a considerable proportion of ferulic acid is excreted as glucuronide or sulfate after PBE consumption, varying over the range 2 to 20% between individuals. The kinetics of excretion associated with the administration of 100 mg PBE was quite similar to that obtained after 200 mg PBE. A a biphasic trend was evident in a number of subjects. All subjects studied here displayed a significant, although variable level of excretion of ferulic acid after supplementation with PBE, Thus, the data provide evidence that at least a part of the phenolic components of PBE are absorbed, metabolized, and eliminated by humans. PMID:10889455

Virgili, F; Pagana, G; Bourne, L; Rimbach, G; Natella, F; Rice-Evans, C; Packer, L

2000-04-15

102

The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy  

PubMed Central

The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5-aminoimidazole-4-carboxamideribotide. Solution NMR spectroscopy of ammonium chloride-titrated samples was used to study the interaction of NH3 with amino acids inside this channel. Although numerous residues showed 15N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78—which is located in the central channel—shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using 1H-15N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon-induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N?-[(5?-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central ?-barrel of HisF and overlaps with the putative ammonia transport channel.

Liebold, Christoph; List, Felix; Kalbitzer, Hans Robert; Sterner, Reinhard; Brunner, Eike

2010-01-01

103

Studies on the chemical composition and possible mechanisms underlying the antispasmodic and bronchodilatory activities of the essential oil of Artemisia maritima L.  

PubMed

This study describes the chemical composition of the essential oil of Artemisia maritima (Am.Oil) and the pharmacological basis for its medicinal use in gut and airways disorders. Twenty five compounds, composing 93.7% of the oil, were identified; among these, chrysanthenyl propionate and elixene were identified for the first time from any Artemisia species. The Am.Oil (0.3-1.0 mg/mL) suppressed spontaneous and high K(+) (80 mM)-induced contractions in isolated rabbit jejunum, suggestive of an antispasmodic effect mediated possibly through calcium channel blockade. The calcium channel blockade activity was confirmed when pre-treatment of the tissue with Am.Oil (0.01-0.03 mg/mL) shifted the Ca(++) concentration-response curves to the right, similar to verapamil and papaverine. In isolated tracheal strips, Am.Oil inhibited carbachol (CCh; 1 ?M)-induced contractions more than that induced by K(+) and shifted the isoprenaline-induced inhibitory CRCs to the left, similar to papaverine, suggestive of potentiation, while, verapamil was more potent against K(+) than CCh-induced contractions and had no potentiating effect on isoprenaline-induced inhibitory CRCs. These data indicate that the Am.Oil exhibited spasmolytic and bronchodilator activities mediated possibly through dual blockade of calcium channels and phosphodiesterase, which provides the pharmacological basis to the medicinal use of Artemisia maritima in colic, diarrhea and possibly asthma. PMID:21910043

Shah, Abdul Jabbar; Gilani, Anwarul-Hassan; Abbas, Kanza; Rasheed, Munawwer; Ahmed, Amir; Ahmad, Viqar Uddin

2011-08-01

104

Enhanced Catalytic Efficiency in Quercetin-4'-glucoside Hydrolysis of Thermotoga maritima ?-Glucosidase A by Site-Directed Mutagenesis.  

PubMed

Te-BglA and Tm-BglA are glycoside hydrolase family 1 ?-glucosidases from Thermoanaerobacter ethanolicus JW200 and Thermotoga maritima, respectively, with 53% sequence identity. However, Te-BglA could more effectively hydrolyze isoflavone glucosides to their aglycones than could Tm-BglA, possibly due to the difference in amino acid residues around their glycone binding pockets. Site-directed mutagenesis was used to replace the amino acid residues of Tm-BglA with the corresponding residues of Te-BglA, generating three single mutants (F221L, N223L, and G224T), as well as the corresponding three double mutants (F221L/N223L, F221L/G224T, and N223L/G224T) and one triple mutant (F221L/N223L/G224T). The seven mutants have been purified, characterized, and compared to the wild-type Tm-BglA. The effects of the mutations on kinetics, enzyme activity, and substrate specificity were determined. All mutants showed pH-activity curves narrower on the basic side and wider on the acid side and had similar optimal pH and stability at pH 6.5-8.3. They were more stable up to 85 °C, but G224T displayed higher optimal temperature than Tm-BglA. Seven mutants indicated an obvious increase in catalytic efficiency toward p-nitrophenyl ?-d-glucopyranoside (pNPG) but an increase or not change in Km. All mutants showed a decrease in catalytic efficiency of isoflavonoid glycosides and were not changed for F221L and lost for N223L in enzymatic hydrolysis on quercetin glucosides. Contrarily, G224T resulted in a dramatic increase conversion of Q4' (35.5%) and Q3,4' (28.6%) in accord with an increased turnover number (kcat, 1.4×) and catalytic efficiency (kcat/Km, 2.2×) as well as a decrease in Km (0.24) for Q4'. Modeling showed that G224T mutation at position 224 may enhance the interaction between G224T and 5-OH and 3-OH on the quercetin backbone of Q4'. PMID:24933681

Sun, Huihui; Xue, Yemin; Lin, Yufei

2014-07-16

105

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

PubMed

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, ? = 90, ? = 90, ? = 120°, indicating that a dimer was present in the asymmetric unit. PMID:24915082

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

106

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

PubMed Central

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 ?????? 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.

Dermoun, Zorah; Foulon, Amelie; 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

107

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

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.

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

108

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

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.

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

2010-05-25

109

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*  

PubMed Central

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 ?(1?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.

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

2009-01-01

110

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

PubMed Central

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.

Nadwodnik, Jan

2008-01-01

111

Properties of an alpha-galactosidase, and structure of its gene galA, within an alpha-and beta-galactoside utilization gene cluster of the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

Thermotoga maritima represents one of the few hyperthermophilic bacteria currently known. The chromosomal alpha-galactosidase gene of T. maritima strain MSB8 has been cloned and its nucleotide sequence was determined. The gene, designated galA, has coding capacity for a 552 residue polypeptide with a calculated molecular mass of 63,653 Da. GalA was found to be flanked by other genes probably involved in galactoside breakdown and utilization. The previously sequenced beta-galactosidase gene, lacZ, is localized immediately upstream of galA while two open reading frames that putatively encode enzymes of galactose catabolism, i.e. galactose-1-phosphate uridylytransferase (galT) and galactokinase (galK), were found downstream of galA. The identified genes are extremely close together or even overlap and have the same orientation, so they could all be part of one galactoside utilization operon of T. maritima MSB8. GalA displayed low-level amino acid sequence similarity with alpha-galactoside of glycosyl hydrolase family 36. However, GalA is smaller than the other members of this enzyme family. The galA gene was expressed in Escherichia coli and the recombinant alpha-galactosidase was purified and characterized. The molecular mass of the recombinant enzyme was estimated at about 62 kDa by denaturting gel electrophoresis. Maximal hydrolysis of the chromogenic substrate p-nitrophenyl-alpha-D-galactopyranoside was measured at pH 5.0-5.5 and 90-95 degrees C (5 min assay). Divalent cations were not required for activity. The enzyme released galactose from raffinose, melibiose and the synthetic substrates p-nitrophenyl-and omicron-nitrophenyl-alpha-D-galactopyranoside. The T. maritima alpha-galactosidase thus was highly specific for the galactose moiety and the alpha-anomeric configuration of the glycosidic linkage. Its extreme thermal stability (t 1/2 = 6.5 h at 85 degrees C) makes this enzyme an interesting candidate for biotechnological applications. PMID:9741105

Liebl, W; Wagner, B; Schellhase, J

1998-03-01

112

Isolation and cloning of Omp alpha, a coiled-coil protein spanning the periplasmic space of the ancestral eubacterium Thermotoga maritima.  

PubMed Central

We have discovered a new oligomeric protein component associated with the outer membrane of the ancestral eubacterium Thermotoga maritima. In electron micrographs, the protein, Omp alpha, appears as a rod-shaped spacer that spans the periplasm, connecting the outer membrane to the inner cell body. Purification, biochemical characterization and sequencing of Omp alpha suggest that it is a homodimer composed of two subunits of 380 amino acids with a calculated M(r) of 43,000 and a pI of 4.54. The sequence of the omp alpha gene indicates a tripartite organization of the protein with a globular NH2-terminal domain of 64 residues followed by a putative coiled-coil segment of 300 residues and a COOH-terminal, membrane-spanning segment. The predicted length of the coiled-coil segment (45 nm) correlates closely with the spacing between the inner and outer membranes. Despite sequence similarity to a large number of coiled-coil proteins and high scores in a coiled-coil prediction algorithm, the sequence of the central rod-shaped domain of Omp alpha does not have the typical 3.5 periodicity of coiled-coil proteins but rather has a periodicity of 3.58 residues. Such a periodicity was also found in the central domain of staphylococcal M protein and beta-giardin and might be indicative of a subclass of fibrous proteins with packing interactions that are distinct from the ones seen in other two-stranded coiled-coils. Images

Engel, A M; Cejka, Z; Lupas, A; Lottspeich, F; Baumeister, W

1992-01-01

113

Structural and thermodynamic studies on a salt-bridge triad in the NADP-binding domain of glutamate dehydrogenase from Thermotoga maritima: cooperativity and electrostatic contribution to stability.  

PubMed

Cooperative interactions within ion-pair networks of hyperthermostable proteins are thought to be a major determinant for extreme protein stability. While the favorable thermodynamic contributions of optimized electrostatics in general as well as those of pairwise interactions have been documented, cooperativity between pairwise interactions has not yet been studied thermodynamically in proteins from hyperthermophiles. In this study we use the isolated cofactor binding domain of glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima to analyze pairwise and cooperative interactions within the salt-bridge triad Arg190-Glu231-Lys193. The X-ray structure of the domain was solved at 1.43 A and reveals the salt-bridge network with surrounding solvent molecules in detail. All three participating charges in the network were mutated to alanine in all combinations. The X-ray structure of the variant lacking all three charges reveals that the removal of the side chains has no effect on the overall conformation of the protein. Using solvent denaturation and thermodynamic cycles, the interaction energies between each pair of residues in the network were determined in the presence and in the absence of the third residue. Both the Arg190-Glu231 ion pair and the Lys193-Glu231 salt bridge in the absence of the third residue, contribute favorably to the free energy for unfolding of the domain in urea. Using guanidinium chloride as denaturant reveals a strong cooperativity between the two ion-pair interactions, the presence of the second ion pair converts the first interaction from destabilizing into stabilizing by as much as 1.09 kcal/mol. The different energetics of the salt-bridge triad in urea and GdmCl are discussed with reference to the observed anion binding in the crystal structure at high ionic strength and their possible role in a highly charged, high-temperature environment such as the cytoplasm of hyperthermophiles. PMID:12501181

Lebbink, Joyce H G; Consalvi, Valerio; Chiaraluce, Roberta; Berndt, Kurt D; Ladenstein, Rudolf

2002-12-31

114

Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase.  

PubMed Central

Triosephosphate isomerase (TIM), from the hyperthermophilic bacterium Thermotoga maritima, has been shown to be covalently linked to phosphoglycerate kinase (PGK) forming a bifunctional fusion protein with TIM as the C-terminal portion of the subunits of the tetrameric protein (Schurig et al., EMBO J 14:442-451, 1995). To study the effect of the anomalous state of association on the structure, stability, and function of Thermotoga TIM, the isolated enzyme was cloned and expressed in Escherichia coli, and compared with its wild-type structure in the PGK-TIM fusion protein. After introducing a start codon at the beginning of the tpi open reading frame, the gene was expressed in E.c.BL21(DE3)/ pNBTIM. The nucleotide sequence was confirmed and the protein purified as a functional dimer of 56.5 kDa molecular mass. Spectral analysis, using absorption, fluorescence emission, near- and far-UV circular dichroism spectroscopy were used to compare the separated Thermotoga enzyme with its homologs from mesophiles. The catalytic properties of the enzyme at approximately 80 degrees C are similar to those of its mesophilic counterparts at their respective physiological temperatures, in accordance with the idea that under in vivo conditions enzymes occupy corresponding states. As taken from chaotropic and thermal denaturation transitions, the separated enzyme exhibits high intrinsic stability, with a half-concentration of guanidinium-chloride at 3.8 M, and a denaturation half-time at 80 degrees C of 2 h. Comparing the properties of the TIM portion of the PGK-TIM fusion protein with those of the isolated recombinant TIM, it is found that the fusion of the two enzymes not only enhances the intrinsic stability of TIM but also its catalytic efficiency.

Beaucamp, N.; Hofmann, A.; Kellerer, B.; Jaenicke, R.

1997-01-01

115

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

SciTech Connect

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.

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

116

A Loose Domain Swapping Organization Confers a Remarkable Stability to the Dimeric Structure of the Arginine Binding Protein from Thermotoga maritima.  

PubMed

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

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

2014-01-01

117

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

SciTech Connect

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.

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

2010-01-01

118

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

SciTech Connect

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.

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

2010-01-01

119

A Loose Domain Swapping Organization Confers a Remarkable Stability to the Dimeric Structure of the Arginine Binding Protein from Thermotoga maritima  

PubMed Central

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.

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

2014-01-01

120

Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.  

PubMed

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 A 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. PMID:20007320

Arragain, Simon; Garcia-Serres, Ricardo; Blondin, Geneviève; Douki, Thierry; Clemancey, Martin; Latour, Jean-Marc; Forouhar, Farhad; Neely, Helen; Montelione, Gaetano T; Hunt, John F; Mulliez, Etienne; Fontecave, Marc; Atta, Mohamed

2010-02-19

121

No male agonistic experience effect on pre-copulatory mate choice in female earwigs  

Microsoft Academic Search

Mating with dominant males may confer considerable benefits, but also incur significant costs, hence intrasexual competitiveness\\u000a is a likely target of mate choice. In addition to established modes of mate assessment, females may use cues or signals associated\\u000a with agonistic experience effects to assess the relative competiveness of males. Experience effects, where the outcome of\\u000a a fight increases the likelihood

Emile van Lieshout; Ellen van Wilgenburg; Mark Adrian Elgar

2009-01-01

122

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

Federal Register 2010, 2011, 2012, 2013

...504), where it is considered an aggressive invasive weed of marshes and wetlands...1-11), and at least 4 particularly aggressive species have severely impacted the native...elevation range due to their particularly aggressive nature and large colony sizes...

2010-06-24

123

Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima  

Microsoft Academic Search

Cold-shock proteins (Csps) are a subgroup of the cold- induced proteins preferentially expressed in bacteria and other organisms on reduction of the growth temperature below the physiological temperature. They are related to the cold-shock domain found in eukaryotes and are some of the most conserved proteins known. Their exact function is still not known, but translational regulation, possibly via RNA

Werner Kremer; Benjamin Schuler; Stefan Harrieder; Matthias Geyer; Wolfram Gronwald; Christine Welker; Rainer Jaenicke; Hans R. Kalbitzer

124

Effects of wrack burial in salt stressed habitats: Batis maritima in a southwest Atlantic marsh  

Microsoft Academic Search

In coastal salt marshes, mats of wrack (dead plant stems) that are deposited on the marsh by high tides can kill underlying vegetation and initiate secondary succession. The importance of wrack disturbance in northwest Atlantic salt marshes has been a topic of recent debate. The importance of wrack disturbance in southwest Atlantic salt marshes, which experience a very different climate

Steven C. Pennings; Christina L. Richards

1998-01-01

125

An analysis of segmentation dynamics throughout embryogenesis in the centipede Strigamia maritima  

PubMed Central

Background Most segmented animals add segments sequentially as the animal grows. In vertebrates, segment patterning depends on oscillations of gene expression coordinated as travelling waves in the posterior, unsegmented mesoderm. Recently, waves of segmentation gene expression have been clearly documented in insects. However, it remains unclear whether cyclic gene activity is widespread across arthropods, and possibly ancestral among segmented animals. Previous studies have suggested that a segmentation oscillator may exist in Strigamia, an arthropod only distantly related to insects, but further evidence is needed to document this. Results Using the genes even skipped and Delta as representative of genes involved in segment patterning in insects and in vertebrates, respectively, we have carried out a detailed analysis of the spatio-temporal dynamics of gene expression throughout the process of segment patterning in Strigamia. We show that a segmentation clock is involved in segment formation: most segments are generated by cycles of dynamic gene activity that generate a pattern of double segment periodicity, which is only later resolved to the definitive single segment pattern. However, not all segments are generated by this process. The most posterior segments are added individually from a localized sub-terminal area of the embryo, without prior pair-rule patterning. Conclusions Our data suggest that dynamic patterning of gene expression may be widespread among the arthropods, but that a single network of segmentation genes can generate either oscillatory behavior at pair-rule periodicity or direct single segment patterning, at different stages of embryogenesis.

2013-01-01

126

Entomological fauna from Reserva Biológica do Atol das Rocas, RN, Brazil: I. Morphospecies composition.  

PubMed

Atol das Rocas, the unique atoll in the South-western Atlantic, is located 144 nautical miles (266 Km) northeast from the city of Natal, NE Brazil and 80 nautical miles from Arquipélago de Fernando de Noronha, with geographic co-ordinates 3 masculine51'S and 33 masculine49"W. It's of volcanic origin and coralline formation. The reef is ellipsoid, its largest axis (E-W) is approximately 3.7 km long, and the shortest (N-S) is 2.5 km. Inside the lagoon, there are two islands: the Ilha do Farol and Ilha do Cemitério, which comprehend 7.2 Km2 of emerged area. The Atol das Rocas lodges 143,000 birds, mainly by Sula dactilatra, S. leucogaster, Anous stolidus, A. minuta and Sterna fuscata. Due to their remote location, the islands remain largely undisturbed by the human activities. Aiming to a first characterization of the entomological diversity and the general trophic niches of atoll's entomofauna, three collects were made (1994, 1995 and 1996) utilizing several methods for a wide sample. One thousand six hundred and six insect specimens were collected belonging to eight orders: 1. Coleoptera - 333 individuals of Dermestidae (Dermestes cadaverinus); Tenebrionidae (Phaleria testacea and morphospecies) and Curculionidae (one morphospecies); 2. Dermaptera - 50 individuals of Carcinophoridae (Anisolabis maritima); 3. Diptera - 281 individuals of Ephydridae (Scatella sp. and Hecamede sp.) and Hippoboscidae (one morphospecies); 4. Hymenoptera - 45 individuals of Formicidae (Brachymyrmex sp.); 5. Lepidoptera - 111 individuals of Microlepidoptera (one morphospecies); 6. Mallophaga - 18 individuals in birds (two morphospecies); 7. Orthoptera - 237 individuals of Acrididae (Schistocerca cancellata), Tridactylidae (one morphospecies) and Blattidae (three morphospecies); 8. Thysanoptera -531 individuals (one morphospecies). Also were collected 112 individuals of Arachnida. The taxa of the Order Araneae were represented by the families: 1. Miturgidae (Cheiracanthium inclusum); 2. Salticidae (two morphospecies) and 3. Segestriidae (Ariadna sp.); 4. Theridiidae (Achaearanea sp. and Latrodectus geometricus). For the Order Scorpionida, only samples of Buthidae (Isometrus maculatus) were collected. Through field observations, it was concluded the most insects are detritophagous and/or necrophagous. It is suggested that which the dimension of ecological niches of the insects are a function of the droppings, trash and corpses of birds. A low diversity in the entomofauna of atoll, with its 25 morphospecies, was ascertained. PMID:10959113

Almeida; Marchon-Silva; Ribeiro; Serpa-Filho; Almeida; Costa

2000-05-01

127

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)

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.

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

2012-05-01

128

Ancient coastal wells of Caesarea Maritima, Israel, an indicator for relative sea level changes during the last 2000 years  

NASA Astrophysics Data System (ADS)

During the detailed excavations of ancient Caesarea, Israel, East Mediterranean, 64 coastal water wells have been examined that date from the early Roman period (with the oldest occurring in the 1st century AD), up to the end of the Crusader period (mid-13th century AD). The depths of these coastal water wells establish the position of the ancient water table and therefore the position of sea level for the first century AD up to 1300 AD. The connection between the coastal water table and changes in sea level has been established from modern observations in several wells on time scales of days and months and this is used to reconstruct sea level during historical time. The results indicate that during the Byzantine period, sea level at Caesarea was higher by about 30 cm than today. The Late Moslem and Crusader data shows greater fluctuations but the data sets are also much smaller than for the earlier periods. The consistency of the data indicates that the near-coastal well data from Caesarea provides a reliable indicator of sea-level change, with an accuracy of about 10-15 cm. These results are consistent with observations for earlier periods and, with comparisons to model-predicted glacio-hydro isostatic sea-level change, indicate that ocean volumes have been constant for much of the past 2000 years. The well data is also consistent with an absence of significant vertical tectonic movement of the coast at Caesarea over about 2000 years.

Sivan, D.; Lambeck, K.; Toueg, R.; Raban, A.; Porath, Y.; Shirman, B.

2004-05-01

129

Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima  

Microsoft Academic Search

Exonuclease VII was first identified in 1974 as a DNA exonuclease that did not require any divalent cations for activity. Indeed, Escherichia coli ExoVII was identified in partially purified extracts in the pre- sence of EDTA. ExoVII is comprised of two subunits (XseA and XseB) that are highly conserved and pre- sent in most sequenced prokaryotic genomes, but are not

Andres A. Larrea; Ilene M. Pedroso; Arun Malhotra; Richard S. Myers

2008-01-01

130

The genetic structure of sea beet (Beta vulgaris ssp. maritima) populations. III. Detection of isolation by distance at microsatellite loci  

Microsoft Academic Search

Variation at three microsatellite loci was investigated in five populations of sea beet on the Dorset coast. Genetic variation among the populations was estimated using two different methods. Estimates of FST were obtained using the program FSTAT, and estimates of RST were obtained using the program AMOVA. These different estimates of genetic distance were used to test for isolation by

A F Raybould; R J Mogg; C Aldam; C J Gliddon; R S Thorpe; R T Clarke

1998-01-01

131

The effect of macrofauna, meiofauna and microfauna on the degradation of Spartina maritima detritus from a salt marsh area  

Microsoft Academic Search

Decomposition of salt marsh plants results from physical, chemical and biological processes including abiotic and biotic fragmentation, microbial decay and chemical transformation. According to literature data, only a few species have the ability to feed directly on living plant material, so fungi and bacteria seem to be the principal competitors for the organic substrates. Nevertheless, by consuming bacteria, protists and

Ana Isabel Lillebø; Mogens R. Flindt; Miguel Ângelo Pardal; João Carlos Marques

1999-01-01

132

Molecular analysis of hyperthermophilic endoglucanase Cel12B from Thermotoga maritima and the properties of its functional residues  

PubMed Central

Background Although many hyperthermophilic endoglucanases have been reported from archaea and bacteria, a complete survey and classification of all sequences in these species from disparate evolutionary groups, and the relationship between their molecular structures and functions are lacking. The completion of several high-quality gene or genome sequencing projects provided us with the unique opportunity to make a complete assessment and thorough comparative analysis of the hyperthermophilic endoglucanases encoded in archaea and bacteria. Results Structure alignment of the 19 hyperthermophilic endoglucanases from archaea and bacteria which grow above 80°C revealed that Gly30, Pro63, Pro83, Trp115, Glu131, Met133, Trp135, Trp175, Gly227 and Glu229 are conserved amino acid residues. In addition, the average percentage composition of residues cysteine and histidine of 19 endoglucanases is only 0.28 and 0.74 while it is high in thermophilic or mesophilic one. It can be inferred from the nodes that there is a close relationship among the 19 protein from hyperthermophilic bacteria and archaea based on phylogenetic analysis. Among these conserved amino acid residues, as far as Cel12B concerned, two Glu residues might be the catalytic nucleophile and proton donor, Gly30, Pro63, Pro83 and Gly227 residues might be necessary to the thermostability of protein, and Trp115, Met133, Trp135, Trp175 residues is related to the binding of substrate. Site-directed mutagenesis results reveal that Pro63 and Pro83 contribute to the thermostability of Cel12B and Met133 is confirmed to have role in enhancing the binding of substrate. Conclusions The conserved acids have been shown great importance to maintain the structure, thermostability, as well as the similarity of the enzymatic properties of those proteins. We have made clear the function of these conserved amino acid residues in Cel12B protein, which is helpful in analyzing other undetailed molecular structure and transforming them with site directed mutagenesis, as well as providing the theoretical basis for degrading cellulose from woody and herbaceous plants.

2014-01-01

133

Effect of procyanidins from Pinus maritima on glutathione levels in endothelial cells challenged by 3-morpholinosydnonimine or activated macrophages.  

PubMed

The effects of reactive nitrogen species on glutathione homeostasis in human endothelial ECV 304 cells challenged by 3-morpholinosydnonimine-N-ethylcarbamide (SIN-1) on RAW 264.7 activated macrophages using a co-culture model were investigated. SIN-1 or macrophages activated by lipopolysaccharide plus interferon-gamma induced a significant glutathione decrease in ECV 304 cells. Pre-incubation of ECV 304 cells with French maritime pine bark extract containing mainly oligomeric procyanidins protected endothelial cells from activated macrophage-induced glutathione depletion. Data demonstrate that reactive nitrogen species generated with different kinetics and mechanisms impair glutathione levels in endothelial cells, and that pine bark extract significantly enhances antioxidant defenses. PMID:10658822

Rimbach, G; Virgili, F; Park, Y C; Packer, L

1999-01-01

134

75 FR 54649 - Endangered Wildlife; Permits  

Federal Register 2010, 2011, 2012, 2013

...endemic to the island of Kauai; to take the flying earwig Hawaiian damselfly (Megalagrion nesiotes), which is endemic to the island of Maui; and to take the Pacific Hawaiian damselfly (Megalagrion pacificum), which is endemic to the islands...

2010-09-08

135

Insectos en Hogares y Bodegas de Alimentos, de Importancia para la Salud Publica (Household and Stored-Food Insects of Public Health Importance and Their Control).  

National Technical Information Service (NTIS)

A variety of drawings to help identify a variety of insects. Short descriptions review insect habitat and chemical control methods. The insects covered include: silverfish, cockroaches, earwigs, ants, moths, chiggers, beetles, grubs and weevils. A bibliog...

1971-01-01

136

The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling  

PubMed Central

Reverse gyrase is the only topoisomerase that can introduce positive supercoils into DNA in an ATP-dependent process. It has a modular structure and harnesses a helicase-like domain to support a topoisomerase activity, thereby creating the unique function of positive DNA supercoiling. The isolated topoisomerase domain can relax negatively supercoiled DNA, an activity that is suppressed in reverse gyrase. The isolated helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain. Inter-domain communication thus appears central for the functional cooperation of the two domains. The latch, an insertion into the helicase-like domain, has been suggested as an important element in coordinating their activities. Here, we have dissected the influence of the latch on nucleotide and DNA binding to the helicase-like domain, and on DNA supercoiling by reverse gyrase. We find that the latch is required for positive DNA supercoiling. It is crucial for the cooperativity of DNA and nucleotide binding to the helicase-like domain. The latch contributes to DNA binding, and affects the preference of reverse gyrase for ssDNA. Thus, the latch coordinates the individual domain activities by modulating the helicase-like domain, and by communicating changes in the nucleotide state to the topoisomerase domain.

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

2011-01-01

137

Interactions between indole-3-acetic acid (IAA) with a lectin from Canavalia maritima seeds reveal a new function for lectins in plant physiology.  

PubMed

Indole-3-acetic acid (IAA) bound is considered a storage molecule and is inactive. However, some studies have proposed an additional possible regulatory mechanism based on the ability of lectins to form complexes with IAA. We report the first crystal structure of ConM in complex with IAA at 2.15 ? resolution. Based on a tetrameric model of the complex, we hypothesize how the lectin controls the availability of IAA during the early seedling stages, indicating a possible new physiological role for these proteins. A free indole group is also bound to the protein. The ConM interaction with different forms of IAA is a strategy to render the phytohormone unavailable to the cell. Thus, this new physiological role proposed for legume lectins might be a novel mechanism by which IAA levels are decreased in addition to the destruction and formation of new complexes in the later stages of seed germination. PMID:23727478

Delatorre, Plinio; Silva-Filho, José Caetano; Rocha, Bruno Anderson Matias; Santi-Gadelha, Tatiane; da Nóbrega, Raphael Batista; Gadelha, Carlos Alberto Almeida; do Nascimento, Kyria Santiago; Nagano, Celso Shiniti; Sampaio, Alexandre Holanda; Cavada, Benildo Sousa

2013-09-01

138

French maritime pine bark (Pinus maritima Lam.) extract (Flavangenol) prevents chronic UVB radiation-induced skin damage and carcinogenesis in melanin-possessing hairless mice.  

PubMed

A French maritime pine bark extract, Flavangenol, is widely used as a nutritional supplement for protection against atherosclerosis, hypertension, diabetes, etc. Chronic exposure to solar UV radiation damages skin, increasing cutaneous thickness, wrinkling and pigmentation, as well as reducing elasticity, and causes skin cancer. The aim of this study was to examine the effects of flavangenol on skin damage and the incidence of skin tumors caused by long-term UVB irradiation in melanin-possessing hairless mice. The oral administration of flavangenol (60, 200 or 600 mg kg(-1), twice daily) significantly inhibited increases in skin thickness, and the formation of wrinkles and melanin granules, as well as increases in the diameter and length of skin blood vessels. Furthermore, it prevented increases in numbers of apoptotic, Ki-67-positive and 8-hydroxy-2'-deoxyguanosine (8-OHdG)-positive cells, and the expression of skin vascular endothelial growth factor (VEGF) induced by chronic UVB irradiation. The effect on these biomarkers was associated with a reduction in the incidence of tumors in mice. The antiphotoaging and anticarcinogenetic activities of flavangenol may be due to inhibition of the expression of Ki-67, 8-OHdG and VEGF through a scavenging effect on reactive oxygen species. PMID:20497364

Kimura, Yoshiyuki; Sumiyoshi, Maho

2010-01-01

139

Anthocyanins of the Squill  

Microsoft Academic Search

IN the course of an investigation of the cardiotonic glycosides and flavonoid content in the squill (Scilla maritima L. or Urginea maritima Baker), several anthocyanins were identified, we believe, for the first time.

F. A. Vega; Consuelo Martin

1963-01-01

140

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

Microsoft Academic Search

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

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

2007-01-01

141

Recent Horizontal Transfer of Mellifera Subfamily Mariner Transposons into Insect Lineages Representing Four Different Orders Shows that Selection Acts Only During Horizontal Transfer  

Microsoft Academic Search

We report the isolation and sequencing of genomic copies of mariner transposons involved in recent horizontal transfers into the genomes of the European earwig, Forficula auricularia; the European honey bee, Apis mellifera; the Mediterranean fruit fly, Ceratitis capitata; and a blister beetle, Epicauta funebris, insects from four different orders. These elements are in the mellifera subfamily and are the second

David J. Lampe; David J. Witherspoon; Felipe N. Soto-Adames; Hugh M. Robertson

2003-01-01

142

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

ERIC Educational Resources Information Center

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

Prince, Christopher G.

2008-01-01

143

Spring staging in Brent Geese Branta bernicla : feeding constraints and the impact of diet on the accumulation of body reserves  

Microsoft Academic Search

The diet composition of Brent Geese Branta bernicla on a salt-marsh was quantified. Puccinellia maritima was the principal food species, while Plantago maritima and Triglochin maritima were less commonly taken. Festuca rubra only acted as a substitute for Puccinellia when production of the latter species dropped. The metabolizable energy of the food plants ranged from 5 to 11 kJ·g-1. By

Jouke Prop; Charlotte Deerenberg

1991-01-01

144

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

PubMed

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

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

2013-09-01

145

Physicochemical, functional and cooking properties of under explored legumes, Canavalia of the southwest coast of India  

Microsoft Academic Search

Nutritionally potential under explored wild legumes viz., Canavalia cathartica and Canavalia maritima are widely distributed in mangroves and sand dunes, respectively, in Southwest coast of India. Physicochemical, functional and cooking properties of dried seeds of these legumes have been evaluated. Seeds and cotyledons of C. cathartica are larger and possessing higher hydration and swelling capacity than that of C. maritima

S. Seena; K. R. Sridhar

2005-01-01

146

An insight into the interaction mode between CheB and chemoreceptor from two crystal structures of CheB methylesterase catalytic domain  

PubMed Central

We have determined 2.2 Å 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 ?/? 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.

Cho, Kwang-Hwi; Crane, Brian R.; Park, SangYoun

2011-01-01

147

An offspring signal of quality affects the timing of future parental reproduction  

PubMed Central

Solicitation signals by offspring are well known to influence parental behaviour, and it is commonly assumed that this behavioural effect translates into an effect on residual reproduction of parents. However, this equivalence assumption concerning behavioural and reproductive effects caused by offspring signals remains largely untested. Here, we tested the effect of a chemical offspring signal of quality on the relative timing and amount of future reproduction in the European earwig (Forficula auricularia). We manipulated the nutritional condition of earwig nymphs and exposed females to their extract, or to solvent as a control. There were no significant main effects of exposure treatment on 2nd clutch production, but exposure to extracts of well-fed nymphs induced predictable timing of the 2nd relative to the 1st clutch. This result demonstrates for the first time that an offspring signal per se, in the absence of any maternal behaviour, affects maternal reproductive timing, possibly through an effect on maternal reproductive physiology.

Mas, Flore; Kolliker, Mathias

2011-01-01

148

Quantitative composition of the defensive secretion of Bledius species (Coleoptera: Staphylinidae: Oxytelinae) is adapted to naturally occurring predators  

Microsoft Academic Search

Summary The adaptation of defensive secretions to their target organisms was examined for the abdominal gland secretions ofBledius furcatus, B. spectabilis andB. arenarius. Therefore the target organisms of the secretion of theseBledius species (i.e. their predators) had to be identified. At the collection sites examined these were the earwigLabidura riparia, the antCataglyphis bicolor, the flyLispe candicans, different carabids of the

Johannes L. M. Steidle; Konrad Dettner

1993-01-01

149

Mesodiplatys venado sp. nov. (Dermaptera: Diplatyidae), probable evidence of contact between Neotropical and Malagasy faunas.  

PubMed

A new earwig of the Malagasy genus Mesodiplatys stat. nov., M. venado sp. nov. (Dermaptera: Diplatyidae) is described from Peru (Departament Junin, Satipo Province). The diagnosis and composition of the genus Mesodiplatys stat. nov. are discussed. A detailed morphological description of the new species is given. The possible biogeographical significance of the find as evidence of link between South American and Malagasy fauna is briefly considered. PMID:24870348

Anisyutkin, Leonid N

2014-01-01

150

Which insect species numerically respond to allochthonous inputs?  

PubMed

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

Sugiura, Shinji; Ikeda, Hiroshi

2013-08-01

151

Protocol for Large-Scale Collection, Processing, and Storage of Seeds of Two Mesohaline Submerged Aquatic Plant Species.  

National Technical Information Service (NTIS)

A previous pilot study (Ailstock and Shafer 2004) established the seed reproductive potential of two species of submerged aquatic angiosperms, Ruppia maritima (widgeon grass) and Potamogeton perfoliatus (redhead grass), that predominate in the mesohaline ...

S. Ailstock D. Shafer

2006-01-01

152

Analysis of condensed and hydrolysable tannins from commercial plant extracts  

Microsoft Academic Search

High performance liquid chromatography (HPLC)\\/DAD and MS qualitative and quantitative analyses of polyphenols, hydrolysable and condensed tannins from Pinus maritima L. and tannic acid (TA) extracts were performed using normal and reverse phase.Normal-phase HPLC was more suitable for pine bark (PBE) and tannic acid extracts analysis. The chromatographic profile revealed that P. maritima L. extract was mainly composed by polymeric

A. Romani; F. Ieri; B. Turchetti; N. Mulinacci; F. F. Vincieri; P. Buzzini

2006-01-01

153

Cues of Maternal Condition Influence Offspring Selfishness  

PubMed Central

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.

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

2014-01-01

154

Inbreeding depression in an insect with maternal care: influences of family interactions, life stage and offspring sex.  

PubMed

Although inbreeding is commonly known to depress individual fitness, the severity of inbreeding depression varies considerably across species. Among the factors contributing to this variation, family interactions, life stage and sex of offspring have been proposed, but their joint influence on inbreeding depression remains poorly understood. Here, we demonstrate that these three factors jointly shape inbreeding depression in the European earwig, Forficula auricularia. Using a series of cross-breeding, split-clutch and brood size manipulation experiments conducted over two generations, we first showed that sib mating (leading to inbred offspring) did not influence the reproductive success of earwig parents. Second, the presence of tending mothers and the strength of sibling competition (i.e. brood size) did not influence the expression of inbreeding depression in the inbred offspring. By contrast, our results revealed that inbreeding dramatically depressed the reproductive success of inbred adult male offspring, but only had little effect on the reproductive success of inbred adult female offspring. Overall, this study demonstrates limited effects of family interactions on inbreeding depression in this species and emphasizes the importance of disentangling effects of sib mating early and late during development to better understand the evolution of mating systems and population dynamics. PMID:23981229

Meunier, J; Kölliker, M

2013-10-01

155

Were the original eubacteria thermophiles?  

NASA Technical Reports Server (NTRS)

Thermotoga maritima is one of the more unusual eubacteria: It is highly thermophilic, growing at temperatures higher than any other eubacterium; its cell wall appears to have a unique structure and its lipids a unique composition; and the organism is surrounded by a loose-fitting sheath of unknown function. Its phenotypic uniqueness is matched by its phylogenetic position; Thermotoga maritima represents the deepest known branching in the eubacterial line of descent, as measured by ribosomal RNA sequence comparisons. T. maritima also represents the most slowly evolving of eubacterial lineages. The fact that the two deepest branchings in the eubacterial line of descent (the other, the green non-sulfur bacteria and relatives, i.e. Chloroflexus, Thermomicrobium, etc.) are both basically thermophilic and slowly evolving, strongly suggests that all eubacteria have ultimately arisen from a thermophilic ancestor.

Achenbach-Richter, L.; Gupta, R.; Stetter, K. O.; Woese, C. R.; Johnson, P. C. (Principal Investigator)

1987-01-01

156

Sugar Transport and Metabolism in Thermotoga  

SciTech Connect

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.

Noll, Kenneth M.; Romano, Antonio H.

2003-02-11

157

Non-target effect of organic insecticides: effect of two plant extracts on soil microbial biomass and enzymatic activities in soil.  

PubMed

Efficacious botanical derivatives can provide an alternative to synthetic pesticides for organic farming systems. However, there is lack of information regarding the side effects of organic pesticides on key soil ecological processes. In this study, we investigated the effects of aqueous extracts from Urginea maritima and Euphorbia myrsinites exhibiting translaminar and systemic activity against pests on microbial biomass and enzymatic activities in soil. Two grams of plant material was extracted with 100 ml of water and then diluted 1:100, 2:100, and 4:100 with distilled water. Diluted plant extracts were applied around hypocotyl of tomato by soil drench. The effect of both plant extracts on microbial biomass C, amount of total N and organic C, and enzymatic activity in soil was significant. After the last application, the highest microbial biomass C was determined in the lowest U. maritima concentration (U 1:100). Soils treated with the highest concentration of U. maritima (U 4:100) had always lower SMBC content than control soil. All concentrations of E. myrsinites decreased microbial biomass C by 18% to 27% compared to the control. Total nitrogen and organic carbon decreased in soils without (control) and with treated U. maritima extract from first application to last application. Phosphatase, urease, and beta-glucosidase activities were monitored in plant extract-treated soils. Except U. maritima 1:100 treatments of second and fourth applications, the other treatments of plant extracts negatively affected enzymatic activity in soil. U. maritima and E. myrsinites plant extracts exhibited different effects on soil microbial biomass and activity, probably because of their different chemical contents. PMID:19415510

Okur, Nur; Tuna, A Levent; Okur, Bülent; Altunlu, Hakan; Kayikçio?lu, H Hüsnü; Civelek, Hasan S

2010-06-01

158

Discontinuous Occurrence of the hsp70 (dnaK) Gene among Archaea and Sequence Features of HSP70 Suggest a Novel Outlook on Phylogenies Inferred from This Protein  

PubMed Central

Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus and Thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacterium Thermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum and Thermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence of hsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70 (dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70 (dnaK) gene.

Gribaldo, Simonetta; Lumia, Valentina; Creti, Roberta; Conway de Macario, Everly; Sanangelantoni, Annamaria; Cammarano, Piero

1999-01-01

159

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

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.

Swithers, Kristen S [University of Connecticut, Storrs; DiPippo, Jonathan L [University of Connecticut, Storrs; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Lykidis, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Stetter, Karl O [Universitat Regensburg, Regensburg, Germany; Nelson, Karen E [J. Craig Venter Institute; Gogarten, Peter [University of Connecticut, Storrs; Noll, Kenneth M [University of Connecticut, Storrs

2011-01-01

160

Molecular characterization of the glucose isomerase from the thermophilic bacterium Fervidobacterium gondwanense.  

PubMed

The gene coding for xylose isomerase from the thermophilic bacterium Fervidobacterium gondwanense was cloned and overexpressed in Escherichia coli. The produced xylose isomerase (XylA), which closely resembles counterparts from Thermotoga maritima and T. neapolitana, was purified and characterized. It is optimally active at 70 degrees C, pH 7.3, with a specific activity of 15.0 U/mg for the interconversion of glucose to fructose. When compared with T. maritima XylA at 85 degrees C, a higher catalytic efficiency was observed. Divalent metal ions Co2+ and Mg2+ were found to enhance the thermostability. PMID:20718290

Kluskens, L D; Zeilstra, J; Geerling, A C M; de Vos, W M; van der Oost, J

2010-09-01

161

Nutritional and antinutritional significance of four unconventional legumes of the genus Canavalia – A comparative study  

Microsoft Academic Search

Developing countries are under the clutch of malnutrition due to a lack of protein rich food. Protein supply can be broadened by exploration and exploitation of alternative legume sources. Even though many wild legume landraces have been identified, their utilization is limited due to insufficient attention. Canavalia gladiata, Canavalia ensiformis, Canavalia maritima and Canavalia cathartica are the common under-exploited legume

K. R. Sridhar; S. Seena

2006-01-01

162

RADIOCARBON CHRONOLOGIES OF HOLOCENE LACUSTRINE SEDIMENTS FROM THE SOUTHERN COAST OF BUENOS AIRES PROVINCE, ARGENTINA  

Microsoft Academic Search

Two lacustrine sediment sequences, La Olla 1 and Laguna del Sauce Grande, on the southern coast of Buenos Aires Province, Argentina, were investigated for carbon reservoir effects, which may influence age-depth chronologies. Fruits of the submerged macrophyte Ruppia cf. maritima from the La Olla 1 sequence, and gastropod shells of Heleobia parchappii from the Laguna del Sauce Grande core, were

Sonia L Fontana

2007-01-01

163

Pycnogenol® Augments Macrophage Phagocytosis and Cytokine Secretion  

Microsoft Academic Search

We previously reported that Pycnogenol , procyanidins extracted from the bark of French maritime ® pine (Pinus maritima Aiton; the official botanical name is now Pinus pinaster Aiton) is a potent free radical scavenger. It has been shown to inhibit macrophage oxidative burst. Macrophages carry out their microbicidal and tumoricidal activities via oxygen-dependent and oxygen-independent mechanisms. The present study investigated

2002-01-01

164

Pycnogenol: A blend of procyanidins with multifaceted therapeutic applications?  

Microsoft Academic Search

Great interest is currently centred on the biologic activities of pycnogenol a standardized plant extract obtained from the bark of the French maritime pine Pinus pinaster (formerly known as Pinus maritima), Aiton, subspecies Atlantica des Villar (Pycnogenol®, Horphag Research Ltd., UK, Geneve, Switzerland), which grows in the coastal southwest France. The quality of this extract is specified in the United

Gabriele D'Andrea

2010-01-01

165

Response of primary producers to nutrient enrichment in a shallow estuary  

USGS Publications Warehouse

Shallow coastal systems worldwide are exhibiting increased algal growth in response to nutrient enrichment. This study evaluates primary production patterns in an estuarine system (Bass Harbor Marsh, ME, USA) receiving low levels of anthropogenic nitrogen. Biomass, areal coverage and in situ oxygen production of green macroalgae, Ruppia Maritima, and Phytoplankton were measured over a growing season to determine net ecosystem production. Macroalgae and R. maritima exhibited seasonal biomass curves with early summer peaks; however, peak biomass of macroalgae [150 g dry weight (wt) m-2] was substantially greater that R. maritima (33 g dry wt m-2) Phytoplankton biomass, measured as chlorophyll a, was low (<1 ??g 1-1) early in the season and peaked (11 ??g 1-1) following a mid-summer decline in macroalgal biomass, suggesting a competitive interaction with macroalgae. Instantaneous net production rates varied over the growing season for all 3 primary producers. R. maritima net production ranged from near zero to 2.7 mg C g-1 dry wt h-1, with higher rates during summer and much of the seasonal variability explained by temperature. Macroalgal (0.88 to 5.0 mg C g-1 dry wt h-1) and phytoplankton (0 to 28 mg C m-3 h-1) net production did not exhibit any clear seasonal signal. Net primary production calculated on an areal basis demonstrated macroalgae's dominance in the lower basin of Bass Harbor Marsh, with peak summer rates (400 mg C m-2 h-1) greatly exceeding maximum rates for both R maritima (70 mg C m-2h-1) and phytoplankton (12 mg C m-2 h-1). When compared to other New England estuarine sites with short residence times, nutrient loading and peak green macroalgal biomass in Bass Harbor Marsh are relatively low; however, the strong dominance of opportunistic green macroalgae is a pattern that is characteristic of shallow coastal systems undergoing eutrophication.

Kinney, E. H.; Roman, C. T.

1998-01-01

166

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

PubMed Central

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.

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

2013-01-01

167

Beneficial Insects  

NSDL National Science Digital Library

Tutorials on insect predators that feed on insect and mite pests. Each tutorial has 50 questions; incorrect answers lead to additional information. Covers brown lacewings, ambush bugs, dragonflies, damselflies, paper wasps, earwigs, long-legged flies, predaceous mites, damsel bugs, minute pirate bug, tiger beetles, tachnid flies, parasitic nematodes, entomopathogenic fungi and viruses. Requires Windows. SOme illustrations may be most apporopriate for the southern U.S. A couple of the questions have rather arbitrary answers; in general, the tutorials are well constructed and the information is accurate. Requires Windows operating system; program must be downloaded to the comptuer's hard drive, but once loaded is easy to launch and use. $15. Part number SW 154.

0002-11-30

168

Effect of habitat quality on diet flexibility in Barbary macaques.  

PubMed

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. Am. J. Primatol. 76:679-693, 2014. © 2014 Wiley Periodicals, Inc. PMID:24573596

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

169

Characterization of ribonuclease P RNAs from thermophilic bacteria.  

PubMed Central

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

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

1993-01-01

170

Large methyl halide emissions from south Texas salt marshes  

NASA Astrophysics Data System (ADS)

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.

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

2014-06-01

171

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

PubMed Central

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.

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-Andre; Schimmel, Paul; Wilson, Ian A.

2010-01-01

172

Structural Biology of S-Adenosylmethionine Decarboxylase  

PubMed Central

S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical enzyme in the polyamine biosynthetic pathway and a subject of many structural and biochemical investigations for anti-cancer and anti-parasitic therapy. The enzyme undergoes an internal serinolysis reaction as a post-translational modification to generate the active site pyruvoyl group for the decarboxylation process. The crystal structures of AdoMetDC from Homo sapiens, Solanum tuberosum, Thermotoga maritima, and Aquifex aeolicus have been determined. Numerous crystal structures of human AdoMetDC and mutants have provided insights into the mechanism of autoprocessing, putrescine activation, substrate specificity, and inhibitor design to the enzyme. The comparison of the human and potato enzyme with the T. maritima and A. aeolicus enzymes supports the hypothesis that the eukaryotic enzymes evolved by gene duplication and fusion. The residues implicated in processing and activity are structurally conserved in all forms of the enzyme, suggesting a divergent evolution of AdoMetDC.

Bale, Shridhar; Ealick, Steven E.

2010-01-01

173

Identification and molecular characterization of an endoglucanase gene, celS , from the extremely thermophilic archaeon Sulfolobus solfataricus  

Microsoft Academic Search

A genomic region upstream of the alcohol dehydrogenase (Ssadh) gene was cloned and sequenced from a library of Sulfolobus solfataricus MT4 strain. The isolated 4,040-bp DNA fragment revealed an open reading frame (celS), lying in the opposite direction to Ssadh, which showed significant similarity to endo-#-1,4-glucanases from Pyrococcus furiosus, Thermotoga maritima, and Thermotoga neapolitana. celS was shown to be a

Danila Limauro; Raffaele Cannio; Gabriella Fiorentino; Mosè Rossi; Simonetta Bartolucci

2001-01-01

174

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

PubMed

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

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

2014-07-01

175

Niche expansion, body size, and survival in Galápagos marine iguanas  

Microsoft Academic Search

Foraging theory predicts that dietary niche breadth should expand as resource availability decreases. However, Galpagos marine\\u000a iguanas often die during algae shortages (El Nios) although land plants abound where they rest and reproduce. On Seymour\\u000a Norte island, a subpopulation of iguanas exhibited unique foraging behavior: they consistently included the succulent beach\\u000a plant B. maritima in their diet. We investigated the

Martin Wikelski; Peter H. Wrege

2000-01-01

176

Effects of ingestion of seeds by sika deer ( Cervus nippon ) and dung presence on their germination in a herbaceous community  

Microsoft Academic Search

In a herbaceous community subjected to continual impacts of sika deer (Cervus\\u000a nippon), I examined the effects of seed ingestion by deer on seeds by comparing the ripening and germination rates of seeds of two\\u000a dominant species, Zoysia japonica and Hydrocotyle maritima, between seeds taken out of fecal pellets (deer-ingested seeds) and mature seeds collected directly from living plants (control

Haruna Ishikawa

2010-01-01

177

Sequential Aldol Condensation Catalyzed by Hyperthermophilic 2-Deoxy-D-Ribose-5Phosphate Aldolase  

Microsoft Academic Search

Genes encoding 2-deoxy-D-ribose-5-phosphate aldolase (DERA) homologues from two hyperthermophiles, the archaeon Pyrobaculum aerophilum and the bacterium Thermotoga maritima, were expressed individually in Escherichia coli, after which the structures and activities of the enzymes produced were characterized and compared with those of E. coli DERA. To our surprise, the two hyperthermophilic DERAs showed much greater catalysis of sequential aldol condensation using

Haruhiko Sakuraba; Kazunari Yoneda; Kumiko Yoshihara; Kyoko Satoh; Ryushi Kawakami; Yoshihiro Uto; Hideaki Tsuge; Katsuyuki Takahashi; Hitoshi Hori; Toshihisa Ohshima

2007-01-01

178

Nectar-carbohydrate production and composition vary in relation to nectary anatomy and location within individual flowers of several species of Brassicaceae  

Microsoft Academic Search

.   Nectar-carbohydrate production and composition were investigated by high-performance liquid chromatography and enzymology\\u000a in nine species from five tribes of the Brassicaceae. In six species (Arabidopsis thaliana (L.) Heynh., Brassica napus L., B. rapa L., Lobularia maritima (L.) Desv., Raphanus sativus L., Sinapis arvensis L.) that produced nectar from both lateral nectaries (associated with the short stamens) and median nectaries

Arthur R. Davis; Jeffrey D. Pylatuik; Joelle C. Paradis; Nicholas H. Low

1998-01-01

179

Nutritional and antinutritional components of Canavalia spp. seeds from the west coast sand dunes of India  

Microsoft Academic Search

Seeds of two coastal sand dune wild legumes, Canavalia cathartica and Canavalia maritima from the west coast of India were analyzed for their nutritional and antinutritional properties. The seeds contained 35.5 and 34.1% crude protein, 52.8 and 50.5% crude carbohydrates, 1.3 and 1.7% crude lipids and 3.1 and 3.5% ash content, respectively. Among the minerals, potassium was the highest followed

A. B. Arun; K. R. Sridhar; N. S. Raviraja; E. Schmidt; K. Jung

2003-01-01

180

Antioxidant activity of procyanidin-containing plant extracts at different pHs  

Microsoft Academic Search

Anti-oxidant activity was measured for a Pinus radiata bark extract (bark 1), a Pinus maritima bark extract (bark 2), two grape seed extracts, three grape skin extracts, catechin, trolox, ascorbic acid (vitamin C) and calcium ascorbate. The activity was analyzed as ability to scavenge superoxide radicals in a hypoxanthine-xanthine oxidase system, using NBT and WST-1 assays. The 50% inhibition (IC50)

Jacqueline E. Wood; Senti T. Senthilmohan; Alexander V. Peskin

2002-01-01

181

Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS 2 and spectral counting  

Microsoft Academic Search

Probing the intracellular proteome of Thermotoga maritima and Caldicellulosiruptor saccharolyticus in pure and co-culture affords a global investigation into the machinery and mechanisms enduring inside the bacterial thermophilic\\u000a cell at the time of harvest. The second of a two part study, employing GeLC-MS2 a variety of proteins were confidently identified with <1% false discovery rate, and spectral counts for label-free

David Muddiman; Genna Andrews; Derrick Lewis; Jaspreet Notey; Robert Kelly

2010-01-01

182

Sulphide tolerance in coastal halophytes  

Microsoft Academic Search

The effect of sulphide on the growth of several species of salt-marsh plants was investigated. Relative growth rates were significantly reduced in two upper-marsh species, Festuca rubra and Atriplex patula, and in the lower-marsh species Puccinellia maritima. However the growth of Salicornia europaea, a species frequently associated with sulphide-containing sediments, was unaffected. In a separate experiment the wide ranging halophyte

D. C. Havill; A. Ingold; J. Pearson

1985-01-01

183

Effects of environmental context on the susceptibility of Atriplex patula to attack by herbivorous beetles  

Microsoft Academic Search

The susceptibility of plants to attack by insect herbivores often depends on local environmental conditions. This study documents\\u000a variation in herbivore damage by the chrysomelid beetle Erynephala maritima to the annual forb Atriplex patula in two microhabitats within New England salt marshes: bare patches and dense matrix vegetation. Environmental conditions\\u000a within bare patches differ from those within matrix vegetation in

Tatyana A. Rand

1999-01-01

184

Invasive alien plants in marine protected areas: the Spartina anglica affair in the European Wadden Sea  

Microsoft Academic Search

The common cord-grass Spartina anglica, a fertile hybrid of S. maritima and S. alterniflora, was planted in the European Wadden Sea extensively during the late 1920s and 1930s to promote sediment accretion. After\\u000a establishment, it colonised as a pioneer plant in the upper tidal zone, where it occurs frequently in coherent swards at the\\u000a seaward front of saltmarshes and in patches on

Stefan Nehring; Karl-Jürgen Hesse

2008-01-01

185

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

NASA Astrophysics Data System (ADS)

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.

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

2004-11-01

186

Studies of Storage Proteins of Higher Plants  

PubMed Central

Concanavalin A, the lectin of the Jack bean, Canavalia ensiformis, was extracted and compared with homologous proteins from Canavalia gladiata and Canavalia maritima. All proteins were bound to Sephadex G-100 and eluted from the gel with buffered glucose solution. Quantitative recoveries indicated that large quantities (23 to 28% of dry seed protein) of these lectins are synthesized by all three species. Antibody preparations made against C. ensiformis lectin failed to discriminate among the three proteins; the pattern of the precipitin bands indicated identical antigenic determinants in the Ouchterlony double-diffusion assay. Native and sodium dodecyl sulfate polyacryl-amide gel electrophoresis also failed to distinguish differences in the proteins. The storage protein active in carbohydrate binding is composed, in each case, of identical subunits. However, the amino acid composition of the subunit chains from the three sources is not identical. In particular, the lectins from C. ensiformis and C. gladiata contain two methionine residues per protein subunit, while only one methionine residue is found in the C. martima lectin. Cyanogen bromide cleavage of the purified subunit from C. maritima yieded two fragments with molecular weights estimated at 20,400 and 4,600, respectively. Amino acid analysis of the separated fragments indicated that the methionine residue at position 130 in C. ensiformis is absent in the lectin from C. maritima. Images

Hague, Donald R.

1975-01-01

187

Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex  

PubMed Central

Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model of T. maritima CheW was constructed using the E. coli CheW NMR structure as a template. The conformational space accessible to the homology models and to the NMR structures was investigated using molecular dynamics and Monte Carlo simulations. The results show that even though static homology models of CheW may be partially structurally different from their corresponding experimentally determined structures, the conformational space they can access through their dynamic variations can be similar, for specific regions of the protein, to that of the experimental NMR structures. When CheW homology models are allowed to explore their local accessible conformational space, modeling can provide a rational path to predicting CheW interactions with the MCP and CheA proteins of the chemotaxis complex. Homology models of CheW (and potentially, of other chemotaxis proteins) should be seen as snapshots of an otherwise larger ensemble of accessible conformational space.

Cashman, Derek J.; Ortega, Davi R.; Zhulin, Igor B.; Baudry, Jerome

2013-01-01

188

GTPase Activity, Structure, and Mechanical Properties of Filaments Assembled from Bacterial Cytoskeleton Protein MreB  

PubMed Central

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells.

Esue, Osigwe; Wirtz, Denis; Tseng, Yiider

2006-01-01

189

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

PubMed Central

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.

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

2012-01-01

190

Sea Surface Temperature Products and Research Associated with GHRSST  

NASA Astrophysics Data System (ADS)

GHRSST serves its user community through the specification of operational Sea Surface Temperature (SST) products (Level 2, Level 3 and Level 4) based on international consensus. Providers of SST data from individual satellites create and deliver GHRSST- compliant near-real time products to a global GHRSST data assembly centre and a long-term stewardship facility. The GHRSST-compliant data include error estimates and supporting data for interpretation. Groups organised within GHRSST perform research on issues relevant to applying SST for air-sea exchange, for instance the Diurnal Variability Working Group (DVWG) analyses the evolution of the skin temperature. Other GHRSST groups concentrate on improving the SST estimate (Estimation and Retrievals Working Group EARWiG) and on improving the error characterization, (Satellite SST Validation Group, ST- VAL) and on improving the methods for SST analysis (Inter-Comparison Technical Advisory Group, IC- TAG). In this presentation we cover the data products and the scientific activities associated with GHRSST which might be relevant for investigating ocean- atmosphere interactions.

Kaiser-Weiss, A. K.; Minnett, P. J.; Kaplan, A.; Wick, G. A.; Castro, S.; Llewellyn-Jones, D.; Merchant, C.; LeBorgne, P.; Beggs, H.; Donlon, C. J.

2012-03-01

191

Mobility of Pb in salt marshes recorded by total content and stable isotopic signature.  

PubMed

Total lead and its stable isotopes were analysed in sediment cores, leaves, stem and roots of Sacorconia fruticosa and Spartina maritima sampled from Tagus (contaminated site) and Guadiana (low anthropogenic pressure) salt marshes. Lead concentration in vegetated sediments from the Tagus marsh largely exceeded the levels in non-vegetated sediments. Depth profiles of (206)Pb/(207)Pb and (206)Pb/(208)Pb showed a decrease towards the surface ((206)Pb/(207)Pb=1.160-1.167) as a result of a higher proportion of pollutant Pb components. In contrast, sediments from Guadiana marsh exhibited low Pb concentrations and an uniform isotopic signature ((206)Pb/(207)Pb=1.172+/-0.003) with depth. This suggests a homogeneous mixing of mine-derived particles and pre-industrial sediments with minor inputs of anthropogenic Pb. Lead concentrations in roots of plants from the two marshes were higher than in leaves and stems, indicating limited transfer of Pb to aerial parts. A similar Pb isotopic signature was found in roots and in vegetated sediments, indicating that Pb uptake by plants reflects the input in sediments as determined by a significant anthropogenic contribution of Pb at Tagus and by mineralogical Pb phases at Guadiana. The accumulation in roots from Tagus marsh (max. 2870 microg g(-1) in S. fruticosa and max. 1755 microg g(-1) in S. maritima) clearly points to the dominant role of belowground biomass in the cycling of anthropogenic Pb. The fraction of anthropogenic Pb in belowground biomass was estimated based on the signature of anthropogenic Pb components in sediments ((206)Pb/(207)Pb=1.154). Since no differences exist between Pb signature in roots and upper sediments, the background and anthropogenic levels of Pb in roots were estimated. Interestingly, both background and anthropogenic Pb in roots exhibited a maximum at the same depth, although the proportion of anthropogenic Pb was relatively constant with depth (83+/-4% for S. fruticosa and 74+/-8% for S. maritima). PMID:17320933

Caetano, Miguel; Fonseca, Nuno; Cesário Carlos Vale, Rute

2007-07-15

192

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)

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.

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

2009-07-01

193

Mucha Ozerov and Ortalischema Frey newly recorded from China with descriptions of two new species (Diptera, Sepsidae).  

PubMed

Eleven genera and 55 species of Sepsidae were known to occur in China. Here two genera, Mucha Ozerov and Ortalischema Frey, are newly reported from China with the following two new species: Mucha liangi sp. nov. and M. yunnanensis sp. nov. Two species, Mucha tzokotucha and Ortalischema maritima, are newly recorded from China. Thus, there are a total of 13 genera of Sepsidae distributed in China. A key to the species of Mucha and a key to the Chinese genera of Sepsidae are provided. PMID:24943611

Li, Xuankun; Yang, Ding

2014-01-01

194

Remote sensing of biomass of salt marsh vegetation in France  

NASA Technical Reports Server (NTRS)

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.

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

1988-01-01

195

H(2) synthesis from pentoses and biomass in Thermotoga spp.  

PubMed

We have investigated H(2) production on glucose, xylose, arabinose, and glycerol in Thermotoga maritima and T. neapolitana. Both species metabolised all sugars with hydrogen yields of 2.7-3.8 mol mol(-1) sugar. Both pentoses were at least comparable to glucose with respect to their qualities as substrates for hydrogen production, while glycerol was not metabolised by either species. Glycerol was also not metabolised by T. elfii. We also demonstrated that T. neapolitana can use wet oxidised wheat straws, in which most sugars are stored in glycoside polymers, for growth and efficient hydrogen production, while glucose, xylose and arabinose are consumed in parallel. PMID:20960218

Eriksen, Niels T; Riis, Martin Leegaard; Holm, Nikolaj Kyndby; Iversen, Niels

2011-02-01

196

Antioxidant activity of wild plants collected in Beni-Sueif governorate, Upper Egypt.  

PubMed

Antioxidant activity of a selection of commonly occurring wild plants growing in Beni-Sueif governorate, Upper Egypt, has been tested. The plants selected are Tamarix nilotica, Ambrosia maritima, Zygophyllum coccenium, Conyza dioscoridis, Chenopodium ambrosioides, and Calotropis procera. The in vitro antioxidant assays used in this study were 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical scavenging activity, superoxide anion scavenging activity and iron chelating activity. Extracts prepared from the leaves and flowers of Tamarix nilotica have shown the highest antioxidant activity in the three kinds of assay. PMID:22504722

Abouzid, S; Elshahaat, A; Ali, S; Choudhary, M I

2008-10-01

197

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

PubMed Central

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.

Chagas-Junior, Amazonas

2013-01-01

198

Screening seeds of Scottish plants for antibacterial activity.  

PubMed

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

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

2002-11-01

199

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

NASA Astrophysics Data System (ADS)

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.

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

2009-04-01

200

Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that may Discriminate Substrates During DNA Repair  

PubMed Central

Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks (DSBs). As x-ray structural information has only been available for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is the Mre11 endo/exonuclease from T. maritima (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only ?20%. However, they differ substantially in their DNA specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA specificity domain are not. The structural differences likely affect how Mre11s from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on ssDNA and dsDNA substrates, respectively.

Das, Debanu; Moiani, Davide; Axelrod, Herbert L.; Miller, Mitchell D.; McMullan, Daniel; Jin, Kevin K.; Abdubek, Polat; Astakhova, Tamara; Burra, Prasad; Carlton, Dennis; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ernst, Dustin; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Grzechnik, Slawomir K.; Han, Gye Won; Jaroszewski, Lukasz; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-Andre; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Tainer, John A.; Wilson, Ian A.

2010-01-01

201

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

PubMed Central

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.

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

2009-01-01

202

Distance to semi-natural grassland influences seed production of insect-pollinated herbs.  

PubMed

Marginal grassland fragments, such as road verges and field margins, may act as important supplemental habitats for grassland plants in the modern agricultural landscape. However, abundance of pollinators in such fragments has been found to decline with distance to larger natural and semi-natural habitats, and this could have corresponding effects on plant pollination. In this study, we performed a field experiment on road verges with three insect-pollinated grassland herbs to examine the relationship between distance to semi-natural grassland and plant reproductive success in two landscapes with contrasting farming intensities. In Lychnis viscaria and Lotus corniculatus, seed production tended to decrease with increasing distance to semi-natural grassland, but only in the landscape with high farming intensity. Seed production in Armeria maritima spp. maritima decreased with distance in both landscapes. Although many studies have investigated effects of natural habitat on crop pollination, little is known about the impact on pollination in native plants. The results from this study indicate that management of semi-natural grasslands improves not only biodiversity within the actual grassland but also pollination of native plants in the surrounding agricultural landscape. PMID:24562471

Jakobsson, Anna; Ågren, Jon

2014-05-01

203

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

PubMed

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

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

2004-02-01

204

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

PubMed

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

Hegazy, A K; Emam, M H

2011-02-01

205

Treating epilepsy: a review of Polish historical sources.  

PubMed

The first surviving Polish publications on epilepsy were written in the 16th and 17th centuries. Many causes of epileptic seizures are quoted and they are divided into two categories: internal and external. Internal causes (causa interna) include imbalance in the basic bodily humors, that is, yellow bile, black bile, phlegm, and blood. According to medieval writers, the principal cause of epilepsy was vapor, a damp, cold volatile substance originating in the excessive production of one of the basic organismic liquids. Vapor allegedly stuck to the openings leading to the cerebral ventricles or blocked them entirely, resulting in convulsions. External causes (causa externa) include overeating and excessive drinking, teething, spoiled milk, poisons, badly treated spots and fever, cold air, moonlight, and wearing donkey hide. Medical treatments for epilepsy included surgical interventions (bloodletting) and pharmacological interventions. The latter included laxatives, sea onion (scilla maritima, urginea maritima), and ground human skull, all of which were supposed to protect the body from vapors. Medical practitioners of that time also advised that the factors and circumstances conducive to epileptic seizures be observed and identified so that patients could be isolated from these alleged causal factors and their seizures reduced or ended. PMID:21775214

Owczarek, Krzysztof

2011-10-01

206

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

PubMed Central

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.

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

2014-01-01

207

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

SciTech Connect

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.

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

208

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

PubMed

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, Escherichia 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 and a systematic mutagenesis study reveal how individual mutations contribute to the rewiring of interaction specificity. Our approach and conclusions have implications for studies of other protein-protein interactions and protein evolution and for the design of novel protein interfaces. PMID:23954504

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

2013-09-01

209

Food habits of mute swans in the Chesapeake Bay  

USGS Publications Warehouse

Unlike the tundra swan (Cygnus columbianus) that migrate to the Bay for the winter, the mute swan (Cygnus olor) is a year long resident and therefore has raised concerns among research managers over reports of conflicts with nesting native water birds and the consumption of submerged aquatic vegetation (SAV). Although data on the reduction of SAV by nesting mute swans and their offspring during the spring and summer are limited, food-habits data show that mute swans rely heavily on SAV during these months. Analyses of the gullet and gizzard of mute swans indicate that widgeon grass (Ruppia maritima) and eelgrass (Zostera marina) were the most important food items to mute swans during the winter and spring. Other organisms were eaten by mute swans, but represent small percentages of food. Corn (Zea mays) fed to the swans by Bay residents in late winter probably supplements their limited vegetative food resources at that time of year.

Perry, M.C.; Osenton, P.C.; Lohnes, E.J.R.

2004-01-01

210

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

PubMed

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

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

2010-11-01

211

A continuous assay of acetate kinase activity: measurement of inorganic phosphate release generated by hydroxylaminolysis of acetyl phosphate.  

PubMed

Acetate kinase, a member of the ASKHA (Acetate and Sugar Kinases, Hsp70, Actin) phosphotransferase superfamily is a central enzyme in prokaryotic carbon and energy metabolism. Recently extensive structural and biochemical studies of acetate kinase and related carboxylate kinases have been conducted. Analysis of the kinetic properties of wild-type and mutant enzymes has been impeded by the nature of the current assays for acetate kinase activity. These assays have the disadvantages of being either discontinuous or insensitive or of utilizing compounds that interfere with activity measurements. We have developed a novel continuous assay that depends on the purine nucleoside phosphorylase-based spectroscopic measurement of the inorganic phosphate generated by hydroxylaminolysis of one of the products of the acetate kinase reaction, acetyl phosphate. This assay has enabled a determination of the kinetic parameters of the Thermotoga maritima acetate kinase that indicates a lower K(m) for acetate than previously published. PMID:18294673

Mukhopadhyay, Soma; Hasson, Miriam S; Sanders, David A

2008-04-01

212

A fungal pathogen in time and space: the population dynamics of Beauveria bassiana in a conifer forest.  

PubMed

The fungal entomopathogen Beauveria bassiana is ubiquitous in below-ground systems; however, there is a dearth of information on the above-ground diversity, temporal and spatial distribution of this fungus. Therefore, we assessed its occurrence in a conifer forest (Pseudotsuga monziesii and Pinus nigra var. maritima) using selective media to isolate B. bassiana from soil, branch and bark samples collected in October 2005, March and June 2006. Fungal density was the highest at all locations in October, declining in March and June, and absent from conifer branches in June. This above-ground decline most likely resulted from more extreme environmental conditions compared with those below ground. Molecular analyses (ISSR-PCR) indicated that B. bassiana is genetically diverse, comprising both distinct microhabitat-specific and seasonal isolates. The occurrence of dissimilar above- and below-ground isolates suggests that B. bassiana occupies various overlapping niches in these systems. PMID:20662927

Ormond, Emma L; Thomas, Alison P M; Pugh, Philip J A; Pell, Judith K; Roy, Helen E

2010-10-01

213

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

PubMed Central

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.

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

2013-01-01

214

Impacts of oil sands process water on fen plants: implications for plant selection in required reclamation projects.  

PubMed

Fen plant growth in peat contaminated with groundwater discharges of oil sands process water (OSPW) was assessed in a greenhouse over two growing seasons. Three treatments (non-diluted OSPW, diluted OSPW and rainwater) were tested on five vascular plants and four mosses. All vascular plants tested can grow in salinity and naphthenic acids levels currently produced by oil sands activity in northwestern Canada. No stress sign was observed after both seasons. Because of plant characteristics, Carex species (C. atherodes and C. utriculata) and Triglochin maritima would be more useful for rapidly restoring vegetation and creating a new peat-accumulating system. Groundwater discharge of OSPW proved detrimental to mosses under dry conditions and ensuring adequate water levels would be crucial in fen creation following oil sands exploitation. Campylium stellatum would be the best choice to grow in contaminated areas and Bryum pseudotriquetrum might be interesting as it has spontaneously regenerated in all treatments. PMID:22575093

Pouliot, Rémy; Rochefort, Line; Graf, Martha D

2012-08-01

215

New highly polymorphic microsatellite markers for the aquatic angiosperm Ruppia cirrhosa reveal population diversity and differentiation.  

PubMed

Ruppia cirrhosa is a clonal monoecious plant phylogenetically associated to seagrass families such as Posidoniaceae and Cymodoceaceae. It inhabits shallow waters that are important for productivity and as a biodiversity reservoir. In this study, we developed 10 polymorphic microsatellite loci for R. cirrhosa. Additionally, we obtained cross-amplification for two microsatellites previously described for Ruppia maritima. These 12 markers were tested in four R. cirrhosa populations from the southwest of Europe. The number of alleles per locus was high for most of the markers, ranging from 4 to 13. Two populations (Sicily and Cádiz) showed heterozygote deficit (p < 0.001). The four populations (Sicily, Murcia, Cádiz, and Tavira) were significantly differentiated (F(ST) ? 0; p < 0.001), corroborating the usefulness of these microsatellites on R. cirrhosa population genetics. PMID:24564216

Martínez-Garrido, J; González-Wangüemert, M; Serrão, E A

2014-01-01

216

Development of genetically encoded fluorescent protein constructs of hyperthermophilic maltose-binding protein.  

PubMed

Circularly permuted green fluorescent protein (cGFP) was inserted into the hyperthermophilic maltose binding protein at two different locations. cGFP was inserted between amino acid residues 206 and 207, or fused to the N-terminal of maltose binding protein from Thermotoga maritima. The cloned DNA constructs were expressed in Escherichia coli cells, and purified by metal chelate affinity chromatography. Conformational change upon ligand binding was monitored by the increase in fluorescence intensity. Both of the fusion proteins developed significant fluorescence change at 0.5 mM maltose concentration, whereas their maltose binding affinities and optimum incubation times were different. Fluorescent biosensors based on mesophilic maltose binding proteins have been described in the literature, but there is a growing interest in biosensors based on thermostable proteins. Therefore, the developed protein constructs could be models for thermophilic protein-based fluorescent biosensors. PMID:24152100

Ozyurt, Canan; Evran, Serap; Telefoncu, Azmi

2014-01-01

217

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

SciTech Connect

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.

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

218

Cloning and characterization of the gene for amylosucrase from Neisseria polysaccharea: production of a linear alpha-1,4-glucan.  

PubMed Central

The gene for the amylosucrase from Neisseria polysaccharea (ATCC 43768) was cloned by use of a functional expression system in Escherichia coli XL1-Blue. The deduced amino acid sequence of the protein has homology to the sequences of the alpha-amylase class of enzymes, with the highest similarities being found to the sequences of the trehalose synthase from Pimelobacter sp. strain R48 (17) and amylomaltase from Thermotoga maritima (11). However, the regions of highest homology within the alpha-amylase class of enzymes, which are essential for the catalytic activity, are only scarcely found in the sequence of amylosucrase. By using the enzyme isolated from culture supernatants of transformed E. coli cells, it is possible to synthesize linear alpha-1,4-glucans from sucrose, indicating that the enzyme is not capable of producing alpha-1,6-glycosidic linkages on its own.

Buttcher, V; Welsh, T; Willmitzer, L; Kossmann, J

1997-01-01

219

Crystal structure of FtsA from Staphylococcus aureus.  

PubMed

The bacterial cell-division protein FtsA anchors FtsZ to the cytoplasmic membrane. But how FtsA and FtsZ interact during membrane division remains obscure. We have solved 2.2Å resolution crystal structure for FtsA from Staphylococcus aureus. In the crystals, SaFtsA molecules within the dimer units are twisted, in contrast to the straight filament of FtsA from Thermotoga maritima, and the half of S12-S13 hairpin regions are disordered. We confirmed that SaFtsZ and SaFtsA associate in vitro, and found that SaFtsZ GTPase activity is enhanced by interaction with SaFtsA. PMID:24746687

Fujita, Junso; Maeda, Yoko; Nagao, Chioko; Tsuchiya, Yuko; Miyazaki, Yuma; Hirose, Mika; Mizohata, Eiichi; Matsumoto, Yoshimi; Inoue, Tsuyoshi; Mizuguchi, Kenji; Matsumura, Hiroyoshi

2014-05-21

220

Homologous Canavalia lectins elicit different patterns of antinociceptive responses.  

PubMed

Canavalia gladiata (CGL), C. maritima (ConM) and C. brasiliensis (ConBr) lectins were evaluated in nociception models. ConBr inhibited first (32%) and second (100%) phases of the formalin test; CGL inhibited only the first (74%) and ConM only the second (59%) phase. Hypernociception evaluated in the Von Frey test was inhibited by ConM (55%), CGL (41%) and ConBr (38%). Acetic acid-induced abdominal writhing was reduced by ConBr (66%), CGL (52%) and ConM (60%). ConBr and CGL effects were reversed by the lectin association with its ligand sugar. The antinociceptive activity of the structural homologous lectins was differentiated by potency, efficacy and mechanisms. PMID:24427956

Pinto, Nilson Vieira; Santos, Cláudia Ferreira; Cavada, Benildo Sousa; do Nascimento, Kyria Santiago; Pereira Junior, Francisco Nascimento; Pires, Alana de Freitas; Assreuy, Ana Maria Sampaio

2013-11-01

221

D-Amino acid dipeptide production utilizing D-alanine-D-alanine ligases with novel substrate specificity.  

PubMed

D-Alanine-D-alanine ligase (Ddl) is an important enzyme in the synthesis of bacterial peptidoglycan. The genes encoding Ddls from Escherichia coli K12 (EcDdlB), Oceanobacillus iheyensis JCM 11309 (OiDdl), Synechocystis sp. PCC 6803 (SsDdl) and Thermotoga maritima ATCC 43589 (TmDdl), the genomic DNA sequences of which have been determined, were cloned and the substrate specificities of these recombinant Ddls were investigated. Although OiDdl had a high substrate specificity for D-alanine; EcDdlB, SsDdl and TmDdl showed broad substrate specificities for D-serine, D-threonine, D-cysteine and glycine, in addition to D-alanine. Four D-amino acid dipeptides were produced using EcDdlB, and D-amino acid homo-dipeptides were successfully produced at high yields except for D-threonyl-D-threonine. PMID:16233841

Sato, Masaru; Kirimura, Kohtaro; Kino, Kuniki

2005-06-01

222

Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase.  

PubMed

The enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) is involved in the biosynthesis of the hypermodified tRNA nucleoside queuosine. It is unprecedented in nature as it uses the cofactor S-adenosylmethionine as the donor of a ribosyl group. We have determined the crystal structure of Bacillus subtilis QueA at a resolution of 2.9A. The structure reveals two domains representing a 6-stranded beta-barrel and an alpha beta alpha-sandwich, respectively. All amino acid residues invariant in the QueA enzymes of known sequence cluster at the interface of the two domains indicating the localization of the substrate binding region and active center. Comparison of the B. subtilis QueA structure with the structure of QueA from Thermotoga maritima suggests a high domain flexibility of this enzyme. PMID:17083917

Grimm, Clemens; Ficner, Ralf; Sgraja, Tanja; Haebel, Peter; Klebe, Gerhard; Reuter, Klaus

2006-12-22

223

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

NASA Astrophysics Data System (ADS)

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.

Warner, Brian D.

2011-04-01

224

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

NASA Technical Reports Server (NTRS)

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.

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

1989-01-01

225

A computational approach to structural properties of glycoside hydrolase family 4 from bacteria.  

PubMed

Structural bioinformatics approaches applied to the alpha- and beta-glycosidases from the GH4 enzyme family reveal that, despite low sequence identity, these enzymes possess quite similar global structural characteristics reflecting a common reaction mechanism. Locally, there are a few distinctive structural characteristics of GH4 alpha- and beta-glycosidases, namely, surface cavities with different geometric characteristics and two regions with highly dissimilar structural organizations and distinct physicochemical properties in the alpha- and beta-glucosidases from Thermotoga maritima. We suggest that these structurally dissimilar regions may be involved in specific protein-protein interactions and this hypothesis is sustained by the predicted distinct functional partners of the investigated proteins. Also, we predict that alpha- and beta-glycosidases from the GH4 enzyme family interact with difenoconazole, a fungicide, but there are different features of these interactions especially concerning the identified structurally distinct regions of the investigated proteins. PMID:24340303

Craciun, Dana; Vlad-Oros, Beatrice; Filimon, Nicoleta; Ostafe, Vasile; Isvoran, Adriana

2013-01-01

226

Inhibition of acetylcholinesterase by extracts and constituents from Angelica archangelica and Geranium sylvaticum.  

PubMed

The aim of this study was to explore the acetylcholinesterase (AChE) inhibition of several Icelandic medicinal herbs. Ethanolic extracts of Angelica archangelica seeds and the aerial parts of Geranium sylvaticum proved effective, with IC50 values of 2.20 mg/ml and 3.56 mg/ml, respectively. The activity of imperatorin and xanthotoxin from A. archangelica was measured. Xanthotoxin proved much more potent than imperatorin, with an IC50 value of 155 microg/ml (0.72 mM) but that for imperatorin was above 274 microg/ml (1.01 mM). However, furanocoumarins seem to have a minor part in the total activity of this extract. Synergistic interaction was observed between the extracts of A. archangelica and G. sylvaticum. Several medicinal herbs (Achillea millefolium, Filipendula ulmaria, Thymus praecox and Matricaria maritima) did not show AChE inhibitory activity. PMID:18069242

Sigurdsson, Steinthor; Gudbjarnason, Sigmundur

2007-01-01

227

Pycnogenol and vitamin E inhibit ethanol-induced apoptosis in rat cerebellar granule cells.  

PubMed

Pycnogenol (PYC), a patented combination of bioflavonoids extracted from the bark of French maritime pine (Pinus maritima), scavenges free radicals and promotes cellular health. The protective capacity of PYC against ethanol toxicity of neurons has not previously been explored. The present study demonstrates that in postnatal day 9 (P9) rat cerebellar granule cells the antioxidants vitamin E (VE) and PYC (1) dose dependently block cell death following 400, 800, and 1600 mg/dL ethanol exposure (2) inhibit the ethanol-induced activation of caspase-3 in the same model system; and (3) reduce neuronal membrane disruption as assayed by phosphatidylserine translocation to the cell surface. These results suggest that both PYC and VE have the potential to act as therapeutic agents, antagonizing the induction of neuronal cell death by ethanol exposure. PMID:15146544

Siler-Marsiglio, Kendra I; Shaw, Gerry; Heaton, Marieta B

2004-06-01

228

Different Dynamical Effects in Mesophilic and Hyperthermophilic Dihydrofolate Reductases  

PubMed Central

The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution (15N, 13C, 2H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis.

2014-01-01

229

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

PubMed

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

Ksouri, Riadh; Megdiche, Wided; Falleh, Hanen; Trabelsi, Nejla; Boulaaba, Mondher; Smaoui, Abderrazak; Abdelly, Chedly

2008-11-01

230

Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate  

PubMed Central

Di-myo-inositol 1,1?-phosphate (DIP) is a major osmoprotecting metabolite in a number of hyperthermophilic species of archaea and bacteria. Although the DIP biosynthesis pathway was previously proposed, genes encoding only two of the four required enzymes, inositol-1-phosphate synthase and inositol monophosphatase, were identified. In this study we used a comparative genomic analysis to predict two additional genes of this pathway (termed dipA and dipB) that remained missing. In Thermotoga maritima both candidate genes (in an originally misannotated locus TM1418) form an operon with the inositol-1-phosphate synthase encoding gene (TM1419). A predicted inositol-mono-phosphate cytidylyltransferase activity was directly confirmed for the purified product of T. maritima gene dipA cloned and expressed in Escherichia coli. The entire DIP pathway was reconstituted in E. coli by cloning of the TM1418–TM1419 operon in pBAD expression vector and confirmed to function in the crude lysate. 31P NMR and MS analysis revealed that DIP synthesis proceeds via a phosphorylated DIP intermediate, P-DIP, which is generated by the dipB-encoded enzyme, now termed P-DIP synthase. This previously unknown intermediate is apparently converted to the final product, DIP, by an inositol monophosphatase-like phosphatase. These findings allowed us to revise the previously proposed DIP pathway. The genomic survey confirmed its presence in the species known to use DIP for osmoprotection. Among several newly identified species with a postulated DIP pathway, Aeropyrum pernix was directly proven to produce this osmolyte.

Rodionov, Dmitry A.; Kurnasov, Oleg V.; Stec, Boguslaw; Wang, Yan; Roberts, Mary F.; Osterman, Andrei L.

2007-01-01

231

Hyperthermophilic Thermotoga Species Differ with Respect to Specific Carbohydrate Transporters and Glycoside Hydrolases  

PubMed Central

Four hyperthermophilic members of the bacterial genus Thermotoga (T. maritima, T. neapolitana, T. petrophila, and Thermotoga sp. strain RQ2) share a core genome of 1,470 open reading frames (ORFs), or about 75% of their genomes. Nonetheless, each species exhibited certain distinguishing features during growth on simple and complex carbohydrates that correlated with genomic inventories of specific ABC sugar transporters and glycoside hydrolases. These differences were consistent with transcriptomic analysis based on a multispecies cDNA microarray. Growth on a mixture of six pentoses and hexoses showed no significant utilization of galactose or mannose by any of the four species. T. maritima and T. neapolitana exhibited similar monosaccharide utilization profiles, with a strong preference for glucose and xylose over fructose and arabinose. Thermotoga sp. strain RQ2 also used glucose and xylose, but was the only species to utilize fructose to any extent, consistent with a phosphotransferase system (PTS) specific for this sugar encoded in its genome. T. petrophila used glucose to a significantly lesser extent than the other species. In fact, the XylR regulon was triggered by growth on glucose for T. petrophila, which was attributed to the absence of a glucose transporter (XylE2F2K2), otherwise present in the other Thermotoga species. This suggested that T. petrophila acquires glucose through the XylE1F1K1 transporter, which primarily serves to transport xylose in the other three Thermotoga species. The results here show that subtle differences exist among the hyperthermophilic Thermotogales with respect to carbohydrate utilization, which supports their designation as separate species.

Frock, Andrew D.; Gray, Steven R.

2012-01-01

232

Stability of endoglucanases from mesophilic fungus and thermophilic bacterium in acidified polyols.  

PubMed

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 5min 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 4.5min in acidified glycerol, indicating that the effectiveness of these enzymes under typical pretreatment times of greater than 15min will be considerably diminished. Attempts have been made to explain the differences in the results obtained between the two enzymes. PMID:24910337

Chong, Barrie Fong; Harrison, Mark D; O'Hara, Ian M

2014-01-01

233

Mother and offspring fitness in an insect with maternal care: phenotypic trade-offs between egg number, egg mass and egg care  

PubMed Central

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.

2014-01-01

234

Hippea jasoniae sp. nov. and Hippea alviniae sp. nov., thermoacidophilic members of the class Deltaproteobacteria isolated from deep-sea hydrothermal vent deposits.  

PubMed

Thirteen novel, obligately anaerobic, thermoacidophilic bacteria were isolated from deep-sea hydrothermal vent sites. Four of the strains, designated EP5-r(T), KM1, Mar08-272r(T) and Mar08-368r, were selected for metabolic and physiological characterization. With the exception of strain EP5-r(T), all strains were short rods that grew between 40 and 72 °C, with optimal growth at 60-65 °C. Strain EP5-r(T) was more ovoid in shape and grew between 45 and 75 °C, with optimum growth at 60 °C. The pH range for growth of all the isolates was between pH 3.5 and 5.5 (optimum pH 4.5 to 5.0). Strain Mar08-272r(T) could only grow up to pH 5.0. Elemental sulfur was required for heterotrophic growth on acetate, succinate, Casamino acids and yeast extract. Strains EP5-r(T), Mar08-272r(T) and Mar08-368r could also use fumarate, while strains EP5-r(T), KM1 and Mar08-272r(T) could also use propionate. All isolates were able to grow chemolithotrophically on H(2), CO(2), sulfur and vitamins. Phylogenetic analysis of 16S rRNA gene sequences placed all isolates within the family Desulfurellaceae of the class Deltaproteobacteria, with the closest cultured relative being Hippea maritima MH(2)(T) (~95-98 % gene sequence similarity). Phylogenetic analysis also identified several isolates with at least one intervening sequence within the 16S rRNA gene. The genomic DNA G+C contents of strains EP5-r(T), KM1, Mar08-272r(T) and Mar08-368r were 37.1, 42.0, 35.6 and 37.9 mol%, respectively. The new isolates differed most significantly from H. maritima MH(2)(T) in their phylogenetic placement and in that they were obligate thermoacidophiles. Based on these phylogenetic and phenotypic properties, the following two novel species are proposed: Hippea jasoniae sp. nov. (type strain Mar08-272r(T) = DSM 24585(T) = OCM 985(T)) and Hippea alviniae sp. nov. (type strain EP5-r(T) = DSM 24586(T) = OCM 986(T)). PMID:21764980

Flores, Gilberto E; Hunter, Ryan C; Liu, Yitai; Mets, Anchelique; Schouten, Stefan; Reysenbach, Anna-Louise

2012-06-01

235

A role for [Fe4S4] clusters in tRNA recognition-a theoretical study.  

PubMed

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

Stiebritz, Martin T

2014-05-01

236

Pycnogenol: a blend of procyanidins with multifaceted therapeutic applications?  

PubMed

Great interest is currently centred on the biologic activities of pycnogenol a standardized plant extract obtained from the bark of the French maritime pine Pinus pinaster (formerly known as Pinus maritima), Aiton, subspecies Atlantica des Villar (Pycnogenol, Horphag Research Ltd., UK, Geneve, Switzerland), which grows in the coastal southwest France. The quality of this extract is specified in the United States Pharmacopeia (USP 28). Between 65% and 75% of Pycnogenol are procyanidins comprising of catechin and epicatechin subunits with varying chain lengths. Other constituents are polyphenolic monomers, phenolic or cinnamic acids and their glycosides. As many studies indicate, pycnogenol components are highly bioavailable. Uniquely, pycnogenol displays greater biologic effects as a mixture than its purified components do individually indicating that the components interact synergistically. Pycnogenol is now utilized throughout the world as a nutritional supplement and as a phytochemical remedy for various diseases ranging from chronic inflammation to circulatory dysfunction, including several impaired psycho-physiological functions. Owing to the basic chemical structure of its components, the most obvious feature of pycnogenol is its strong antioxidant activity. In fact, phenolic acids, polyphenols, and in particular flavonoids, are composed of one (or more) aromatic rings bearing one or more hydroxyl groups and are therefore potentially able to quench free radicals by forming resonance-stabilized phenoxyl radicals. In this review, emphasizing the molecular, cellular, and functional bases of therapy, data appearing in the peer-reviewed literature and focussing the main therapeutic applications of pycnogenol will be summarized and critically evaluated. PMID:20598812

D'Andrea, Gabriele

2010-10-01

237

Effect of pycnogenol on glucose transport in mature 3T3-L1 adipocytes.  

PubMed

Pycnogenol, a procyanidins-enriched extract of Pinus maritima bark, possesses antidiabetic properties, which improves the altered parameters of glucose metabolism that are associated with type 2 diabetes mellitus (T2DM). Since the insulin-stimulated antidiabetic activities of natural bioactive compounds are mediated by GLUT4 via the phosphatidylinositol-3-kinase (PI3K) and/or p38 mitogen activated protein kinase (p38-MAPK) pathway, the effects of pycnogenol were examined on the molecular mechanism of glucose uptake by the glucose transport system. 3T3-L1 adipocytes were treated with various concentrations of pycnogenol, and glucose uptake was examined using a non-radioisotope enzymatic assay and by molecular events associated with the glucose transport system using semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). The results show that pycnogenol increased glucose uptake in fully differentiated 3T3-L1 adipocytes and increased the relative abundance of both GLUT4 and Akt mRNAs through the PI3K pathway in a dose dependent manner. Furthermore, pycnogenol restored the PI3K antagonist-induced inhibition of glucose uptake in the presence of wartmannin, an inhibitor of the PI3K. Overall, these results indicate that pycnogenol may stimulate glucose uptake via the PI3K dependent tyrosine kinase pathways involving Akt. Further the results suggest that pycnogenol might be useful in maintaining blood glucose control. PMID:20658573

Lee, Hee-Hyun; Kim, Kui-Jin; Lee, Ok-Hwan; Lee, Boo-Yong

2010-08-01

238

A new approach to assess and predict the functional roles of proteins across all known structures.  

PubMed

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

Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping; McLaughlin, William A

2011-03-01

239

Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis.  

PubMed Central

The three-dimensional structure of the Acetogenium kivui surface layer (S-layer) has been determined to a resolution of 1.7 nm by electron crystallographic techniques. Two independent reconstructions were made from layers negatively stained with uranyl acetate and Na-phosphotungstate. The S-layer has p6 symmetry with a center-to-center spacing of approximately 19 nm. Within the layer, six monomers combine to form a ring-shaped core surrounded by a fenestrated rim and six spokes that point towards the axis of threefold symmetry and provide lateral connectivity to other hexamers in the layer. The structure of the A. kivui S-layer protein is very similar to that of the Bacillus brevis middle wall protein, with which it shares an N-terminal domain of homology. This domain is found in several other extracellular proteins, including the S-layer proteins from Bacillus sphaericus and Thermus thermophilus, Omp alpha from Thermotoga maritima, an alkaline cellulase from Bacillus strain KSM-635, and xylanases from Clostridium thermocellum and Thermoanaerobacter saccharolyticum, and may serve to anchor these proteins to the peptidoglycan. To our knowledge, this is the first example of a domain conserved in several S-layer proteins. Images

Lupas, A; Engelhardt, H; Peters, J; Santarius, U; Volker, S; Baumeister, W

1994-01-01

240

Host-driven divergence in the parasitic plant Orobanche minor Sm. (Orobanchaceae).  

PubMed

Many parasitic angiosperms have a broad host range and are therefore considered to be host generalists. Orobanche minor is a nonphotosynthetic root parasite that attacks a range of hosts from taxonomically disparate families. In the present study, we show that O. minor sensu lato may comprise distinct, genetically divergent races isolated by the different ecologies of their hosts. Using a three-pronged approach, we tested the hypothesis that intraspecific taxa O. minor var. minor and O. minor ssp. maritima parasitizing either clover (Trifolium pratense) or sea carrot (Daucus carota ssp.gummifer), respectively, are in allopatric isolation. Morphometric analysis revealed evidence of divergence but this was insufficient to define discrete, host-specific taxa. Intersimple sequence repeat (ISSR) marker-based data provided stronger evidence of divergence, suggesting that populations were isolated from gene flow. Phylogenetic analysis, using sequence-characterized amplified region (SCAR) markers derived from ISSR loci, provided strong evidence for divergence by clearly differentiating sea carrot-specific clades and mixed-host clades. Low levels of intrapopulation SCAR marker sequence variation and floral morphology suggest that populations on different hosts are probably selfing and inbreeding. Morphologically cryptic Orobanche taxa may therefore be isolated from gene flow by host ecology. Together, these data suggest that host specificity may be an important driver of allopatric speciation in parasitic plants. PMID:19378406

Thorogood, C J; Rumsey, F J; Harris, S A; Hiscock, S J

2008-10-01

241

ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex.  

PubMed

DNA double-strand breaks (DSBs) threaten genome stability in all kingdoms of life and are linked to cancerogenic chromosome aberrations in humans. The Mre11:Rad50 (MR) complex is an evolutionarily conserved complex of two Rad50 ATPases and a dimer of the Mre11 nuclease that senses and processes DSBs and tethers DNA for repair. ATP binding and hydrolysis by Rad50 is functionally coupled to DNA-binding and tethering, but also regulates Mre11's nuclease in processing DNA ends. To understand how ATP controls the interaction between Mre11 and Rad50, we determined the crystal structure of Thermotoga maritima (Tm) MR trapped in an ATP/ADP state. ATP binding to Rad50 induces a large structural change from an open form with accessible Mre11 nuclease sites into a closed form. Remarkably, the NBD dimer binds in the Mre11 DNA-binding cleft blocking Mre11's dsDNA-binding sites. An accompanying large swivel of the Rad50 coiled coil domains appears to prepare the coiled coils for DNA tethering. DNA-binding studies show that within the complex, Rad50 likely forms a dsDNA-binding site in response to ATP, while the Mre11 nuclease module retains a ssDNA-binding site. Our results suggest a possible mechanism for ATP-dependent DNA tethering and DSB processing by MR. PMID:21937514

Möckel, Carolin; Lammens, Katja; Schele, Alexandra; Hopfner, Karl-Peter

2012-01-01

242

The Mre11:Rad50 structure shows an ATP dependent molecular clamp in DNA double-strand break repair  

PubMed Central

Summary The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to cancer development. MR can recognize and process DNA ends even if they are blocked and misfolded. To reveal its mechanism, we determined the crystal structure of the catalytic head of Thermotoga maritima MR and analyzed ATP dependent conformational changes. MR adopts an open form with a central Mre11 nuclease dimer and two peripheral Rad50 molecules, a form suited for sensing obstructed breaks. The Mre11 C-terminal helix-loop-helix domain binds Rad50 and attaches flexibly to the nuclease domain, enabling large conformational changes. ATP binding to the two Rad50 subunits induces a rotation of the Mre11 helix-loop-helix and Rad50 coiled-coil domains, creating a clamp conformation with increased DNA binding activity. The results suggest that MR is an ATP controlled transient molecular clamp at DNA double-strand breaks

Lammens, Katja; Bemeleit, Derk J.; Mockel, Carolin; Clausing, Emanuel; Schele, Alexandra; Hartung, Sophia; Schiller, Christian B.; Lucas, Maria; Angermuller, Christof; Soding, Johannes; Strasser, Katja; Hopfner, Karl-Peter

2011-01-01

243

The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair.  

PubMed

The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to cancer development. MR can recognize and process DNA ends even if they are blocked and misfolded. To reveal its mechanism, we determined the crystal structure of the catalytic head of Thermotoga maritima MR and analyzed ATP-dependent conformational changes. MR adopts an open form with a central Mre11 nuclease dimer and two peripheral Rad50 molecules, a form suited for sensing obstructed breaks. The Mre11 C-terminal helix-loop-helix domain binds Rad50 and attaches flexibly to the nuclease domain, enabling large conformational changes. ATP binding to the two Rad50 subunits induces a rotation of the Mre11 helix-loop-helix and Rad50 coiled-coil domains, creating a clamp conformation with increased DNA-binding activity. The results suggest that MR is an ATP-controlled transient molecular clamp at DNA double-strand breaks. PMID:21458667

Lammens, Katja; Bemeleit, Derk J; Möckel, Carolin; Clausing, Emanuel; Schele, Alexandra; Hartung, Sophia; Schiller, Christian B; Lucas, Maria; Angermüller, Christof; Söding, Johannes; Strässer, Katja; Hopfner, Karl-Peter

2011-04-01

244

ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex  

PubMed Central

DNA double-strand breaks (DSBs) threaten genome stability in all kingdoms of life and are linked to cancerogenic chromosome aberrations in humans. The Mre11:Rad50 (MR) complex is an evolutionarily conserved complex of two Rad50 ATPases and a dimer of the Mre11 nuclease that senses and processes DSBs and tethers DNA for repair. ATP binding and hydrolysis by Rad50 is functionally coupled to DNA-binding and tethering, but also regulates Mre11's nuclease in processing DNA ends. To understand how ATP controls the interaction between Mre11 and Rad50, we determined the crystal structure of Thermotoga maritima (Tm) MR trapped in an ATP/ADP state. ATP binding to Rad50 induces a large structural change from an open form with accessible Mre11 nuclease sites into a closed form. Remarkably, the NBD dimer binds in the Mre11 DNA-binding cleft blocking Mre11's dsDNA-binding sites. An accompanying large swivel of the Rad50 coiled coil domains appears to prepare the coiled coils for DNA tethering. DNA-binding studies show that within the complex, Rad50 likely forms a dsDNA-binding site in response to ATP, while the Mre11 nuclease module retains a ssDNA-binding site. Our results suggest a possible mechanism for ATP-dependent DNA tethering and DSB processing by MR.

Mockel, Carolin; Lammens, Katja; Schele, Alexandra; Hopfner, Karl-Peter

2012-01-01

245

Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA  

PubMed Central

Ribonuclease (RNase) P is the universal ribozyme responsible for 5?-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNAPhe. The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor, and mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts, and base pairing interactions. Soaks with a pre-tRNA 5? leader sequence with and without metal help identify the 5? substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P/tRNA contacts suggest a universal mechanism of catalysis by RNase P.

Reiter, Nicholas J.; Osterman, Amy; Torres-Larios, Alfredo; Swinger, Kerren K.; Pan, Tao; Mondragon, Alfonso

2010-01-01

246

Rising from the sea: correlations between sulfated polysaccharides and salinity in plants.  

PubMed

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

Aquino, Rafael S; Grativol, Clicia; Mourão, Paulo A S

2011-01-01

247

Fluorescence in insects  

NASA Astrophysics Data System (ADS)

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.

Welch, Victoria L.; Van Hooijdonk, Eloise; Intrater, Nurit; Vigneron, Jean-Pol

2012-10-01

248

Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism  

PubMed Central

Sirtuins are protein deacetylases regulating metabolism and stress responses. The seven human Sirtuins (Sirt1–7) are attractive drug targets, but Sirtuin inhibition mechanisms are mostly unidentified. We report the molecular mechanism of Sirtuin inhibition by 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide (Ex-527). Inhibitor binding to potently inhibited Sirt1 and Thermotoga maritima Sir2 and to moderately inhibited Sirt3 requires NAD+, alone or together with acetylpeptide. Crystal structures of several Sirtuin inhibitor complexes show that Ex-527 occupies the nicotinamide site and a neighboring pocket and contacts the ribose of NAD+ or of the coproduct 2’-O-acetyl-ADP ribose. Complex structures with native alkylimidate and thio-analog support its catalytic relevance and show, together with biochemical assays, that only the coproduct complex is relevant for inhibition by Ex-527, which stabilizes the closed enzyme conformation preventing product release. Ex-527 inhibition thus exploits Sirtuin catalysis, and kinetic isoform differences explain its selectivity. Our results provide insights in Sirtuin catalysis and inhibition with important implications for drug development.

Gertz, Melanie; Fischer, Frank; Nguyen, Giang Thi Tuyet; Lakshminarasimhan, Mahadevan; Schutkowski, Mike; Weyand, Michael; Steegborn, Clemens

2013-01-01

249

Construction of a chimeric thermoacidophilic beta-endoglucanase  

PubMed Central

Background The archeaon Sulfolobus solfataricus P2 encodes a thermoacidophilic cellulase which shows an extreme acid and thermal stability with a pH optimum at 1.8 and a temperature optimum at 80°C. This extraordinary enzyme could be useful for biotechnological exploitation but the expression and purification in expression hosts like E. coli is unsatisfactory due to the high aggregation tendency of the recombinant enzyme. The thermophilic cellulase CelA from Thermotoga maritima belongs to the same glycoside hydrolase family (GH12) but has a neutral pH optimum. In contrast to SSO1949 this enzyme is expressed partially soluble in E. coli. Results We aimed to constructed a hybrid enzyme based on these two beta-endoglucanases which should successfully combine the advantageous properties of both cellulases, i.e. recombinant expression in E. coli, acidophily and thermophily. We constructed two hybrid proteins after bioinformatic analysis: both hybrids are expressed insoluble in E. coli, but one hybrid enzyme was successfully refolded from washed inclusion bodies. Conclusions The refolded active chimeric enzyme shows a temperature optimum of approximately 85°C and a pH optimum of approximately pH 3 thus retaining the advantageous properties of the Sulfolobus parent enzyme. This study suggests that the targeted construction of chimeric enzymes is an alternative to point mutational engineering efforts as long as parent enzymes with the wanted properties are available.

2013-01-01

250

Molecular Diagnostics, Taxonomy, and Phylogeny of the Stem Nematode Ditylenchus dipsaci Species Complex Based on the Sequences of the Internal Transcribed Spacer-rDNA.  

PubMed

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

Subbotin, Sergei A; Madani, Mehrdad; Krall, Eino; Sturhan, Dieter; Moens, Maurice

2005-11-01

251

The Root-Knot Nematode Producing Galls on Spartina alterniflora Belongs to the Genus Meloidogyne: Rejection of Hypsoperine and Spartonema spp.  

PubMed Central

Root-knot nematodes are a major group of plant-parasitic nematodes, but their sister group within the Tylenchida remains to be identified. To find the sister group and for any investigation of the evolutionary biology of the genus Meloidogyne, it would be useful to identify the most basal species within Meloidogyninae. Meloidogyne spartinae, a root-knot nematode parasitic on cordgrass (Spartina spp.), constitutes a potentially interesting early diverging (or at least highly divergent) root-knot nematode because it was originally described in a different genus, Hypsoperine (and later Spartonema), due to its unique anatomy and biology (although it was later put in synonymy by some, but not all, taxonomists). We have sequenced the whole 18S rDNA of this species and compared it to other sequences of this region that are available in GenBank for numerous Meloidogyne species. Phylogenetic analysis unambiguously locates the branch corresponding to M. spartinae as a lately diverging species, more closely related to M. maritima, M. duytsi or the M. ardenensis-hapla group. Thus, the distinction of a separate genus (Hypsoperine or Spartonema) for this species is not justified.

Plantard, Olivier; Valette, Sylvie; Gross, Michael F.

2007-01-01

252

Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an inositol monophosphatase family protein (SAS2203) from Staphylococcus aureus MSSA476  

PubMed Central

The gene product of the sas2203 ORF of Staphylococcus aureus MSSA476 encodes a 30?kDa molecular-weight protein with a high sequence resemblance (29% identity) to tetrameric inositol monophosphatase from Thermotoga maritima. The protein was cloned, expressed, purified to homogeneity and crystallized. Crystals appeared in several conditions and good diffraction-quality crystals were obtained from 0.2?M Li2SO4, 20% PEG 3350, 0.1?M HEPES pH 7.0 using the sitting-drop vapour-diffusion method. A complete diffraction data set was collected to 2.6?Å resolution using a Rigaku MicroMax-007 HF Cu?K? X-­ray generator and a Rigaku R-AXIS IV++ detector. The diffraction data were consistent with the orthorhombic space group P212121, with unit-cell parameters a = 49.98, b = 68.35, c = 143.79?Å, ? = ? = ? = 90°, and the crystal contained two molecules in the asymmetric unit.

Bhattacharyya, Sudipta; Dutta, Debajyoti; Ghosh, Ananta Kumar; Das, Amit Kumar

2011-01-01

253

Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27.  

PubMed

The C-terminal 176 amino acids of a Thermotoga maritima mannanase (Man5) constitute a carbohydrate binding module (CBM) that has been classified into CBM family 27. The isolated CBM27 domain, named TmCBM27, binds tightly (K(a)s 10(5)-10(6) M(-1)) to beta-1, 4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. The X-ray crystal structures of native TmCBM27, a TmCBM27-mannohexaose complex, and a TmCBM27-6(3),6(4)-alpha-D-galactosyl-mannopentaose complex at 2.0 A, 1.6 A, and 1.35 A, respectively, reveal the basis of TmCBM27's specificity for mannans. In particular, the latter complex, which is the first structure of a CBM in complex with a branched plant cell wall polysaccharide, illustrates how the architecture of the binding site can influence the recognition of naturally substituted polysaccharides. PMID:12791255

Boraston, Alisdair B; Revett, Timothy J; Boraston, Catherine M; Nurizzo, Didier; Davies, Gideon J

2003-06-01

254

The biological soil crusts of the San Nicolas Island: Enigmatic algae from a geographically isolated ecosystem  

USGS Publications Warehouse

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.

Flechtner, V. R.; Johansen, J. R.; Belnap, J.

2008-01-01

255

Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex  

PubMed Central

Redox-sensing repressor Rex was previously implicated in the control of anaerobic respiration in response to the cellular NADH/NAD+ levels in Gram-positive bacteria. We utilized the comparative genomics approach to infer candidate Rex-binding DNA motifs and assess the Rex regulon content in 119 genomes from 11 taxonomic groups. Both DNA-binding and NAD-sensing domains are broadly conserved in Rex orthologs identified in the phyla Firmicutes, Thermotogales, Actinobacteria, Chloroflexi, Deinococcus-Thermus, and Proteobacteria. The identified DNA-binding motifs showed significant conservation in these species, with the only exception detected in Clostridia, where the Rex motif deviates in two positions from the generalized consensus, TTGTGAANNNNTTCACAA. Comparative analysis of candidate Rex sites revealed remarkable variations in functional repertoires of candidate Rex-regulated genes in various microorganisms. Most of the reconstructed regulatory interactions are lineage specific, suggesting frequent events of gain and loss of regulator binding sites in the evolution of Rex regulons. We identified more than 50 novel Rex-regulated operons encoding functions that are essential for resumption of the NADH:NAD+ balance. The novel functional role of Rex in the control of the central carbon metabolism and hydrogen production genes was validated by in vitro DNA binding assays using the TM0169 protein in the hydrogen-producing bacterium Thermotoga maritima.

Ravcheev, Dmitry A.; Li, Xiaoqing; Latif, Haythem; Zengler, Karsten; Leyn, Semen A.; Korostelev, Yuri D.; Kazakov, Alexey E.; Novichkov, Pavel S.; Osterman, Andrei L.

2012-01-01

256

Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine  

PubMed Central

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 Å 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.

Seckute, Jolita; McCloskey, Diane E; Thomas, H Jeanette; Secrist, John A; Pegg, Anthony E; Ealick, Steven E

2011-01-01

257

New compatible solutes related to Di-myo-inositol-phosphate in members of the order Thermotogales.  

PubMed Central

The accumulation of intracellular organic solutes was examined in six species of the order Thermotogales by nuclear magnetic resonance spectroscopy. The newly discovered compounds di-2-O-beta-mannosyl-di-myo-inositol-1,1'(3,3')-phosphate and di-myo-inositol-1,3'-phosphate were identified in Thermotoga maritima and Thermotoga neapolitana. In the latter species, at the optimum temperature and salinity the organic solute pool was composed of di-myo-inositol-1,1'(3,3')-phosphate, beta-glutamate, and alpha-glutamate in addition to di-myo-inositol-1,3'-phosphate and di-2-O-beta-mannosyl-di-myo-inositol-1,1'(3,3')-phosphate. The concentrations of the last two solutes increased dramatically at supraoptimal growth temperatures, whereas beta-glutamate increased mainly in response to a salinity stress. Nevertheless, di-myo-inositol-1,1'(3,3')-phosphate was the major compatible solute at salinities above the optimum for growth. The amino acids alpha-glutamate and proline were identified under optimum growth conditions in Thermosipho africanus, and beta-mannosylglycerate, trehalose, and glycine betaine were detected in Petrotoga miotherma. Organic solutes were not detected, under optimum growth conditions, in Thermotoga thermarum and Fervidobacterium islandicum, which have a low salt requirement or none.

Martins, L O; Carreto, L S; Da Costa, M S; Santos, H

1996-01-01

258

Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria).  

PubMed

Nucleoside modification has been studied in unfractionated tRNA from 11 thermophilic archaea (archaebacteria), including phylogenetically diverse representatives of thermophilic methanogens and sulfur-metabolizing hyperthermophiles which grow optimally in the temperature range of 56 (Thermoplasma acidophilum) to 105 degrees C (Pyrodictium occultum), and for comparison from the most thermophilic bacterium (eubacterium) known, Thermotoga maritima (80 degrees C). Nine nucleosides are found to be unique to the archaea, six of which are structurally novel in being modified both in the base and by methylation in ribose and occur primarily in tRNA from the extreme thermophiles in the Crenarchaeota of the archaeal phylogenetic tree. 2-Thiothymine occurs in tRNA from Thermococcus sp., and constitutes the only known occurrence of the thymine moiety in archaeal RNA, in contrast to its near-ubiquitous presence in tRNA from bacteria and eukarya. A total of 33 modified nucleosides are rigorously characterized in archaeal tRNA in the present study, demonstrating that the structural range of posttranscriptional modifications in archaeal tRNA is more extensive than previously known. From a phylogenetic standpoint, certain tRNA modifications occur in the archaea which are otherwise unique to either the bacterial or eukaryal domain, although the overall patterns of modification are more typical of eukaryotes than bacteria. PMID:1708763

Edmonds, C G; Crain, P F; Gupta, R; Hashizume, T; Hocart, C H; Kowalak, J A; Pomerantz, S C; Stetter, K O; McCloskey, J A

1991-05-01

259

Composition, abundance, biomass, and production of macrofauna in a New England estuary: comparisons among eelgrass meadows and other nursery habitats  

USGS Publications Warehouse

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.

Heck, K. L., Jr.; Able, K. W.; Roman, C. T.; Fahay, M. P.

1995-01-01

260

Structure and electrostatic property of cytoplasmic domain of ZntB transporter.  

PubMed

ZntB is the distant homolog of CorA Mg(2+) transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn(2+) and Cd(2+), but not Mg(2+). Here, we report the 1.90 A 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(2+) or Cd(2+) binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl(-) 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(-) ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport. PMID:19653298

Tan, Kemin; Sather, Alicia; Robertson, Janice L; Moy, Shiu; Roux, Benoît; Joachimiak, Andrzej

2009-10-01

261

A role for [Fe4S4] clusters in tRNA recognition--a theoretical study  

PubMed Central

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.

Stiebritz, Martin T.

2014-01-01

262

The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor  

PubMed Central

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 Å 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 ?-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.

Korolev, Sergey; Ikeguchi, Yoshihiko; Skarina, Tatiana; Beasley, Steven; Arrowsmith, Cheryl; Edwards, Aled; Joachimiak, Andrzej; Pegg, Anthony E.; Savchenko, Alexei

2009-01-01

263

Retention of tannic acid and condensed tannin by Fe-oxide-coated quartz sand.  

PubMed

This paper intends to shed light on the interactions between tannin and mineral soil particles. For that purpose, aqueous solution of condensed tannin (CT) (derived from Black pine (Pinus nigra var. maritima)) and commercially available tannic acid (TA) were added to purified quartz (Qtz) sand and quartz sand coated with either goethite (Gt) or ferrihydrite (Fh). After solvent removal by evaporation the samples were extracted by water. The extracts were analysed for organic carbon, total phenolics and CT. The extractability of the two tannins was small and increased in the order Qtz-Fh < Qtz-Gt < Qtz. For all mineral samples, TA was more extractable than CT. Bonding of tannins to the mineral samples and the partial peptisation of the Fe oxide coatings upon the binding resulted in complex tannin release curves. Our results suggest that the inextractability of tannins from natural soils and the absence of tannins in soil leachates might be caused by strong adsorption on soil minerals such as Qtz and Fe (oxy)(hydr)oxides. The results of competition experiments with mixtures of both tannins demonstrate that the CTs, and TA in particular, can release large amounts of Fe (oxides), suggesting that the tannins are excellent metal-mobilising agents. We therefore suggest that the fate of tannins in the mineral soil environment is highly dependent on the abundance of weakly bonded secondary oxides. PMID:15914150

Kaal, J; Nierop, K G J; Verstraten, J M

2005-07-01

264

Crystal structure of the RNA component of bacterial ribonuclease P  

SciTech Connect

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.

Torres-Larios, Alfredo; Swinger, Kerren K.; Krasilnikov, Andrey S.; Pan, Tao; Mondragon, Alfonso (NWU); (UC)

2010-03-08

265

Evolutionary relationships of bacterial and archaeal glutamine synthetase genes.  

PubMed

Glutamine synthetase (GS), an essential enzyme in ammonia assimilation and glutamine biosynthesis, has three distinctive types: GSI, GSII and GSIII. Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in eukaryotes and a few soil-dwelling bacteria. GSIII genes have been found in only a few bacterial species. Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii. Our phylogenetic analysis, which included most available GS sequences, revealed two significant prokaryotic GSI subdivisions: GSI-alpha and GSI-beta. GSI-alpha-genes are found in the thermophilic bacterium, Thermotoga maritima, the low G+C Gram-positive bacteria, and the Euryarchaeota (includes methanogens, halophiles, and some thermophiles). GSI-beta-type genes occur in all other bacteria. GSI-alpha- and GSI-beta-type genes also differ with respect to a specific 25-amino-acid insertion and adenylylation control of GS enzyme activity, both absent in the former but present in the latter. Cyanobacterial genes lack adenylylation regulation of GS and may have secondarily lost it. The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision. PMID:7916055

Brown, J R; Masuchi, Y; Robb, F T; Doolittle, W F

1994-06-01

266

Phylogenetic conservation of antigenic determinants in archaebacterial elongation factors (Tu proteins).  

PubMed

By using affinity chromatography methods, we have purified elongation factor Tu (EF-Tu) proteins from a host of archaebacteria covering all known divisions in the archaebacterial tree except halophiles, and from such distantly related eubacteria as Thermotoga maritima and Escherichia coli. Polyclonal antibodies were raised against the Tu proteins of Sulfolobus solfataricus, Thermoproteus tenax, Thermococcus celer, Pyrococcus wosei, Archaeoglobus fulgidus, Methanococcus thermolitotrophicus, Thermoplasma acidophilum, and Thermotoga and used to probe the immunochemical relatedness of elongation factors both within and across kingdom boundaries. A selection of the results, presented here, indicates that (i) every archaebacterial EF-Tu is closer (immunochemically) to every other archaebacterial EF-Tu than to the functionally analogous proteins of eubacteria and eukaryotes, with only one possible exception concerning the recognition of eukaryotic (EF-1 alpha) factors by Thermococcus EF-Tu antibodies, and (ii) within the archaebacteria there appears to be a correlation between EF-Tu immunochemical similarities and the phylogenetic relatedness of the organisms inferred from other (sequence) criteria. On the whole, immunochemical similarity data argue against the proposal that the archaebacterial taxon should be split and redistributed between two superkingdoms. PMID:2470483

Cammarano, P; Tiboni, O; Sanangelantoni, A M

1989-01-01

267

Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine  

SciTech Connect

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.

Š e; #269; kut; #279; , Jolita; McCloskey, Diane E.; Thomas, H. Jeanette; Secrist III, John A.; Pegg, Anthony E.; Ealick, Steven E. (Cornell); (Southern Research); (UPENN-MED)

2011-11-17

268

Molecular details of ligand selectivity determinants in a promiscuous ?-glucan periplasmic binding protein  

PubMed Central

Background Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. Results A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying ?-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. Conclusions The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands.

2013-01-01

269

Improving small-angle X-ray scattering data for structural analyses of the RNA world  

PubMed Central

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 tRNAval, and yeast tRNAphe 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.

Rambo, Robert P.; Tainer, John A.

2010-01-01

270

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA.  

PubMed

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

De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

2002-12-01

271

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA  

PubMed Central

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.

De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

2002-01-01

272

Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis.  

PubMed

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 Mg(2+)-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

Liu, Xiuying; Yin, Yan; Wu, Jinjun; Liu, Zhenfeng

2014-01-01

273

A thermostable exo-?-fructosidase immobilised through rational design.  

PubMed

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 22.2g 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

Martínez, Duniesky; Cutiño-Avila, Bessy; Pérez, Enrique Rosendo; Menéndez, Carmen; Hernández, Lázaro; Del Monte-Martínez, Alberto

2014-02-15

274

Assembly and mechanism of a group II ECF transporter  

PubMed Central

Energy-coupling factor (ECF) transporters are a recently discovered family of primary active transporters for micronutrients and vitamins, such as biotin, thiamine, and riboflavin. Found exclusively in archaea and bacteria, including the human pathogens Listeria, Streptococcus, and Staphylococcus, ECF transporters may be the only means of vitamin acquisition in these organisms. The subunit composition of ECF transporters is similar to that of ATP binding cassette (ABC) importers, whereby both systems share two homologous ATPase subunits (A and A?), a high affinity substrate-binding subunit (S), and a transmembrane coupling subunit (T). However, the S subunit of ECF transporters is an integral membrane protein, and the transmembrane coupling subunits do not share an obvious sequence homology between the two transporter families. Moreover, the subunit stoichiometry of ECF transporters is controversial, and the detailed molecular interactions between subunits and the conformational changes during substrate translocation are unknown. We have characterized the ECF transporters from Thermotoga maritima and Streptococcus thermophilus. Our data suggests a subunit stoichiometry of 2S:2T:1A:1A? and that S subunits for different substrates can be incorporated into the same transporter complex simultaneously. In the first crystal structure of the A–A? heterodimer, each subunit contains a novel motif called the Q-helix that plays a key role in subunit coupling with the T subunits. Taken together, these findings suggest a mechanism for coupling ATP binding and hydrolysis to transmembrane transport by ECF transporters.

Karpowich, Nathan K.; Wang, Da-Neng

2013-01-01

275

Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis  

PubMed Central

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.

Liu, Xiuying; Yin, Yan; Wu, Jinjun; Liu, Zhenfeng

2014-01-01

276

Disease concepts and treatment practices relating to schistosomiasis haematobium in Upper Egypt.  

PubMed

Disease concepts and medical treatment practices surrounding schistosomiasis haematobium were studied among males in Upper Egyptian villages and towns using interview methods. Most informants considered bilharzia to be a serious disease for which they commonly sought treatment. Its occurrence was attributed primarily to natural causes, particularly various aquatic worms and insects, dirts, excrement, dead animals, toxins and stagnant and vegetated waters, mostly large canals. Contact with water from the Nile river was generally thought to be quite safe. Drug treatment was weakly associated with amount of education. All groups reported use of antischistosomal drugs and plant medicines. Seventy-four per cent of the sample had a treatment history, 64% having taken oral drugs and/or injections, 40% plant medicines and 29% both. Drinking decoctions of damsissa (Ambrosia maritima) was the most commonly used household remedy. Plant materials were usually obtained from fields, gardens and local markets and patent medicines from nearby clinics and private physicians in towns. Recommendations are made for the national mass chemotherapy programme. PMID:7097828

Kloos, H; Sidrak, W; Michael, A A; Mohareb, E W; Higashi, G I

1982-06-01

277

The structure of the TrmE GTP-binding protein and its implications for tRNA modification.  

PubMed

TrmE is a 50 kDa guanine nucleotide-binding protein conserved between bacteria and man. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. The precise role of TrmE in the modification reaction is hitherto unknown. Here, we report the X-ray structure of TrmE from Thermotoga maritima. The structure reveals a three-domain protein comprising the N-terminal alpha/beta domain, the central helical domain and the G domain, responsible for GTP binding and hydrolysis. The N-terminal domain induces dimerization and is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase. Biochemical and structural studies show that TrmE indeed binds formyl-tetrahydrofolate. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. We propose a reaction mechanism whereby TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. PMID:15616586

Scrima, Andrea; Vetter, Ingrid R; Armengod, M Eugenia; Wittinghofer, Alfred

2005-01-12

278

The structure of the TrmE GTP-binding protein and its implications for tRNA modification  

PubMed Central

TrmE is a 50 kDa guanine nucleotide-binding protein conserved between bacteria and man. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. The precise role of TrmE in the modification reaction is hitherto unknown. Here, we report the X-ray structure of TrmE from Thermotoga maritima. The structure reveals a three-domain protein comprising the N-terminal ?/? domain, the central helical domain and the G domain, responsible for GTP binding and hydrolysis. The N-terminal domain induces dimerization and is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase. Biochemical and structural studies show that TrmE indeed binds formyl-tetrahydrofolate. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. We propose a reaction mechanism whereby TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate.

Scrima, Andrea; Vetter, Ingrid R; Armengod, M Eugenia; Wittinghofer, Alfred

2005-01-01

279

Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass-derived substrates.  

PubMed

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 thermocellum (T(opt) = 55 °C), Caldicellulosiruptor obsidiansis (T(opt) = 78 °C) and the fermentative hyperthermophiles, Pyrococcus furiosus (T(opt) = 100 °C) and Thermotoga maritima (T(opt) = 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 OD(600). 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. PMID:22843398

Hamilton-Brehm, Scott D; Vishnivetskaya, Tatiana A; Allman, Steve L; Mielenz, Jonathan R; Elkins, James G

2012-01-01

280

Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.  

PubMed

B(12)-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH(3)-H(4)folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH(3)-H(4)folate. These substrate-binding domains are (beta alpha)(8) barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH(3)-H(4)folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by approximately 50 A. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites. PMID:14752199

Evans, John C; Huddler, Donald P; Hilgers, Mark T; Romanchuk, Gail; Matthews, Rowena G; Ludwig, Martha L

2004-03-16

281

Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase  

PubMed Central

B12-dependent methionine synthase (MetH) is a large modular enzyme that utilizes the cobalamin cofactor as a methyl donor or acceptor in three separate reactions. Each methyl transfer occurs at a different substrate-binding domain and requires a different arrangement of modules. In the catalytic cycle, the cobalamin-binding domain carries methylcobalamin to the homocysteine (Hcy) domain to form methionine and returns cob(I)alamin to the folate (Fol) domain for remethylation by methyltetrahydrofolate (CH3-H4folate). Here, we describe crystal structures of a fragment of MetH from Thermotoga maritima comprising the domains that bind Hcy and CH3-H4folate. These substrate-binding domains are (??)8 barrels packed tightly against one another with their barrel axes perpendicular. The properties of the domain interface suggest that the two barrels remain associated during catalysis. The Hcy and CH3-H4folate substrates are bound at the C termini of their respective barrels in orientations that position them for reaction with cobalamin, but the two active sites are separated by ?50 Å. To complete the catalytic cycle, the cobalamin-binding domain must travel back and forth between these distant active sites.

Evans, John C.; Huddler, Donald P.; Hilgers, Mark T.; Romanchuk, Gail; Matthews, Rowena G.; Ludwig, Martha L.

2004-01-01

282

Microbiological evidence for Fe(III) reduction on early Earth  

NASA Astrophysics Data System (ADS)

It is generally considered that sulphur reduction was one of the earliest forms of microbial respiration, because the known microorganisms that are most closely related to the last common ancestor of modern life are primarily anaerobic, sulphur-reducing hyperthermophiles. However, geochemical evidence indicates that Fe(III) is more likely than sulphur to have been the first external electron acceptor of global significance in microbial metabolism. Here we show that Archaea and Bacteria that are most closely related to the last common ancestor can reduce Fe(III) to Fe(II) and conserve energy to support growth from this respiration. Surprisingly, even Thermotoga maritima, previously considered to have only a fermentative metabolism, could grow as a respiratory organism when Fe(III) was provided as an electron acceptor. These results provide microbiological evidence that Fe(III) reduction could have been an important process on early Earth and suggest that microorganisms might contribute to Fe(III) reduction in modern hot biospheres. Furthermore, our discovery that hyperthermophiles that had previously been thought to require sulphur for cultivation can instead be grown without the production of toxic and corrosive sulphide, should aid biochemical investigations of these poorly understood organisms.

Vargas, Madeline; Kashefi, Kazem; Blunt-Harris, Elizabeth L.; Lovley, Derek R.

1998-09-01

283

Persistent organochlorine levels in six prey species of the gyrfalcon Falco rusticolus in Iceland.  

PubMed

Our previous investigations have revealed very high levels of organochlorines (OCs) in the Icelandic gyrfalcon Falco rusticolus, a resident top predator. We now examine six potential prey species of birds, both resident and migratory, in order to elucidate the most likely route of the OCs to the gyrfalcon. The ptarmigan Lagopus mutus, the most important prey of the gyrfalcon, contained very low levels of OCs. Bioaccumulation of polychlorinated biphenyls (PCBs) and DDTs in mallards Anas platyrhynchos, tufted ducks Aythya fuligula, golden plovers Pluvialis apricaria, purple sandpipers Calidris maritima, and black guillemots Cepphus grylle reflected their position in the foodchain. The differences in OC-levels seem nevertheless too high just to reflect the different food-chain levels of these species in Iceland. The winter grounds of the migratory golden plovers and tufted ducks appear to be more contaminated than the Icelandic terrestrial habitat of ptarmigans or the freshwater habitat as reflected in mallards, both resident species. However, spending the winter on the coast in Iceland, results in high levels of contaminants in purple sandpipers and black guillemots. Our results indicate OC contamination of the marine ecosystem in Iceland while the terrestrial and freshwater ecosystems are little affected. It is postulated that gyrfalcons receive the major part of the observed contamination from prey other than ptarmigan, especially birds associated with the marine ecosystem and also from migratory birds. PMID:11234542

Olafsdóttir, K; Petersen, A E; Magnúsdóttir, E V; Björnsson, T; Jóhannesson, T

2001-01-01

284

Effects of two plant extracts on larval leafminer Liriomyza trifolii (Diptera: Agromyzidae) in tomatoes.  

PubMed

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

Civelek, H S; Weintraub, P G

2004-10-01

285

Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography.  

PubMed

The relative amounts of the five nucleosides (deoxycytidine, 5-methyldeoxycytidine, deoxyadenosine, deoxyguanosine and thymidine) in the DNA of nine plant species, one plant satellite DNA, and one animal species were determined by high performance liquid chromatography. The method allows the clean separation of the nucleosides from 10 microgram samples with 15 min. The following values for the proportion of methylated cytosines among all cytosines were obtained: Lobularia maritima 18.5%, Nicotiana tabacum 32.6%, Pisum sativum 23.2%, Rhinanthus minor 29.2%, Sinapsis alba 12.2%, Vicia faba 30.5%, Viscum album 23.2%, Cymbidium pumilum 18.8%, Cymbidium pumilum AT-rich satellite DNA 15.8%, Triticum aestivum 22.4%. DNA of an animal, the gerbil, Meriones unguiculatus, had a methylation percentage of 3.1%. An estimate of the GC content based on the buoyant density of DNA tends to be lower than the actual value, an estimate based on the melting temperature tends to be higher. This supports the finding by other authors that DNA methylation decreases the buoyant density and may increase the melting temperature at high m5C concentration. PMID:7272310

Wagner, I; Capesius, I

1981-06-26

286

Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage.  

PubMed

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 Zn(2+) finger motifs in the CTD. The Zn(2+) 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 Zn(2+) 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 Zn(2+) fingers from the mycobacterial topoI could be associated with Zn(2+) export and homeostasis. PMID:23771144

Ahmed, Wareed; Bhat, Anuradha Gopal; Leelaram, Majety Naga; Menon, Shruti; Nagaraja, Valakunja

2013-08-01

287

Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage  

PubMed Central

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.

Ahmed, Wareed; Bhat, Anuradha Gopal; Leelaram, Majety Naga; Menon, Shruti; Nagaraja, Valakunja

2013-01-01

288

Chemical and in vitro assessment of Alaskan coastal vegetation antioxidant capacity.  

PubMed

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 ?g 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 ?g/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

Kellogg, Joshua; Lila, Mary Ann

2013-11-20

289

Trophic plasticity of the gastropod Hydrobia ulvae within an intertidal bay (Roscoff, France): A stable isotope evidence  

NASA Astrophysics Data System (ADS)

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.

Riera, P.

2010-01-01

290

DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations  

PubMed Central

The compaction of DNA by the HU protein from Thermotoga maritima (TmHU) is analysed on a single-molecule level by the usage of an optical tweezers-assisted force clamp. The condensation reaction is investigated at forces between 2 and 40 pN applied to the ends of the DNA as well as in dependence on the TmHU concentration. At 2 and 5 pN, the DNA compaction down to 30% of the initial end-to-end distance takes place in two regimes. Increasing the force changes the progression of the reaction until almost nothing is observed at 40 pN. Based on the results of steered molecular dynamics simulations, the first regime of the length reduction is assigned to a primary level of DNA compaction by TmHU. The second one is supposed to correspond to the formation of higher levels of structural organisation. These findings are supported by results obtained by atomic force microscopy.

Olbrich, Carsten; Brutzer, Hergen; Salomo, Mathias; Kleinekathofer, Ulrich; Keyser, Ulrich F.; Kremer, Friedrich

2010-01-01

291

Effects of Posidonia oceanica beach-cast on germination, growth and nutrient uptake of coastal dune plants.  

PubMed

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

Del Vecchio, Silvia; Marbà, Núria; Acosta, Alicia; Vignolo, Clara; Traveset, Anna

2013-01-01

292

Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification  

PubMed Central

In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a truncated tRNA. The RNA is mainly bound by the N-terminal ferredoxin-like domain (NFLD) and the THUMP domain of one subunit within the ThiI homo-dimer thereby positioning the U8 close to the catalytic center in the pyrophosphatase domain of the other subunit. The recognition of the 3’-CCA end by the THUMP domain yields a molecular ruler defining the specificity for U8 thiolation. This first structure of a THUMP/NFLD-RNA complex might serve as paradigm for the RNA recognition by THUMP domains of other proteins. The ternary ThiI–RNA–ATP complex shows no significant structural changes due to adenosine triphosphate (ATP) binding, but two different states of active site loops are observed independent of the nucleotide loading state. Thereby conformational changes of the active site are coupled with conformational changes of the bound RNA. The ThiI–RNA complex structures indicate that full-length tRNA has to adopt a non-canonical conformation upon binding to ThiI.

Neumann, Piotr; Naumann, Peter-Thomas; Erwin, Whitney M.; Lauhon, Charles T.; Ficner, Ralf

2014-01-01

293

Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates  

SciTech Connect

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.

Hamilton-Brehm, Scott [ORNL; Vishnivetskaya, Tatiana A [ORNL; Allman, Steve L [ORNL; Mielenz, Jonathan R [ORNL; Elkins, James G [ORNL

2012-01-01

294

Effects of Canavalia lectins on acute inflammation in sensitized and non-sensitized rats.  

PubMed

The anti-inflammatory activity of Canavalia seed lectins (Canavalia gladiata [CGL], Canavalia maritima [ConM] and Canavalia brasiliensis [ConBr]) was evaluated by intravenous administration in rats. In non-sensitized rats, cellular edema elicited by carrageenan was reduced (45-51 %) by ConM and (44-59 %) by CGL. Osmotic edema elicited by dextran was reduced by ConM and CGL in 27 % and 29 %. ConM and CGL reduced the edema elicited by L-arginine in 53 % and that of prostaglandin E2 in 48 % and 36 %. Leukocyte migration elicited by carrageenan was reduced in 49 % by ConM and in 55 % by CGL (attenuated in 4× by glucose) and peritoneal TNF-? content in 82 %. In rats sensitized, ConM inhibited the paw edema and leukocyte migration elicited by ovalbumin in 34 % and 70 %. ConM and CGL are anti-inflammatory, mainly in cellular events mediated by prostaglandin E?, nitric oxide and TNF-? in non-sensitized rats. However, only ConM is anti-inflammatory in sensitized rats. CGL effect involves the lectin domain. PMID:23377963

Pinto, Nilson Vieira; Cavada, Benildo Sousa; Brito, Lucas Ferreira; Pereira, Ronniery Ilario; da Silva, Mayara Torquato Lima; Castro, Rondinelle Ribeiro; de Freitas Pires, Alana; Assreuy, Ana Maria Sampaio

2013-06-01

295

Isolation and characterization of a novel gene encoding alpha-L-arabinofuranosidase from Aspergillus oryzae.  

PubMed

We cloned and characterized a novel gene (abfA) encoding alpha-L-arabinofuranosidase (alpha-L-AFase) from Aspergillus oryzae. One clone homologous to the alpha-L-AFase gene of Thermotoga maritima was found in an expressed sequence tag (EST) library of A. oryzae and a corresponding gene was isolated. Molecular analysis showed that the abfA gene carried six exons interrupted by five introns and had an open reading frame encoding 481 amino acid residues. The amino acid sequence similarity at active sites to the alpha-L-AFases from other organisms indicated that the alpha-L-AFase encoded by abfA was classified as a family 51 glycoside hydrolase. When the abfA was overexpressed in the homologous hyperexpression system of A. oryzae, a large amount of alpha-L-AFase was produced as intracellular protein. The apparent molecular mass of the purified enzyme was estimated to be 228,000 by gel filtration and that of its subunit as 55,000 by SDS-PAGE, suggesting that the enzyme is a tetramer. The enzyme hydrolyzed p-nitrophenyl-alpha-L-arabinofuranoside but not other p-nitrophenyl glycosides. These results demonstrated that the abfA gene encodes a functional alpha-L-AFase. PMID:16233670

Matsumura, Kengo; Obata, Hiroshi; Hata, Yoji; Kawato, Akitsugu; Abe, Yasuhisa; Akita, Osamu

2004-01-01

296

Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.  

PubMed

In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a truncated tRNA. The RNA is mainly bound by the N-terminal ferredoxin-like domain (NFLD) and the THUMP domain of one subunit within the ThiI homo-dimer thereby positioning the U8 close to the catalytic center in the pyrophosphatase domain of the other subunit. The recognition of the 3'-CCA end by the THUMP domain yields a molecular ruler defining the specificity for U8 thiolation. This first structure of a THUMP/NFLD-RNA complex might serve as paradigm for the RNA recognition by THUMP domains of other proteins. The ternary ThiI-RNA-ATP complex shows no significant structural changes due to adenosine triphosphate (ATP) binding, but two different states of active site loops are observed independent of the nucleotide loading state. Thereby conformational changes of the active site are coupled with conformational changes of the bound RNA. The ThiI-RNA complex structures indicate that full-length tRNA has to adopt a non-canonical conformation upon binding to ThiI. PMID:24705700

Neumann, Piotr; Lakomek, Kristina; Naumann, Peter-Thomas; Erwin, Whitney M; Lauhon, Charles T; Ficner, Ralf

2014-06-01

297

Structural Dynamics of the Magnesium-bound Conformation of CorA in a lipid bilayer  

PubMed Central

Summary The transmembrane conformation of Thermotoga maritima CorA, a Magnesium transport system, has been studied in it’s Mg2+-bound form by site-directed spin labeling and electron paramagnetic resonance spectroscopy. Probe mobility together with accessibility data were used to evaluate the overall dynamics and relative arrangement of individual transmembrane segments TM1 and TM2. TM1 extends toward the cytoplasmic side creating a water filled cavity, while TM2 is located in the periphery of the oligomer, contacting the lipid bilayer. A structural model for the conserved extracellular loop was generated based on EPR data and MD simulations, in which residue E316 is located towards the fivefold symmetry axis in position to electrostatically influence divalent ion translocation. Electrostatic analyses of our model suggest that, in agreement with the crystal structure, Mg2+ -bound CorA is in a close conformation. The present results suggest that long-range structural rearrangements are necessary to allow Mg2+ translocation.

Dalmas, Olivier; Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien; Roux, Benoit; Perozo, Eduardo

2010-01-01

298

A model for the effect of submerged aquatic vegetation on turbulence induced by an oscillating grid  

NASA Astrophysics Data System (ADS)

The aim of this study is to model, under controlled laboratory conditions, the effect of submerged aquatic vegetation (SAV) on turbulence generated in a water column by an oscillating grid turbulence (OGT). Velocity profiles have been measured by an acoustic Doppler velocimeter (MicroADV). Experimental conditions are analysed in two canopy models (rigid and semi-rigid), using nine plant-to-plant distances (ppd), three stem diameters (d), four types of natural SAV (Cladium mariscus, Potamogeton nodosus, Myriophyllum verticillatum and Ruppia maritima) and two oscillation grid frequencies (f). To quantify this response, we have developed a non-dimensional model, with a specific turbulent kinetic energy (TKE), f, stroke (s), d, ppd, distance from the virtual origin to the measurement (zm) and space between grid bars (M). The experimental data show that, at zm/zc < 1 the turbulent kinetic energy decays with zm, according to the well-known power law, zm-2, and does not depend on the vegetation characteristics. In contrast, at zm/zc > 1, TKE decreases faster with zm and scales to the model variables according to TKE/(f·s)?(·(. Therefore, at zm/zc > 1 the TKE is affected by the geometric characteristics of the plants (both diameter and plant-to-plant distance), an effect called sheltering. Results from semi-rigid canopies and natural SAV are found to scale with the non-dimensional model proposed for rigid canopies. We also discuss the practical implications for field conditions (wind and natural SAV).

Pujol, Dolors; Colomer, Jordi; Serra, Teresa; Casamitjana, Xavier

2012-12-01

299

Prediction of signal recognition particle RNA genes  

PubMed Central

We describe a method for prediction of genes that encode the RNA component of the signal recognition particle (SRP). A heuristic search for the strongly conserved helix 8 motif of SRP RNA is combined with covariance models that are based on previously known SRP RNA sequences. By screening available genomic sequences we have identified a large number of novel SRP RNA genes and we can account for at least one gene in every genome that has been completely sequenced. Novel bacterial RNAs include that of Thermotoga maritima, which, unlike all other non-gram-positive eubacteria, is predicted to have an Alu domain. We have also found the RNAs of Lactococcus lactis and Staphylococcus to have an unusual UGAC tetraloop in helix 8 instead of the normal GNRA sequence. An investigation of yeast RNAs reveals conserved sequence elements of the Alu domain that aid in the analysis of these RNAs. Analysis of the human genome reveals only two likely genes, both on chromosome 14. Our method for SRP RNA gene prediction is the first convenient tool for this task and should be useful in genome annotation.

Regalia, Marco; Rosenblad, Magnus Alm; Samuelsson, Tore

2002-01-01

300

An unusual triosephosphate isomerase from the early divergent eukaryote Giardia lamblia.  

PubMed

Recombinant triosephosphate isomerase from the parasite Giardia lamblia (GlTIM) was characterized and immunolocalized. The enzyme is distributed uniformly throughout the cytoplasm. Size exclusion chromatography of the purified enzyme showed two peaks with molecular weights of 108 and 55 kDa. Under reducing conditions, only the 55-kDa protein was detected. In denaturing gel electrophoresis without dithiothreitol, the enzyme showed two bands with molecular weights of 28 and 50 kDa; with dithiotretitol, only the 28-kDa protein was observed. These data indicate that GlTIM may exist as a tetramer or a dimer and that, in the former, the two dimers are covalently linked by disulfide bonds. The kinetics of the dimer were similar to those of other TIMs. The tetramer exhibited half of the kcat of the dimer without changes in the Km. Studies on the thermal stability and the apparent association constants between monomers showed that the tetramer was slightly more stable than the dimer. This finding suggests the oligomerization is not related to enzyme thermostability as in Thermotoga maritima. Instead, it could be that oligomerization is related to the regulation of catalytic activity in different states of the life cycle of this mesophilic parasite. PMID:15146481

López-Velázquez, Gabriel; Molina-Ortiz, Dora; Cabrera, Nallely; Hernández-Alcántara, Gloria; Peon-Peralta, Jorge; Yépez-Mulia, Lilian; Pérez-Montfort, Ruy; Reyes-Vivas, Horacio

2004-06-01

301

The Structural and Biochemical Characterization of Human RNase H2 Complex Reveals the Molecular Basis for Substrate Recognition and Aicardi-Gouti?res Syndrome Defects*  

PubMed Central

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 ? 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.

Figiel, Malgorzata; Chon, Hyongi; Cerritelli, Susana M.; Cybulska, Magdalena; Crouch, Robert J.; Nowotny, Marcin

2011-01-01

302

The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects.  

PubMed

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 ? 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

Figiel, Ma?gorzata; Chon, Hyongi; Cerritelli, Susana M; Cybulska, Magdalena; Crouch, Robert J; Nowotny, Marcin

2011-03-25

303

Rising from the Sea: Correlations between Sulfated Polysaccharides and Salinity in Plants  

PubMed Central

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.

Aquino, Rafael S.; Grativol, Clicia; Mourao, Paulo A. S.

2011-01-01

304

Status and threats on seagrass beds using GIS in Vietnam  

NASA Astrophysics Data System (ADS)

Seagrasses, marine flowering plants, are widely distributed along temperate and tropical coastlines of the world. Seagrasses have key ecological roles in coastal ecosystems and can form extensive meadows supporting high biodiversity. Till now, fourteen seagrass species belonging to four families were found in Vietnam: Halophila beccarii, H. decipiens, H. ovalis, H. minor, Thalassia hemprichii, Enhalus acoroides, Ruppia maritima, Halodule pinifolia, H. uninervis, Syringodium isoetifolium, Cymadocea rotundata, C. serrulata and Thalassodendron ciliatum. A total area of seagrass beds in Vietnam is estimated to be approximately 17000 ha by satellite images and GIS technology. In recent years, the distribution areas and densities of seagrass beds in Vietnam have been serious decreased compared with those 10-15 years ago. The decline level depended on the impacts by the natural process, the economical activities and the conservation awareness of local people. Thus, it is different at each coastal area. Generally speaking, the distribution areas and densities of seagrass beds were decreased by more than 50%. Seagrasses on tidal flats in some areas such as Quang Ninh, Hai Phong, Phu Quoc seem to be nearly lost. The distribution areas of seagrass beds in 2009 at Tam Giang-Cau Hai lagoon and Cua Dai estuary was decreased by 50-70% of those in early 1990s.

Luong, Cao Van; Thao, Nguyen Van; Komatsu, Teruhisa; Ve, Nguyen Dac; Tien, Dam Duc

2012-10-01

305

Bird colonies cause seagrass enrichment in a subtropical estuary: Observational and experimental evidence  

NASA Astrophysics Data System (ADS)

Colonies/roosts of piscivorous birds in Florida Bay, a subtropical estuary, concentrate nutrients by feeding away from their colonies/roosts and returning with food for young and to defaecate. Seagrass beds surrounding the colony islands were markedly different from those around similar islands that did not contain colonies. Seagrass standing crop was enhanced up to 200 m from bird colony islands compared with islands without colonies. The species of seagrass were also different at colonies, where Halodule wrightii and Ruppia maritima predominated in zones close to the colony islands. Around islands without colonies, only Thalassia testudinum was present. Experimental bird perches placed to stimulate concentrated bird presence produced changes in adjacent seagrass meadows that were similar to differences between islands with colonies and those without. Over 5 years, seagrass standing crop increased around the experimental perches, and species dominance shifted from T. testudinum to H. wrightii. No similar changes occurred at control locations. These experimental results indicate that the bird concentrations are responsible for the observed differences in seagrass communities surrounding islands that contain colonies. These enriched areas are significant to the seagrass ecosystem because many seagrasses in Florida Bay appear to be nutrient-limited. Demersal fish and invertebrate density and species richness have been shown to be a function of the seagrass standing crop and species composition, so the changes in seagrasses stimulated by localized bird concentrations have the capacity to alter the entire community structure.

Powell, George V. N.; Fourqurean, James W.; Kenworthy, W. Judson; Zieman, Joseph C.

1991-06-01

306

Effects of Posidonia Oceanica Beach-Cast on Germination, Growth and Nutrient Uptake of Coastal Dune Plants  

PubMed Central

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.

Del Vecchio, Silvia; Marba, Nuria; Acosta, Alicia; Vignolo, Clara; Traveset, Anna

2013-01-01

307

Functional Characterization of Two M42 Aminopeptidases Erroneously Annotated as Cellulases  

PubMed Central

Several aminopeptidases of the M42 family have been described as tetrahedral-shaped dodecameric (TET) aminopeptidases. A current hypothesis suggests that these enzymes are involved, along with the tricorn peptidase, in degrading peptides produced by the proteasome. Yet the M42 family remains ill defined, as some members have been annotated as cellulases because of their homology with CelM, formerly described as an endoglucanase of Clostridium thermocellum. Here we describe the catalytic functions and substrate profiles CelM and of TmPep1050, the latter having been annotated as an endoglucanase of Thermotoga maritima. Both enzymes were shown to catalyze hydrolysis of nonpolar aliphatic L-amino acid-pNA substrates, the L-leucine derivative appearing as the best substrate. No significant endoglucanase activity was measured, either for TmPep1050 or CelM. Addition of cobalt ions enhanced the activity of both enzymes significantly, while both the chelating agent EDTA and bestatin, a specific inhibitor of metalloaminopeptidases, proved inhibitory. Our results strongly suggest that one should avoid annotating members of the M42 aminopeptidase family as cellulases. In an updated assessment of the distribution of M42 aminopeptidases, we found TET aminopeptidases to be distributed widely amongst archaea and bacteria. We additionally observed that several phyla lack both TET and tricorn. This suggests that other complexes may act downstream from the proteasome.

Dutoit, Raphael; Brandt, Nathalie; Legrain, Christianne; Bauvois, Cedric

2012-01-01

308

Protective mechanisms of pycnogenol in ethanol-insulted cerebellar granule cells.  

PubMed

Pycnogenol (PYC), a patented combination of bioflavonoids extracted from the bark of French maritime pine (Pinus maritima), inhibits apoptosis and necrosis of developing neurons exposed acutely to ethanol (EtOH). The present study shows that the protective mechanisms of PYC in EtOH-exposed postnatal day 9 cerebellar granule cells (P9 CGCs) include (1) reduction of reactive oxygen species (ROS) production; (2) counteraction of suppressed copper/zinc superoxide dismutase (Cu/Zn SOD) and glutathione peroxidase/reductase (GSH-Px/GSSG-R) system activities; (3) upregulation of Cu/Zn SOD protein expression; (4) mitigation of the EtOH-mediated exacerbation of catalase (CAT) activity; and, (5) specific binding and inhibition of active caspase-3. These results indicate that the mechanisms by which PYC antagonizes EtOH-induced oxidative stress include oxidant scavenging and modulation of endogenous, cellular proteins. Using findings from the present and previous studies, a model delineating the mechanisms of EtOH effects on the system of antioxidant enzymes in developing CGCs is presented. PMID:15389691

Siler-Marsiglio, Kendra I; Paiva, Michael; Madorsky, Irina; Serrano, Yahaira; Neeley, Andy; Heaton, Marieta B

2004-11-01

309

Crystal structure of the N-terminal domain of MinC dimerized via domain swapping  

PubMed Central

Proper cell division at the mid-site of gram-negative bacteria reflects critical regulation by the min system (MinC, MinD and MinE) of the cytokinetic Z ring, which is a polymer composed of FtsZ subunits. MinC and MinD act together to inhibit aberrantly positioned Z-ring formation. MinC consists of two domains: an N-terminal domain (MinCNTD), which interacts with FtsZ and inhibits FtsZ polymerization, and a C-terminal domain (MinCCTD), which interacts with MinD and inhibits the bundling of FtsZ filaments. These two domains reportedly function together, and both are essential for normal cell division. The full-length dimeric structure of MinC from Thermotoga maritima has been reported, and shows that MinC dimerization occurs via MinCCTD; MinCNTD is not involved in dimerization. Here the crystal structure of Escherichia coli MinCNTD (EcoMinCNTD) is reported. EcoMinCNTD forms a dimer via domain swapping between the first ? strands in each subunit. It is therefore suggested that the dimerization of full-length EcoMinC occurs via both MinCCTD and MinCNTD, and that the dimerized EcoMinCNTD likely plays an important role in inhibiting aberrant Z-ring localization.

An, Jun Yop; Kim, Tae Gyun; Park, Kyoung Ryoung; Lee, Jung-Gyu; Youn, Hyung-Seop; Lee, Youngjin; Kang, Jung Youn; Kang, Gil Bu; Eom, Soo Hyun

2013-01-01

310

A study of antioxidant activity, enzymatic inhibition and in vitro toxicity of selected traditional sudanese plants with anti-diabetic potential  

PubMed Central

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.

2014-01-01

311

The Periplasmic Loop Provides Stability to the Open State of the CorA Magnesium Channel*  

PubMed Central

Crystal structures of the CorA Mg2+ channel have suggested that metal binding in the cytoplasmic domain stabilizes the pentamer in a closed conformation. The open “metal free” state of the channel is, however, still structurally uncharacterized. Here, we have attempted to map conformational states of CorA from Thermotoga maritima by determining which residues support the pentameric structure in the presence or absence of Mg2+. We find that when Mg2+ is present, the pentamer is stabilized by the putative gating sites (M1/M2) in the cytoplasmic domain. Strikingly however, we find that the conserved and functionally important periplasmic loop is vital for the integrity of the pentamer when Mg2+ is absent from the M1/M2 sites. Thus, although the periplasmic loops were largely disordered in the x-ray structures of the closed channel, our data suggests a prominent role for the loops in stabilizing the open conformation of the CorA channels.

Palombo, Isolde; Daley, Daniel O.; Rapp, Mikaela

2012-01-01

312

Development of a novel fluorescent protein construct by genetically fusing green fluorescent protein to the N-terminal of aspartate dehydrogenase.  

PubMed

We developed a fluorescent protein construct by genetically fusing green fluorescent protein (GFP) to aspartate dehydrogenase from Thermotoga maritima. The fusion protein was cloned, heterologously expressed in Escherichia coli cells, and purified by Ni-chelate affinity chromatography. It was then introduced into a measurement cuvette to monitor its fluorescence signal. Aspartate dehydrogenase functioned as the biorecognition element, and aspartate-induced conformational change was converted to a fluorescence signal by GFP. The recombinant protein responded to l-aspartate (l-Asp) linearly within the concentration range of 1-50 mM, and it was capable of giving a fluorescence signal in 1 Min. Although a linear response was also observed for l-Glu, the fluorescence signal was 2.7 times lower than that observed for l-Asp. In the present study, we describe two novelties: development of a genetically encoded fluorescent protein construct for monitoring of l-Asp in vitro, and employment of aspartate dehydrogenase scaffold as a biorecognition element. A few genetically encoded amino-acid biosensors have been described in the literature, but to our knowledge, a protein has not been constructed solely for determination of l-Asp. Periplasmic ligand binding proteins offer high binding affinity in the micromolar range, and they are frequently used as biorecognition elements. Instead of choosing a periplasmic l-Asp binding protein, we attempted to use the substrate specificity of aspartate dehydrogenase enzyme. PMID:24033594

Ozyurt, Canan; Evran, Serap; Telefoncu, Azmi

2013-01-01

313

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters  

PubMed Central

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.

Nicolet, Yvain; Rohac, Roman; Martin, Lydie; Fontecilla-Camps, Juan C.

2013-01-01

314

Ingestion, enzymatic digestion and absorption of particles derived from different vegetal sources by the cockle Cerastoderma edule  

NASA Astrophysics Data System (ADS)

Ingestion, enzymatic digestion and absorption of particulate detrital matter derived from six different vegetal sources by the common cockle Cerastoderma edule was analyzed in a series of seasonal experiments performed in March, May and October 2005. Two green macroalgae: Ulva lactuca and Enteromorpha sp; two vascular plants: Spartina maritima and Juncus maritimus, the red macroalgae Gracilaria gracilis; and the microalgae Isochrysis galbana were used in experiments. Detrital matter was elaborated by freeze-drying, grinding and sieving (< 63 ?m) vegetal tissues. Mono-specific detrital diets of similar organic content (? 60-70%) were elaborated by mixing detritus with ashed silt. We measured i) the biochemical composition of different detritus, ii) physiological components of the absorptive balance (i.e. clearance, ingestion, rejection and absorption rate and absorption efficiency), iii) the capability of the digestive gland to hydrolyze carbohydrates from different detritus (digestibility), as well as iv) glandular cellulase and xylanase activities. Detritus type, season and the interaction detritus-season exerted significant effects upon all the physiological components of absorptive balance. Effects were light at the pre-absorptive level, however, huge variations associated to absorption efficiency promoted large significant differences in absorption rates (AR) of different kind of detritus: irrespective of season, highest values corresponded to cockles fed the green macroalgae ( Ulva and Enteromorpha) and lowest to those fed the vascular plant Juncus maritimus. Recorded significant differences in enzymatic digestibility among detritus were found to explain ? 40% of differences recorded in AR, and the following regression could be fitted: AR = 0.232 (± 0.032) * Digestibility + 0,072 (± 0.015); r 2 = 0.415; F = 51.036; p < 0.001. Digestibility of Ulva and Enteromorpha was found to be significantly correlated with cellulase activity in the digestive gland, whereas digestibility of Juncus, Spartina and Gracilaria was correlated with xylanase activity. Obtained correlations are discussed in the frame of contrasting conclusions in the literature regarding the importance of detritus as a food source for bivalves.

Arambalza, U.; Urrutia, M. B.; Navarro, E.; Ibarrola, I.

2010-10-01

315

Toward a molecular understanding of metal transport by P(1B)-type ATPases.  

PubMed

The P(1B) 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 (P(1B-1)-P(1B-5)) on the basis of their transported substrates (Cu(+), Zn(2+), Cu(2+), and Co(2+)) 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 Zn(2+)-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 P(1B)-ATPases. PMID:23046649

Rosenzweig, Amy C; Argüello, José M

2012-01-01

316

Annexation of a high-activity enzyme in a synthetic three-enzyme complex greatly decreases the degree of substrate channeling.  

PubMed

The self-assembled three-enzyme complex containing triosephosphate isomerase (TIM), aldolase (ALD), and fructose 1,6-biphosphatase (FBP) was constructed via a mini-scaffoldin containing three different cohesins and the three dockerin-containing enzymes. This enzyme complex exhibited 1 order of magnitude higher initial reaction rates than the mixture of noncomplexed three enzymes. In this enzyme cascade reactions, the reaction mediated by ALD was the rate-limiting step. To understand the in-depth role of the rate-limiting enzyme ALD in influencing the substrate channeling effect of synthetic enzyme complexes, low-activity ALD from Thermotoga maritima was replaced with a similar-size ALD isolated from Thermus thermophilus, where the latter had more than 5 times specific activity of the former. The synthetic three-enzyme complexes annexed with either low-activity or high-activity ALDs exhibited higher initial reaction rates than the mixtures of the two-enzyme complex (TIM-FBP) and the nonbound low-activity or high activity ALD at the same enzyme concentration. It was also found that the annexation of more high-activity ALD in the synthetic enzyme complexes drastically decreased the degree of substrate channeling from 7.5 to 1.5. These results suggested that the degree of substrate channeling in synthetic enzyme complexes depended on the enzyme choice. This study implied that the construction of synthetic enzyme enzymes in synthetic cascade pathways could be a very important tool to accrelerate rate-limiting steps controlled by low-activity enzymes. PMID:24283966

You, Chun; Zhang, Y-H Percival

2014-06-20

317

Structural Diversity Within the Mononuclear and Binuclear Active Sites of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase  

SciTech Connect

NagA catalyzes the hydrolysis of N-acetyl-D-glucosamine-6-phosphate to D-glucosamine-6-phosphate and acetate. X-ray crystal structures of NagA from Escherichia coli were determined to establish the number and ligation scheme for the binding of zinc to the active site and to elucidate the molecular interactions between the protein and substrate. The three-dimensional structures of the apo-NagA, Zn-NagA, and the D273N mutant enzyme in the presence of a tight-binding N-methylhydroxyphosphinyl-D-glucosamine-6-phosphate inhibitor were determined. The structure of the Zn-NagA confirms that this enzyme binds a single divalent cation at the beta-position in the active site via ligation to Glu-131, His-195, and His-216. A water molecule completes the ligation shell, which is also in position to be hydrogen bonded to Asp-273. In the structure of NagA bound to the tight binding inhibitor that mimics the tetrahedral intermediate, the methyl phosphonate moiety has displaced the hydrolytic water molecule and is directly coordinated to the zinc within the active site. The side chain of Asp-273 is positioned to activate the hydrolytic water molecule via general base catalysis and to deliver this proton to the amino group upon cleavage of the amide bond of the substrate. His-143 is positioned to help polarize the carbonyl group of the substrate in conjunction with Lewis acid catalysis by the bound zinc. The inhibitor is bound in the {alpha}-configuration at the anomeric carbon through a hydrogen bonding interaction of the hydroxyl group at C-1 with the side chain of His-251. The phosphate group of the inhibitor attached to the hydroxyl at C-6 is ion paired with Arg-227 from the adjacent subunit. NagA from Thermotoga maritima was shown to require a single divalent cation for full catalytic activity.

Hall,R.; Brown, S.; Fedorov, A.; Fedorov, E.; Xu, C.; Babbitt, P.; Almo, S.; Raushel, F.

2007-01-01

318

The utility of mitochondrial DNA sequences for the identification of forensically important blowflies (Diptera: Calliphoridae) in southeastern Australia.  

PubMed

The applicability of mitochondrial DNA (mtDNA) sequencing was investigated for the identification of the following forensically important species of blowflies from southeastern Australia: Calliphora albifrontalis, C. augur, C. dubia, C. hilli hilli, C. maritima, C. stygia, C. vicina, Chrysomya rufifacies, Ch. varipes and Onesia tibialis. All breed in carrion except O. tibialis, which is an earthworm parasitoid. Emphasis was placed on Calliphora species because they predominate among the carrion-breeding blowfly fauna of southern Australia and their immatures are difficult to identify morphologically. A partial sequence of the mitochondrial COII gene was determined for all species and for COI for C. albifrontalis, C. augur, C. dubia and C. stygia only. Five other species of blowflies, Chrysomya albiceps, Ch. rufifacies, Protophormia terraenovae, Lucilia illustris and L. sericata, for which sequence data were already available, were also included. Analysis of the COI and COII sequences revealed abundant phylogenetically informative nucleotide substitutions that could identify blowfly species to species group. In contrast, because of the low level of sequence divergence of sister species, the data could not distinguish among taxa from the same species group, i.e. the species within the C. augur and C. stygia groups. The molecular data support the existing species group separation of the taxa within Calliphora. Because of the speed and accuracy of current nucleotide sequencing technology and the abundant apomorphic substitutions available from mtDNA sequences, this approach, with the analysis of additional taxa and genes, is likely to enable the reliable identification of carrion-breeding blowflies in Australia. PMID:11457611

Wallman, J F; Donnellan, S C

2001-08-15

319

Complete sucrose hydrolysis by heat-killed recombinant Pichia pastoris cells entrapped in calcium alginate  

PubMed Central

Background An ideal immobilized biocatalyst for the industrial-scale production of invert sugar should stably operate at elevated temperatures (60-70°C) and high sucrose concentrations (above 60%, w/v). Commercial invertase from the yeast Saccharomyces cerevisiae is thermolabile and suffers from substrate inhibition. Thermotoga maritima ?-fructosidase (BfrA) is the most thermoactive and thermostable sucrose-hydrolysing enzyme so far identified and allows complete inversion of the substrate in highly concentrated solutions. Results In this study, heat-killed Pichia pastoris cells bearing N-glycosylated BfrA in the periplasmic space were entrapped in calcium alginate beads. The immobilized recombinant yeast showed maximal sucrose hydrolysis at pH 5–7 and 90°C. BfrA was 65% active at 60°C and had no activity loss after incubation without the substrate at this temperature for 15 h. Complete inversion of cane sugar (2.04 M) at 60°C was achieved in batchwise and continuous operation with respective productivities of 4.37 and 0.88 gram of substrate hydrolysed per gram of dry beads per hour. The half-life values of the biocatalyst were 14 and 20 days when operated at 60°C in the stirred tank and the fixed-bed column, respectively. The reaction with non-viable cells prevented the occurrence of sucrose fermentation and the formation of by-products. Six-month storage of the biocatalyst in 1.46 M sucrose (pH 5.5) at 4°C caused no reduction of the invertase activity. Conclusions The features of the novel thermostable biocatalyst developed in this study are more attractive than those of immobilized S. cerevisiae cells for application in the enzymatic manufacture of inverted sugar syrup in batch and fixed-bed reactors.

2014-01-01

320

Thermophilic anaerobic oxidation of methane by marine microbial consortia  

PubMed Central

The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ?25?°C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70?°C with an apparent optimum between 45 and 60?°C. AOM was absent at temperatures ?75?°C. Long-term enrichment of AOM was fastest at 50?°C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60?°C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats.

Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

2011-01-01

321

Crystal structure of ?-galactosidase from Lactobacillus acidophilus NCFM: insight into tetramer formation and substrate binding.  

PubMed

Lactobacillus acidophilus NCFM is a probiotic bacterium known for its beneficial effects on human health. The importance of ?-galactosidases (?-Gals) for growth of probiotic organisms on oligosaccharides of the raffinose family present in many foods is increasingly recognized. Here, the crystal structure of ?-Gal from L. acidophilus NCFM (LaMel36A) of glycoside hydrolase (GH) family 36 (GH36) is determined by single-wavelength anomalous dispersion. In addition, a 1.58-Å-resolution crystallographic complex with ?-d-galactose at substrate binding subsite -1 was determined. LaMel36A has a large N-terminal twisted ?-sandwich domain, connected by a long ?-helix to the catalytic (?/?)(8)-barrel domain, and a C-terminal ?-sheet domain. Four identical monomers form a tightly packed tetramer where three monomers contribute to the structural integrity of the active site in each monomer. Structural comparison of LaMel36A with the monomeric Thermotoga maritima ?-Gal (TmGal36A) reveals that O2 of ?-d-galactose in LaMel36A interacts with a backbone nitrogen in a glycine-rich loop of the catalytic domain, whereas the corresponding atom in TmGal36A is from a tryptophan side chain belonging to the N-terminal domain. Thus, two distinctly different structural motifs participate in substrate recognition. The tetrameric LaMel36A furthermore has a much deeper active site than the monomeric TmGal36A, which possibly modulates substrate specificity. Sequence analysis of GH36, inspired by the observed structural differences, results in four distinct subgroups having clearly different active-site sequence motifs. This novel subdivision incorporates functional and architectural features and may aid further biochemical and structural analyses within GH36. PMID:21827767

Fredslund, Folmer; Hachem, Maher Abou; Larsen, René Jonsgaard; Sørensen, Pernille Gerd; Coutinho, Pedro M; Lo Leggio, Leila; Svensson, Birte

2011-09-23

322

Breeding productivity of Smith Island black ducks  

USGS Publications Warehouse

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.

Haramis, G.M.; Jorde, D.G.; Olsen, G.H.; Stotts, D.B.; Harrison, M.K.

2002-01-01

323

Improved recombinant cellulase expression in chloroplast of tobacco through promoter engineering and 5' amplification promoting sequence.  

PubMed

Economical production of bioethanol from lignocellulosic biomass still faces many technical limitations. Cost-effective production of fermentable sugars is still not practical for large-scale production of bioethanol due to high costs of lignocellulolytic enzymes. Therefore, plant molecular farming, where plants are used as bioreactors, was developed for the mass production of cell wall degrading enzymes that will help reduce costs. Subcellular targeting is also potentially more suitable for the accumulation of recombinant cellulases. Herein, we generated transgenic tobacco plants (Nicotiana tabacum cv. SR1) that accumulated Thermotoga maritima BglB cellulase, which was driven by the alfalfa RbcsK-1A promoter and contained a small subunit of the rubisco complex transit peptide. The generated transformants possessed high specific BglB activity and did not show any abnormal phenotypes. Furthermore, we genetically engineered the RbcsK-1A promoter (MRbcsK-1A) and fused the amplification promoting sequence (aps) to MRbcsK-1A promoter to obtain high expression of BglB in transgenic plants. AMRsB plant lines with aps-MRbcsK-1A promoter showed the highest specific activity of BglB, and the accumulated BglB protein represented up to 9.3 % of total soluble protein. When BglB was expressed in Arabidopsis and tobacco plants, the maximal production capacity of recombinant BglB was 0.59 and 1.42 mg/g wet weight, respectively. These results suggests that suitable recombinant expression of cellulases in subcellular compartments such as chloroplasts will contribute to the cost-effective production of enzymes, and will serve as the solid foundation for the future commercialization of bioethanol production via plant molecular farming. PMID:23771581

Jung, Sera; Lee, Dae-Seok; Kim, Yeon-Ok; Joshi, Chandrashekhar P; Bae, Hyeun-Jong

2013-11-01

324

Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme  

PubMed Central

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.

Hayashi, Takahiro; Caranto, Jonathan D.; Wampler, David A.; Kurtz, Donald M.; Moenne-Loccoz, Pierre

2010-01-01

325

Laboratory Directed Research & Development program. Annual report to the Department of Energy  

SciTech Connect

This report briefly discusses the following projects coordinated at Brookhaven National Laboratory: investigation of the utility of max-entropy methods for the analysis of powder diffraction data; analysis of structures and interactions of nucleic acids and proteins by small angle x-ray diffraction; relaxographic MRI and functional MRI; very low temperature infra-red laser absorption as a potential analytical tool; state-resolved measurements of H{sub 2} photodesorption: development of laser probes of H{sub 2} for in-situ accelerator measurements; Siberian snake prototype development for RHIC; synthesis and characterization of novel microporous solids; ozone depletion, chemistry and physics of stratospheric aerosols; understanding the molecular basis for the synthesis of plant fatty acids possessing unusual double bond positions; structure determination of outer surface proteins of the Lyme disease spirochete; low mass, low-cost multi-wire proportional chambers for muon systems of collider experiments; theory of self-organized criticality; development of the PCR-SSCP technique for the detection, at the single cell level, of specific genetic changes; feasibility of SPECT in imaging of F-18 FDG accumulation in tumors; visible free electron laser oscillator experiment; study of possible 2 + 2 TeV muon-muon collider; ultraviolet FEL R & D; precision machining using hard x-rays; new directions in in-vivo enzyme mapping: catechol-O-methyltransferase; proposal to develop a high rate muon polarimeter; development of intense, tunable 20-femtosecond laser systems; use of extreme thermophilic bacterium thermatoga maritima as a source of ribosomal components and translation factors for structural studies; and biochemical and structural studies of Chaperon proteins from thermophilic bacteria and other experiments.

Ogeka, G.J.; Romano, A.J.

1995-12-01

326

Ethnopharmacological survey of wild medicinal plants in Showbak, Jordan.  

PubMed

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

Al-Qura'n, S

2009-05-01

327

The mute swan, its status, behavior, and history in the U. K  

USGS Publications Warehouse

For many years the mute swan has been considered a royal bird. It is a prominent resident throughout the United Kingdom (U.K.), often found on the inland waterways. Some people consider it to be a nonmigratory native bird because it doesn't tend to move large distances and doesn't often venture far from freshwater. A mute swan may often live out its life cycle in the same river valley in which it hatched. Over the last 30-40 years, a large amount of research has been carried out on their life cycle, behavior, and mortality caused by such factors as lead poisoning from fishing weights. Throughout the U.K., there are a number of areas where mute swans may be found in large numbers, including (1) the River Thames (which passes through London), (2) Slimbridge Wetlands Center, (3) Berwick-upon- Tweed (the second largest mute swan colony in Britain), and (4) Abbotsbury Swannery (the worlds only managed swan colony). This last site is a truly unique area, and each year it often has over 150 nesting pairs producing between 2-12 eggs per nest. The management is minimal, and the site is ideal for their requirements because it is close to a number of freshwater sources, and has good nesting sites and large quantities of eelgrass Zostera marina and widgeon grass Ruppia maritima, their preferred food sources. The Swannery is located on the south coast of England at the western end of the Fleet Lagoon, a micro-tidal estuary, which borders the English Channel.

Lohnes, E. J. R.

2004-01-01

328

Reining in Polyoma Virus Associated Nephropathy: Design and Characterization of a Template Mimicking BK Viral Coat Protein Cellular Binding  

PubMed Central

The BK polyoma virus is a leading cause of chronic post kidney transplantation rejection. One target for therapeutic intervention is the initial association of the BK virus with the host cell. We hypothesize that the rate of BKV infection can be curbed by competitively preventing viral binding to cells. The x-ray structures of homologous viruses complexed with N-terminal glycoproteins suggest that the BC and HI loops of the viral coat are determinant for binding and thereby, infection of the host cell. The large size of the viral coat precludes it from common biophysical and small molecule screening studies. Hence, we sought to develop a smaller protein template incorporating the identified binding loops of the BK viral coat in a manner that adequately mimics the binding activity of the BK virus coat protein to cells. Such a mimic may serve as a tool for the identification of inhibitors of BK viral progression. Herein, we report the design and characterization of a reduced-size and soluble template derived from a four helix protein—TM1526 of Thermatoga maritima archaea bacteria—which maintains the topological display of the BC and HI loops as found in the viral coat protein, VP1, of BKV. We demonstrate that the GT1b and GD1b sialogangliosides, which bind to the VP1 of BKV, also associate with our BKV-template. Employing a GFP-tagged template, we show host cell association that is dose dependent and that can be reduced by neuraminidase treatment. These data demonstrate that the BKV-template mimics the host-cell binding observed for the wild-type virus coat protein, VP1.

Audu, Christopher O.; O'Hara, Bethany; Pellegrini, Maria; Wang, Lei; Atwood, Walter J.; Mierke, Dale F.

2012-01-01

329

Molecular cloning and biochemical characterization of a heat-stable type I pullulanase from Thermotoga neapolitana.  

PubMed

The gene encoding a type I pullulanase from the hyperthermophilic anaerobic bacterium Thermotoga neapolitana (pulA) was cloned in Escherichia coli and sequenced. The pulA gene from T. neapolitana showed 91.5% pairwise amino acid identity with pulA from Thermotoga maritima and contained the four regions conserved in all amylolytic enzymes. pulA encodes a protein of 843 amino acids with a 19-residue signal peptide. The pulA gene was subcloned and overexpressed in E. coli under the control of the T7 promoter. The purified recombinant enzyme (rPulA) produced a 93-kDa protein with pullulanase activity. rPulA was optimally active at pH 5-7 and 80°C and had a half-life of 88 min at 80°C. rPulA hydrolyzed pullulan, producing maltotriose, and hydrolytic activities were also detected with amylopectin, starch, and glycogen, but not with amylose. This substrate specificity is typical of a type I pullulanase. Thin layer chromatography of the reaction products in the reaction with pullulan and aesculin showed that the enzyme had transglycosylation activity. Analysis of the transfer product using NMR and isoamylase treatment revealed it to be ?-maltotriosyl-(1,6)-aesculin, suggesting that the enzyme transferred the maltotriosyl residue of pullulan to aesculin by forming ?-1,6-glucosidic linkages. Our findings suggest that the pullulanase from T. neapolitana is the first thermostable type I pullulanase which has ?-1,6-transferring activity. PMID:22112909

Kang, Jinho; Park, Kyung-Min; Choi, Kyoung-Hwa; Park, Cheon-Seok; Kim, Go-Eun; Kim, Doman; Cha, Jaeho

2011-03-01

330

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)

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 ?13C and ?15N 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.

Vinagre, C.; Salgado, J.; Costa, M. J.; Cabral, H. N.

2008-01-01

331

Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel That Evolved by Gene Duplication  

PubMed Central

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 (??)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)3Zn 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·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.

2005-01-01

332

Isotopic variation of fishes in freshwater and estuarine zones of a large subtropical coastal lagoon  

NASA Astrophysics Data System (ADS)

We used stable C and N isotope ratios of tissues from 29 fish species from a large subtropical lagoon in southern Brazil to examine spatial variability in isotopic composition and vertical trophic structure across freshwater and estuarine habitats. Nitrogen isotope ratios indicated a smooth gradation in trophic positions among species, with most fishes occupying the secondary and tertiary consumer level. Fish assemblages showed a significant shift in their carbon isotopic signatures between freshwater and estuarine sites. Depleted carbon signatures (from -24.7‰ to -17.8‰) were found in freshwater, whereas more enriched signatures (from -19.1‰ to -12.3‰) were obtained within the estuarine zone downstream. Based on our survey of the C 3 and C 4 plants and isotopic values for phytoplankton and benthic microalgae reported for ecosystems elsewhere, we hypothesized that the observed ?13C differences in the fish assemblage between freshwater and estuarine sites is due to a shift from assimilating organic matter ultimately derived from C 3 freshwater marsh vegetation and phytoplankton at the freshwater site ( ?13C ranging from -25‰ to -19‰), to C 4 salt-marsh (e.g. Spartina) and widgeon grass ( Ruppia maritima), benthic microalgae and marine phytoplankton at the estuarine sites (from -18‰ to -12‰). Our results suggested that fish assemblages are generally supported by autochthonous primary production. Freshwater fishes that likely were displaced downstream into the estuary during periods of high freshwater discharge had depleted ?13C values that were characteristic of the upper lagoon. These results suggest that spatial foodweb subsidies can occur within the lagoon.

Garcia, A. M.; Hoeinghaus, D. J.; Vieira, J. P.; Winemiller, K. O.

2007-07-01

333

Starch biosynthetic genes and enzymes are expressed and active in the absence of starch accumulation in sugar beet tap-root  

PubMed Central

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.

2014-01-01

334

Metagenomic cellulases highly tolerant towards the presence of ionic liquids--linking thermostability and halotolerance.  

PubMed

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

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

335

Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643.  

PubMed

The open reading frame TM1643 of Thermotoga maritima belongs to a large family of proteins, with homologues in bacteria, archaea, and eukaryotes. TM1643 is found in an operon with two other genes that encode enzymes involved in the biosynthesis of NAD. In several bacteria, the gene in the position occupied by TM1643 encodes an aspartate oxidase (NadB), which synthesizes iminoaspartate as a substrate for NadA, the next enzyme in the pathway. The amino acid sequence of TM1643 does not share any recognizable homology with aspartate oxidase or with other proteins of known functions or structures. To help define the biological functions of TM1643, we determined its crystal structure at 2.6A resolution and performed a series of screens for enzymatic function. The structure reveals the presence of an N-terminal Rossmann fold domain with a bound NAD(+) cofactor and a C-terminal alpha+beta domain. The structural information suggests that TM1643 may be a dehydrogenase and the active site of the enzyme is located at the interface between the two domains. The enzymatic characterization of TM1643 revealed that it possesses NAD or NADP-dependent dehydrogenase activity toward l-aspartate but no aspartate oxidase activity. The product of the aspartate dehydrogenase activity is also iminoaspartate. Therefore, our studies demonstrate that two different enzymes, an oxidase and a dehydrogenase, may have evolved to catalyze the first step of NAD biosynthesis in prokaryotes. TM1643 establishes a new class of amino acid dehydrogenases. PMID:12496312

Yang, Zhiru; Savchenko, Alexei; Yakunin, Alexander; Zhang, Rongguang; Edwards, Aled; Arrowsmith, Cheryl; Tong, Liang

2003-03-01

336

Testing introgressive hybridization hypotheses using statistical network analysis of nuclear and cytoplasmic haplotypes in the leaf beetle Timarcha goettingensis species complex.  

PubMed

Previous studies of leaf beetles (Chrysomelidae) in the Timarcha goettingensis species complex using mitochondrial (cox2) and nuclear (ITS-2 rRNA) markers revealed two main clades confined to the Iberian Peninsula and the rest of Europe but showing incongruent distributions indicative of gene exchange between both groups. Because of the anastomosing nature of hybridization, which disrupts the cladistic structure of character variation, phylogenetic trees might be inappropriate to represent and study this process. Here we test for evidence of hybridization in the T. goettingensis complex by analyzing the extra homoplasy arising in hybrid genomes from the simultaneous analysis of genetically independent markers. Haplotype networks obtained by Templeton's statistical parsimony analysis were generated for combined (concatenated) cox2 and ITS-2 sequences from 167 individuals of the T. goettingensis complex. Networks were used to detect runs of homoplasious characters physically clustered along a nucleotide sequence, as evidence for recombination between both gene partitions. A hypergeometric tail probability for the chance occurrence of physically clustered character changes on the connections linking networks of genotypes was applied. The test recognized two instances of statistically significant clustering, indicating the presence of cox2-ITS-2 mosaic genotypes and reticulation of both main T. goettingensis clades, supporting the reticulate origin of samples of T. maritima in southwestern France and T. sinuatocollis/T. monserratensis in the eastern Pyrenees. Although the assessment of reticulation in DNA sequences does not provide direct proof for hybridization, the geographical distribution of mosaic genotypes in the vicinity of "pure" genotypes supports the effect of gene flow between the two divergent lineages. The study demonstrates the utility of statistical parsimony networks for the detection of hybrids in the growing number of phylogeographic studies based on multiple gene markers. PMID:16557341

Gómez-Zurita, J; Vogler, A P

2006-04-01

337

New cultural approaches for microaerophilic hyperthermophiles.  

PubMed

This article reports on a new culture system designed for studying the effects of nutritional factors on the growth of hyperthermophilic and chemolithotrophic microorganisms. The system comprises 5-l stainless steel jars, an automatic gas dispenser, propylene microplates, and a robotic platform. The culture system was validated using Aquifex aeolicus, a hyperthermophilic, chemolithotrophic, and microaerophilic bacterium, which requires hydrogen, oxygen, CO?, and minerals for growth. We demonstrated that the cell densities measured on 147 cultures of A. aeolicus microplated in jar at 80°C under partial pressures (in kPa) of water vapor (47), H? (117.7), O? (28.1), CO? (31.4), and N? (3.9), followed a normal distribution, with a mean of 0.72 and a standard deviation of 0.04 (variation coefficient: 5.7%). In addition, cross-comparison of the growth kinetics of A. aeolicus in serum bottles and in a jar system highlighted similar kinetics patterns (both mean growth rates were 0.18 and 0.17 h-1, respectively), whereas the maximum cell densities reached were slightly lower in jar than in bottle (0.73 vs. 0.88 OD units, respectively). Furthermore, these results showed that, contrary to bottles, the total pressure of gas in jars remained constant throughout the biotic experiments, even with seven microplates completely filled with grown cultures. In addition, this system has been validated also for hyperthermophilic strictly anaerobes such as Thermotoga maritima or aerobes such as Sulfolobus solfataricus. This new culture system offers an interesting alternative for cultivating hyperthermophiles, using gas as substrate under constant pressure, thus making it possible to miniaturize experiments and study a large number of nutritional factors in one experimental run. PMID:20676678

Uzarraga, Rafael; Auria, Richard; Davidson, Sylvain; Navarro, David; Combet-Blanc, Yannick

2011-02-01

338

Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis*  

PubMed Central

The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Thermotoga maritima DAH7PS (TmaDAH7PS) is tetrameric, with monomer units comprised of a core catalytic (?/?)8 barrel and an N-terminal domain. This enzyme is inhibited strongly by tyrosine and to a lesser extent by the presence of phenylalanine. A truncated mutant of TmaDAH7PS lacking the N-terminal domain was catalytically more active and completely insensitive to tyrosine and phenylalanine, consistent with a role for this domain in allosteric inhibition. The structure of this protein was determined to 2.0 ?. In contrast to the wild-type enzyme, this enzyme is dimeric. Wild-type TmaDAH7PS was co-crystallized with tyrosine, and the structure of this complex was determined to a resolution of 2.35 ?. Tyrosine was found to bind at the interface between two regulatory N-terminal domains, formed from diagonally located monomers of the tetramer, revealing a major reorganization of the regulatory domain with respect to the barrel relative to unliganded enzyme. This significant conformational rearrangement observed in the crystal structures was also clearly evident from small angle X-ray scattering measurements recorded in the presence and absence of tyrosine. The closed conformation adopted by the protein on tyrosine binding impedes substrate entry into the neighboring barrel, revealing an unusual tyrosine-controlled gating mechanism for allosteric control of this enzyme.

Cross, Penelope J.; Dobson, Renwick C. J.; Patchett, Mark L.; Parker, Emily J.

2011-01-01

339

Structure of FliM Provides Insight into Assembly of the Switch Complex in the Bacterial Flagella Motor  

SciTech Connect

Bacteria switch the direction their flagella rotate to control movement. FliM, along with FliN and FliG, compose a complex in the motor that, upon binding phosphorylated CheY, reverses the sense of flagellar rotation. The 2.0- Angstroms resolution structure of the FliM middle domain (FliMM) from Thermotoga maritima reveals a pseudo-2-fold symmetric topology similar to the CheY phosphatases CheC and CheX. A variable structural element, which, in CheC, mediates binding to CheD ({alpha}2') and, in CheX, mediates dimerization ({beta}x), has a truncated structure unique to FliM ({alpha}2'). An exposed helix of FliMM ({alpha}1) does not contain the catalytic residues of CheC and CheX but does include positions conserved in FliM sequences. Cross-linking experiments with site-directed cysteine mutants show that FliM self-associates through residues on {alpha}1 and {alpha}2'. CheY activated by BeF3- binds to FliM with {approx}40-fold higher affinity than CheY (Kd = 0.04 {micro}M vs. 2 {micro}M). Mapping residue conservation, suppressor mutation sites, binding data, and deletion analysis onto the FliMM surface defines regions important for contacts with the stator-interacting protein FliG and for either counterclockwise or clockwise rotation. Association of 33-35 FliM subunits would generate a 44- to 45-nm-diameter disk, consistent with the known dimensions of the C-ring. The localization of counterclockwise- and clockwise-biasing mutations to distinct surfaces suggests that the binding of phosphorylated CheY cooperatively realigns FliM around the ring.

Park,S.; Lowder, B.; Bilwes, A.; Blair, D.; Crane, B.

2006-01-01

340

Ocean Acidification and the Loss of Phenolic Substances in Marine Plants  

PubMed Central

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.

Arnold, Thomas; Mealey, Christopher; Leahey, Hannah; Miller, A. Whitman; Hall-Spencer, Jason M.; Milazzo, Marco; Maers, Kelly

2012-01-01

341

Structural Basis for Substrate Binding and the Catalytic Mechanism of Type III Pantothenate Kinase  

SciTech Connect

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.

Yang, Kun; Strauss, Erick; Huerta, Carlos; Zhang, Hong (Stellenbosch); (UTSMC)

2008-07-15

342

Crystal Structure of a Type III Pantothenate Kinase: Insight into the Mechanism of an Essential Coenzyme A Biosynthetic Enzyme Universally Distributed in Bacteria†  

PubMed Central

Pantothenate kinase (PanK) catalyzes the first step in the five-step universal pathway of coenzyme A (CoA) biosynthesis, a key transformation that generally also regulates the intracellular concentration of CoA through feedback inhibition. A novel PanK protein encoded by the gene coaX was recently identified that is distinct from the previously characterized type I PanK (exemplified by the Escherichia coli coaA-encoded PanK protein) and type II eukaryotic PanKs and is not inhibited by CoA or its thioesters. This type III PanK, or PanK-III, is widely distributed in the bacterial kingdom and accounts for the only known PanK in many pathogenic species, such as Helicobacter pylori, Bordetella pertussis, and Pseudomonas aeruginosa. Here we report the first crystal structure of a type III PanK, the enzyme from Thermotoga maritima (PanKTm), solved at 2.0-Å resolution. The structure of PanKTm reveals that type III PanKs belong to the acetate and sugar kinase/heat shock protein 70/actin (ASKHA) protein superfamily and that they retain the highly conserved active site motifs common to all members of this superfamily. Comparative structural analysis of the PanKTm active site configuration and mutagenesis of three highly conserved active site aspartates identify these residues as critical for PanK-III catalysis. Furthermore, the analysis also provides an explanation for the lack of CoA feedback inhibition by the enzyme. Since PanK-III adopts a different structural fold from that of the E. coli PanK—which is a member of the “P-loop kinase”superfamily—this finding represents yet another example of convergent evolution of the same biological function from a different protein ancestor.

Yang, Kun; Eyobo, Yvonne; Brand, Leisl A.; Martynowski, Dariusz; Tomchick, Diana; Strauss, Erick; Zhang, Hong

2006-01-01

343

Depositional History of a Saline Blue Hole on Eleuthera Island, Bahamas: Implications for Sea Level History and Climate Change  

NASA Astrophysics Data System (ADS)

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.

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

344

Iron-sulfur cluster biosynthesis: characterization of IscU-IscS complex formation and a structural model for sulfide delivery to the [2Fe-2S] assembly site.  

PubMed

Recent work on the bacterial iron-sulfur cluster (isc) family of gene products, and eukaryotic homologs, has advanced the molecular understanding of cellular mechanisms of iron-sulfur cluster biosynthesis. Members of the IscS family are pyridoxyl-5'-phosophate dependent proteins that deliver inorganic sulfide during assembly of the [2Fe-2S] cluster on the IscU scaffold protein. Herein it is demonstrated through calorimetry, fluorescence, and protein stability measurements that Thermotoga maritima IscS forms a 1:1 complex with IscU in a concentration-dependent manner (K(D) varying from 6 to 34 microM, over an IscS concentration range of approximately 2-50 microM). Docking simulations of representative IscU and IscS proteins reveal critical contact surfaces at the N-terminal helix of IscU and a C-terminal loop comprising a chaperone binding domain. Consistent with the isothermal titration calorimetry results described here, an overall dominant contribution of charged surfaces with a change in the molar heat capacity of binding, DeltaC(p) approximately 199.8 kcal K(-1) mol(-1), is observed that accounts for approximately 10% of the total accessible surface area at the binding interface. Both apo and holo IscUs and homologs were found to bind to IscS in an enthalpically driven reaction with comparable K(D) values. Both helix and loop regions are highly conserved among phylogenetically diverse organisms from a pool of archael, bacterial, fungal, and mammalian representatives. PMID:19308466

Nuth, Manunya; Cowan, J A

2009-08-01

345

Oxidase activity of a flavin-dependent thymidylate synthase.  

PubMed

Flavin-dependent thymidylate synthases (FDTS) catalyze the production of dTMP from dUMP and N(5),N(10)-methylene-5,6,7,8-tetrahydrofolate (CH(2)H(4)folate). In contrast to human and other classical thymidylate synthases, the activity of FDTS depends on a FAD coenzyme, and its catalytic mechanism is very different. Several human pathogens rely on this recently discovered enzyme, making it an attractive target for novel antibiotics. Like many other flavoenzymes, FDTS can function as an oxidase, which catalyzes the reduction of O(2) to H(2)O(2), using reduced NADPH or other reducing agents. In this study, we exploit the oxidase activity of FDTS from Thermatoga maritima to probe the binding and release features of the substrates and products during its synthase activity. Results from steady-state and single-turnover experiments suggest a sequential kinetic mechanism of substrate binding during FDTS oxidase activity. CH(2)H(4)folate competitively inhibits the oxidase activity, which indicates that CH(2)H(4)folate and O(2) compete for the same reduced and dUMP-activated enzymatic complex (FDTS-FADH(2)-NADP(+)-dUMP). These studies imply that the binding of CH(2)H(4)folate precedes NADP(+) release during FDTS activity. The inhibition constant of CH(2)H(4)folate towards the oxidase activity was determined to be rather small (2 microm), which indicates a tight binding of CH(2)H(4)folate to the FDTS-FADH(2)-NADP(+)-dUMP complex. PMID:19459936

Wang, Zhen; Chernyshev, Anatoly; Koehn, Eric M; Manuel, Tony D; Lesley, Scott A; Kohen, Amnon

2009-05-01

346

Mechanistic studies of a flavin-dependent thymidylate synthase.  

PubMed

The ThyA gene that encodes for thymidylate synthase (TS) is absent in the genomes of a large number of bacteria, including several human pathogens. Many of these bacteria also lack the genes for dihydrofolate reductase (DHFR) and thymidine kinase and are totally dependent on an alternative enzyme for thymidylate synthesis. Thy1 encodes flavin-dependent TS (FDTS, previously denoted as TSCP) and shares no sequence homology with classical TS genes. Mechanistic studies of a FDTS from Thermotoga maritima (TM0449) are presented here. Several isotopic labeling experiments reveal details of the catalyzed reaction, and a chemical mechanism that is consistent with the experimental data is proposed. The reaction proceeds via a ping-pong mechanism where nicotinamide binding and release precedes the oxidative half-reaction. The enzyme is primarily pro-R specific with regard to the nicotinamide (NADPH), the oxidation of which is the rate-limiting step of the whole catalytic cascade. An enzyme-bound flavin is reduced with an isotope effect of 25 (consistent with H-tunneling) and exchanges protons with the solvent prior to the reduction of an intermediate methylene. A quantitative assay was developed, and the kinetic parameters were measured. A significant NADPH substrate inhibition and large K(M) rationalized the slow activity reported for this enzyme in the past. These and other findings are compared with classical TS (ThyA) catalysis in terms of kinetic and molecular mechanisms. The differences between the FDTS proposed mechanism and that of the classical TS are striking and invoke the notion that mechanism-based drugs will selectively inhibit FDTS and will not have much effect on human (and other eukaryotes) TS. Since TS activity is essential to DNA replication, the unique mechanism of FDTS makes it an attractive target for antibiotic drug development. PMID:15301527

Agrawal, Nitish; Lesley, Scott A; Kuhn, Peter; Kohen, Amnon

2004-08-17

347

Oxidase Activity of a Flavin-Dependent Thymidylate Synthase  

PubMed Central

Summary Flavin-dependent thymidylate synthases (FDTSs) catalyze the production of 2?-deoxythymidine-5?-monophosphate (dTMP) from 2?-deoxyuridine-5?-monophosphate (dUMP) and N5, N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate). In contrast to human and other classical thymidylate synthases, the activity of FDTS depends on a flavin adenine dinucleotide (FAD) coenzyme, and its catalytic mechanism is very different. Several human pathogens rely on this recently discovered enzyme, making it an attractive target for novel antibiotics. Like many other flavoenzymes, FDTS can function as an oxidase, which catalyzes the reduction of oxygen (O2) to hydrogen peroxide (H2O2) using reduced nicotinamide adenine dinucleotide 2?-phosphate (NADPH) or other reducing agents. In the present study we exploit the oxidase activity of FDTS from Thermatoga maritima to probe the binding and release features of the substrates and products during its synthase activity. The results from both steady state and single turnover experiments suggest a sequential kinetic mechanism of substrate binding during FDTS oxidase activity. CH2H4folate competitively inhibits the oxidase activity, which indicates that CH2H4folate and O2 compete for the same reduced and dUMP-activated enzymatic complex (FDTS-FADH2-NADP+-dUMP). These studies imply that the binding of CH2H4folate precedes NADP+ release during FDTS synthase activity. The inhibition constant of CH2H4folate towards the oxidase activity was determined to be rather small (2 ?M), which indicates a tight binding of CH2H4folate to the FDTS-FADH2-NADP+-dUMP complex.

Wang, Zhen; Chernyshev, Anatoly; Koehn, Eric M.; Manuel, Antonio; Lesley, Scott A.; Kohen, Amnon

2009-01-01

348

Expression of myriapod pair rule gene orthologs  

PubMed Central

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.

2011-01-01

349

Single-minded and the evolution of the ventral midline in arthropods.  

PubMed

In insects and crustaceans, ventral midline cells are present that subdivide the CNS into bilateral symmetric halves. In both arthropod groups unpaired midline neurons and glial cells have been identified that contribute to the embryonic patterning mechanisms. In the fruitfly Drosophila melanogaster, for example, the midline cells are involved in neural cell fate specification along the dorso-ventral axis but also in axonal pathfinding and organisation of the axonal scaffold. Both in insects and malacostracan crustaceans, the bHLH-PAS transcription factor single-minded is the master regulator of ventral midline development and homology has been suggested for individual midline precursors in these groups. The conserved arrangement of the axonal scaffold as well as the regular pattern of neural precursors in all euarthropod groups raises the question whether the ventral midline system is conserved in this phylum. In the remaining euarthropod groups, the chelicerates and myriapods, a single-minded homologue has been identified in the spider Achaearanea tepidariorum (chelicerate), however, the gene is not expressed in the ventral midline but in the median area of the ventral neuroectoderm. Here we show that At-sim is not required for ventral midline development. Furthermore, we identify sim homologues in representatives of arthropods that have not yet been analysed: the myriapod Strigamia maritima and a representative of an outgroup to the euarthropods, the onychophoran Euperipatoides kanangrensis. We compare the expression patterns to the A. tepidariorum sim homologue expression and furthermore analyse the nature of the arthropod midline cells. Our data suggest that in arthropods unpaired midline precursors evolved from the bilateral median domain of the ventral neuroectoderm in the last common ancestor of Mandibulata (insects, crustaceans, myriapods). We hypothesize that sim was expressed in this domain and recruited to ventral midline development. Subsequently, sim function has evolved in parallel to the evolution of midline cell function in the individual Mandibulata lineages. PMID:22306923

Linne, Viktoria; Eriksson, Bo Joakim; Stollewerk, Angelika

2012-04-01

350

Establishing Minimum Flow Requirements Based on Benthic Vegetation: What are Some Issues Related to Identifying Quantity of Inflow and Tools Used to Quantify Ecosystem Response?  

NASA Astrophysics Data System (ADS)

Establishing minimum flow requirements in aquatic ecosystems is one way to stipulate controls on water withdrawals in a watershed. The basis of the determination is to identify the amount of flow needed to sustain a threshold ecological function. To develop minimum flow criteria an understanding of ecological response in relation to flow is essential. Several steps are needed including: (1) identification of important resources and ecological functions, (2) compilation of available information, (3) determination of historical conditions, (4) establishment of technical relationships between inflow and resources, and (5) identification of numeric criteria that reflect the threshold at which resources are harmed. The process is interdisciplinary requiring the integration of hydrologic and ecologic principles with quantitative assessments. The tools used quantify the ecological response and key questions related to how the quantity of flow influences the ecosystem are examined by comparing minimum flow determination in two different aquatic systems in South Florida. Each system is characterized by substantial hydrologic alteration. The first, the Caloosahatchee River is a riverine system, located on the southwest coast of Florida. The second, the Everglades- Florida Bay ecotone, is a wetland mangrove ecosystem, located on the southern tip of the Florida peninsula. In both cases freshwater submerged aquatic vegetation (Vallisneria americana or Ruppia maritima), located in areas of the saltwater- freshwater interface has been identified as a basis for minimum flow criteria. The integration of field studies, laboratory studies, and literature review was required. From this information we developed ecological modeling tools to quantify and predict plant growth in response to varying environmental variables. Coupled with hydrologic modeling tools questions relating to the quantity and timing of flow and ecological consequences in relation to normal variability are addressed.

Hunt, M. J.; Nuttle, W. K.; Cosby, B. J.; Marshall, F. E.

2005-05-01

351

Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX  

PubMed Central

In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes.

Laptenok, Sergey P.; Bouzhir-Sima, Latifa; Lambry, Jean-Christophe; Myllykallio, Hannu; Liebl, Ursula; Vos, Marten H.

2013-01-01

352

Structural Analysis of the Domain Interface in DrrB, a Response Regulator of the OmpR/PhoB Subfamily  

PubMed Central

The N-terminal regulatory domains of bacterial response regulator proteins catalyze phosphoryl transfer and function as phosphorylation-dependent regulatory switches to control the output activities of C-terminal effector domains. Structures of numerous isolated regulatory and effector domains have been determined. However, a detailed understanding of regulatory interactions among these domains has been limited by the relative paucity of structural data for intact multidomain response regulator proteins. The first multidomain structures determined, those of transcription factor NarL and methylesterase CheB, both revealed extensive interdomain interfaces. The regulatory domains obstruct access to the functional sites of the effector domains, indicating a regulatory mechanism based on inhibition. In contrast, the recently determined structure of the OmpR/PhoB homologue DrrD revealed no significant interdomain interface, suggesting that the domains are tethered by a flexible linker and lack a fixed orientation relative to each other. To address the generality of this feature, we have determined the 1.8-Å resolution crystal structure of Thermotoga maritima DrrB, providing a second structure of a multidomain response regulator of the OmpR/PhoB subfamily. The structure reveals an extensive domain interface of 751 Å2 and therefore differs greatly from that observed in DrrD. Residues that are crucial players in defining the activation state of the regulatory domain contribute to this interface, implying that conformational changes associated with phosphorylation will influence these intramolecular contacts. The DrrB and DrrD structures are suggestive of different signaling mechanisms, with intramolecular communication between N- and C-terminal domains making substantially different contributions to effector domain regulation in individual members of the OmpR/PhoB family.

Robinson, Victoria L.; Wu, Ti; Stock, Ann M.

2003-01-01

353

Effect of lectins from Diocleinae subtribe against oral Streptococci.  

PubMed

Surface colonization is an essential step in biofilm development. The ability of oral pathogens to adhere to tooth surfaces is directly linked with the presence of specific molecules at the bacterial surface that can interact with enamel acquired pellicle ligands. In light of this, the aim of this study was to verify inhibitory and antibiofilm action of lectins from the Diocleinaesubtribe against Streptococcus mutans and Streptococcus oralis. The inhibitory action against planctonic cells was assessed using lectins from Canavaliaensi formis (ConA), Canavalia brasiliensis (ConBr), Canavalia maritima (ConM), Canavalia gladiata (CGL) and Canavalia boliviana (ConBol). ConBol, ConBr and ConM showed inhibitory activity on S. mutans growth. All lectins, except ConA, stimulated significantly the growth of S. oralis. To evaluate the effect on biofilm formation, clarified saliva was added to 96-well, flat-bottomed polystyrene plates, followed by the addition of solutions containing 100 or 200 µg/mL of the selected lectins. ConBol, ConM and ConA inhibited the S. mutans biofilms. No effects were found on S. oralis biofilms. Structure/function analysis were carried out using bioinformatics tools. The aperture and deepness of the CRD (Carbohydrate Recognition Domain) permit us to distinguish the two groups of Canavalia lectins in accordance to their actions against S. mutans and S. oralis. The results found provide a basis for encouraging the use of plant lectins as biotechnological tools in ecological control and prevention of caries disease. PMID:21525793

Cavalcante, Theodora Thays Arruda; Anderson Matias da Rocha, Bruno; Alves Carneiro, Victor; Vassiliepe Sousa Arruda, Francisco; Fernandes do Nascimento, Antônia Sâmia; Cardoso Sá, Nairley; do Nascimento, Kyria Santiago; Sousa Cavada, Benildo; Holanda Teixeira, Edson

2011-01-01

354

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene  

PubMed Central

Background There are three pathways of L-threonine catabolism. The enzyme L-threonine aldolase (TA) has been shown to catalyse the conversion of L-threonine to yield glycine and acetaldehyde in bacteria, fungi and plants. Low levels of TA enzymatic activity have been found in vertebrates. It has been suggested that any detectable activity is due to serine hydroxymethyltransferase and that mammals lack a genuine threonine aldolase. Results The 7-exon murine L-threonine aldolase gene (GLY1) is located on chromosome 11, spanning 5.6 kb. The cDNA encodes a 400-residue protein. The protein has 81% similarity with the bacterium Thermotoga maritima TA. Almost all known functional residues are conserved between the two proteins including Lys242 that forms a Schiff-base with the cofactor, pyridoxal-5'-phosphate. The human TA gene is located at 17q25. It contains two single nucleotide deletions, in exons 4 and 7, which cause frame-shifts and a premature in-frame stop codon towards the carboxy-terminal. Expression of human TA mRNA was undetectable by RT-PCR. In mice, TA mRNA was found at low levels in a range of adult tissues, being highest in prostate, heart and liver. In contrast, serine/threonine dehydratase, another enzyme that catabolises L-threonine, is expressed very highly only in the liver. Serine dehydratase-like 1, also was most abundant in the liver. In whole mouse embryos TA mRNA expression was low prior to E-15 increasing more than four-fold by E-17. Conclusion Mice, the western-clawed frog and the zebrafish have transcribed threonine aldolase/GLY1 genes, but the human homolog is a non-transcribed pseudogene. Serine dehydratase-like 1 is a putative L-threonine catabolising enzyme.

Edgar, Alasdair J

2005-01-01

355

Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes.  

PubMed

A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of 1/72 bp, 1 in 58 bp in non-coding sequences, increasing to 1/47 bp upon the addition of the remaining genotypes. Within analysed DNA fragments, alleles at different SNP positions displayed linkage disequilibrium indicative of haplotype structures. On average 2.7 haplotypes were found in sugar beet lines, and haplotype conservation in expressed genes appeared to exceed 500 bp in length. Seven different genotyping techniques including SNP detection by MALDI-TOF mass spectrometry, pyrosequencing and fluorescence scanning of labelled nucleotides were employed to perform 712 segregation analyses for 538 markers in three F(2) populations. Functions were predicted for 492 mapped sequences. Genetic maps comprised 305 loci covering 599.8 cM in population K1, 241 loci distributed over 636.6 cM in population D2, and 166 loci over 507.1 cM in population K2, respectively. Based on 156 markers common to more than one population an integrated map was constructed with 524 loci covering 664.3 cM. For 377 loci the genome positions of the most similar sequences from A. thaliana were identified, but little evidence for previously presented ancestral genome structures was found. PMID:17622508

Schneider, Katharina; Kulosa, Dagmar; Soerensen, Thomas Rosleff; Möhring, Silke; Heine, Martin; Durstewitz, Gregor; Polley, Andreas; Weber, Eberhard; Jamsari; Lein, Jens; Hohmann, Uwe; Tahiro, Emma; Weisshaar, Bernd; Schulz, Britta; Koch, Georg; Jung, Christian; Ganal, Martin

2007-09-01

356

Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain  

SciTech Connect

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.

Miller, D.J.; Ouellette, N.; Evodokimova, E.; Savchenko, A.; Edwards, A.; Anderson, W.F. (Toronto); (NWU)

2010-03-08

357

Mobile dunes and eroding salt marshes  

NASA Astrophysics Data System (ADS)

The paper deals with general outlines of salt marsh and dune vegetation in the Ellenbogen and Listland area on Sylt (Schleswig-Holstein, FRG). The composition of current salt marsh vegetation is considered to be mainly the result of a long-lasting process of tidal inundation, grazing, and a permanent influence of groundwater seepage from the surrounding dunes. The lower salt marsh communities have shown constancy for 67 years, due to the effect of heavy grazing. The mid-upper salt marsh communities demonstrated a succession from a Puccinellia maritima-dominated community of the lower marsh to a Juncus gerardii-dominated community of the mid-upper salt marsh, which may be due to the transport of sand — over a short time — on the surface of the marsh. The area covered by plant communities of annuals below Mean High Water (MHW) seemed to diminish. Salt marsh soils, especially of the mid-upper marsh, indicate sandy layers resulting from sand drift of the dunes. Dry and wet successional series of the dunes in the Listland/Ellenbogen area both show grassy stages shifting to dwarf shrubs as final stages. White primary dunes can only be found on the accreting shoreline of the Ellenbogen, which is also grazed by sheep; vegetation cover therefore remains dominated by grasses, mosses and lichens. Three mobile dunes (as the most prominent features of this landscape) have been left unaffected by seeding and planting by local authorities. Grazing is considered to be an inadequate tool in nature conservation as long as natural processes are to prevail in the landscape as major determinants.

Neuhaus, R.

1994-06-01

358

Seagrass distribution and abundance in Eastern Gulf of Mexico coastal waters  

NASA Astrophysics Data System (ADS)

The marine angiosperms Thalassia testudinum, Syringodium filiforme, and Halodule wrightii form two of the largest reported seagrass beds along the northwest and southern coasts of Florida where they cover about 3000 square km in the Big Bend area and about 5500 square km in Florida Bay, respectively. Most of the leaf biomass in the Big Bend area and outer Florida Bay was composed of Thalassia testudinum and Syringodium filiforme which were distributed throughout the beds but which were more abundant in shallow depths. A short-leaved form of Halodule wrightii grew in monotypic stands in shallow water near the inner edges of the beds, while Halophila decipiens and a longer-leaved variety of H. wrightii grew scattered throughout the beds, in monotypic stands near the outer edges of the beds, and in deeper water outside the beds. Halophila engelmanni was observed scattered at various depths throughout the seagrass beds and in monospecific patches in deep water outside the northern bed. Ruppia maritima grew primarily in brackish water around river mouths. The cross-shelf limits of the two major seagrass beds are controlled nearshore by increased water turbidity and lower salinity around river mouths and off-shore by light penetration to depths which receive 10% or more of sea surface photosynthetically active radiation. Seagrasses form large beds only along low energy reaches of the coast. The Florida Bay seagrass bed contained about twice the short-shoot density of both Thalassia testudinum and Syringodium filiforme, for data averaged over all depths, and about four times the average short-shoot density of both species in shallow water compared with the Big Bend seagrass bed. The differences in average seagrass abundance between Florida Bay and the Big Bend area may be a consequence of the effects of greater seasonal solar radiation and water temperature fluctuations experienced by plants in the northern bed, which lies at the northern distribution limit for American Tropical seagrasses.

Iverson, Richard L.; Bittaker, Henry F.

1986-05-01

359

Photorespiration and Carbon Limitation Determine Productivity in Temperate Seagrasses  

PubMed Central

The gross primary productivity of two seagrasses, Zostera marina and Ruppia maritima, and one green macroalga, Ulva intestinalis, was assessed in laboratory and field experiments to determine whether the photorespiratory pathway operates at a substantial level in these macrophytes and to what extent it is enhanced by naturally occurring shifts in dissolved inorganic carbon (DIC) and O2 in dense vegetation. To achieve these conditions in laboratory experiments, seawater was incubated with U. intestinalis in light to obtain a range of higher pH and O2 levels and lower DIC levels. Gross photosynthetic O2 evolution was then measured in this pretreated seawater (pH, 7.8–9.8; high to low DIC:O2 ratio) at both natural and low O2 concentrations (adjusted by N2 bubbling). The presence of photorespiration was indicated by a lower gross O2 evolution rate under natural O2 conditions than when O2 was reduced. In all three macrophytes, gross photosynthetic rates were negatively affected by higher pH and lower DIC. However, while both seagrasses exhibited significant photorespiratory activity at increasing pH values, the macroalga U. intestinalis exhibited no such activity. Rates of seagrass photosynthesis were then assessed in seawater collected from the natural habitats (i.e., shallow bays characterized by high macrophyte cover and by low DIC and high pH during daytime) and compared with open baymouth water conditions (where seawater DIC is in equilibrium with air, normal DIC, and pH). The gross photosynthetic rates of both seagrasses were significantly higher when incubated in the baymouth water, indicating that these grasses can be significantly carbon limited in shallow bays. Photorespiration was also detected in both seagrasses under shallow bay water conditions. Our findings indicate that natural carbon limitations caused by high community photosynthesis can enhance photorespiration and cause a significant decline in seagrass primary production in shallow waters.

Buapet, Pimchanok; Rasmusson, Lina M.; Gullstrom, Martin; Bjork, Mats

2013-01-01

360

A New Root-Knot Nematode Parasitizing Sea Rocket from Spanish Mediterranean Coastal Dunes: Meloidogyne dunensis n. sp. (Nematoda: Meloidogynidae)  

PubMed Central

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.

Palomares Rius, J. E.; Vovlas, N.; Troccoli, A.; Liebanas, G.; Landa, B. B.; Castillo, P.

2007-01-01

361

Insertion of Endocellulase Catalytic Domains into Thermostable Consensus Ankyrin Scaffolds: Effects on Stability and Cellulolytic Activity  

PubMed Central

Degradation of cellulose for biofuels production holds promise in solving important environmental and economic problems. However, the low activities (and thus high enzyme-to-substrate ratios needed) of hydrolytic cellulase enzymes, which convert cellulose into simple sugars, remain a major barrier. As a potential strategy to stabilize cellulases and enhance their activities, we have embedded cellulases of extremophiles into hyperstable ?-helical consensus ankyrin domain scaffolds. We found the catalytic domains CelA (CA, GH8; Clostridium thermocellum) and Cel12A (C12A, GH12; Thermotoga maritima) to be stable in the context of the ankyrin scaffold and to be active against both soluble and insoluble substrates. The ankyrin repeats in each fusion are folded, although it appears that for the C12A catalytic domain (CD; where the N and C termini are distant in the crystal structure), the two flanking ankyrin domains are independent, whereas for CA (where termini are close), the flanking ankyrin domains stabilize each other. Although the activity of CA is unchanged in the context of the ankyrin scaffold, the activity of C12A is increased between 2- and 6-fold (for regenerated amorphous cellulose and carboxymethyl cellulose substrates) at high temperatures. For C12A, activity increases with the number of flanking ankyrin repeats. These results showed ankyrin arrays to be a promising scaffold for constructing designer cellulosomes, preserving or enhancing enzymatic activity and retaining thermostability. This modular architecture will make it possible to arrange multiple cellulase domains at a precise spacing within a single polypeptide, allowing us to search for spacings that may optimize reactivity toward the repetitive cellulose lattice.

Cunha, Eva S.; Hatem, Christine L.

2013-01-01

362

Conformational Transition of Response Regulator RR468 in a Two-Component System Signal Transduction Process.  

PubMed

Signal transduction can be accomplished via a two-component system (TCS) consisting of a histidine kinase (HK) and a response regulator (RR). In this work, we simulate the response regulator RR468 from Thermotoga maritima, in which phosphorylation and dephosphorylation of a conserved aspartate residue acts as a switch via a large conformational change concentrated in three proximal loops. A detailed view of the conformational transition is obscured by the lack of stability of the intermediate states, which are difficult to detect using common structural biology techniques. Molecular dynamics (MD) trajectories of the inactive and active conformations were run, and show that the inactive (or active) trajectories do not exhibit sampling of the active (or inactive) conformations on this time scale. Targeted MD (TMD) was used to generate trajectories that span the inactive and active conformations and provide a view of how a localized event like phosphorylation can lead to conformational changes elsewhere in the protein, especially in the three proximal loops. The TMD trajectories are clustered to identify stages along the transition path. Residue interaction networks are identified that point to key residues having to rearrange in the process of transition. These are identified using both hydrogen bond analysis and residue interaction strength measurements. Potentials of mean force are generated for key residue rearrangements to ascertain their free energy barriers. We introduce methods that attempt to extrapolate from one conformation to the other and find that the most fluctuating proximal loop can transit part way from one to the other, suggesting that this conformational information is embedded in the sequence. PMID:24731214

Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

2014-05-01

363

Involvement of NADH:Acceptor Oxidoreductase and Butyryl Coenzyme A Dehydrogenase in Reversed Electron Transport during Syntrophic Butyrate Oxidation by Syntrophomonas wolfei? †  

PubMed Central

Methanogenic oxidation of butyrate to acetate requires a tight cooperation between the syntrophically fermenting Syntrophomonas wolfei and the methanogen Methanospirillum hungatei, and a reversed electron transport system in S. wolfei was postulated to shift electrons from butyryl coenzyme A (butyryl-CoA) oxidation to the redox potential of NADH for H2 generation. The metabolic activity of butyrate-oxidizing S. wolfei cells was measured via production of formazan and acetate from butyrate, with 2,3,5-triphenyltetrazolium chloride as electron acceptor. This activity was inhibited by trifluoperazine (TPZ), an antitubercular agent known to inhibit NADH:menaquinone oxidoreductase. In cell extracts of S. wolfei, the oxidation of NADH could be measured with quinones, viologens, and tetrazolium dyes as electron acceptors, and also this activity was inhibited by TPZ. The TPZ-sensitive NADH:acceptor oxidoreductase activity appeared to be membrane associated but could be dissociated from the membrane as a soluble protein and was semipurified by anion-exchange chromatography. Recovered proteins were identified by peptide mass fingerprinting, which indicated the presence of an NADH:acceptor oxidoreductase as part of a three-component [FeFe] hydrogenase complex and a selenocysteine-containing formate dehydrogenase. Furthermore, purification of butyryl-CoA dehydrogenase (Bcd) activity and peptide mass fingerprinting revealed two Bcd proteins different from the Bcd subunit of the Bcd/electron-transfer flavoprotein complex (Bcd/EtfAB) predicted from the genome sequence of S. wolfei. The results suggest that syntrophic oxidation of butyrate in S. wolfei involves a membrane-associated TPZ-sensitive NADH:acceptor oxidoreductase as part of a hydrogenase complex similar to the recently discovered “bifurcating” hydrogenase in Thermotoga maritima and butyryl-CoA dehydrogenases that are different from Bcd of the Bcd/EtfAB complex.

Muller, Nicolai; Schleheck, David; Schink, Bernhard

2009-01-01

364

Structure, diversity and evolution of myriapod hemocyanins.  

PubMed

Oxygen transport in the hemolymph of many arthropods is mediated by hemocyanins, large copper-containing proteins that are well-studied in Chelicerata and Crustacea, but had long been considered unnecessary in the subphylum of Myriapoda. Only recently has it become evident that hemocyanins are present in Scutigeromorpha (Chilopoda) and Spirostreptida (Diplopoda). Here we present evidence for a more widespread occurrence of hemocyanin in the myriapods. By means of RT-PCR, western blotting and database searches, hemocyanins were identified in the symphylans Hanseniella audax and Symphylella vulgaris, the chilopod Scolopendra subspinipes dehaani and the diplopod Polydesmus angustus. No hemocyanins were found in the diplopods Polyxenus lagurus, Cylindroiulus punctatus, Glomeris marginata, Glomeris pustulata and Arthrosphaera brandtii, or the chilopods Lithobius forficatus, Geophilus flavus and Strigamia maritima. This suggests multiple independent losses in myriapod taxa. Two independent hemocyanin subunits were found that were already present in the myriapod stem line. We specifically investigated the structure of the hemocyanin of P. angustus, which consists of three distinct subunits that occur in an approximately equimolar ratio. As deduced by 3D electron microscopy, the quaternary structure is a 3 × 6-mer that resembles the half structure of the 6 × 6-mer hemocyanin from Scutigera coleoptrata. It was analyzed more closely by homology modeling of 1 × 6-mers and their rigid-body fitting to the electron density map of the 3 × 6-mer. In addition, we obtained the cDNA sequence of a putative myriapod phenoloxidase. Phenoloxidases are related to the arthropod hemocyanins, but diverged before radiation of the arthropod subphyla. PMID:24520955

Pick, Christian; Scherbaum, Samantha; Hegedüs, Elöd; Meyer, Andreas; Saur, Michael; Neumann, Ruben; Markl, Jürgen; Burmester, Thorsten

2014-04-01

365

Domain-swapping of mesophilic xylanase with hyper-thermophilic glucanase  

PubMed Central

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.

2012-01-01

366

Ancestral Patterning of Tergite Formation in a Centipede Suggests Derived Mode of Trunk Segmentation in Trilobites  

PubMed Central

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.

Ortega-Hernandez, Javier; Brena, Carlo

2012-01-01

367

Where on Earth...? MISR Mystery Image Quiz #6  

NASA Technical Reports Server (NTRS)

Here's another chance to play geographical detective! This Multi-angle Imaging SpectroRadiometer (MISR) image covers an area of about 298 kilometers x 358 kilometers, and was captured by the instrument's vertical-viewing (nadir) camera on December 27, 2001. Use any reference materials you like and answer the following five questions: The large lagoon in the image is named for a particular type of bird. Name the bird. Note the sediment plume emanating from the southern end of the lagoon. Sailors in the 16th century imagined this outlet to be the mouth of a large river. What did they call the river? A series of wave-like points and curls form 'cusps' on the inner shores of the lagoon. Which ONE of the following is most responsible for the formation of these cusps? Violent storm impacts on erosion and accretion Wind and tide-driven sediment transport and circulation Tectonic folding associated with nearby mountain ridges Bathymetric effects of dredging operations True or false: Changes in regional precipitation associated with large scale atmospheric circulation patterns have no effect on the salinity of the lagoon's water. Which one of these is NOT distributed within the area covered by this image? Ruppia maritima Chelonia mydas Tapirus bairdii Microcystis aeruginosa E-mail your answers, name (initials are acceptable if you prefer), and your hometown by Tuesday, February 19, 2002 to suggestions@mail-misr.jpl.nasa.gov. Answers will be published on the MISR web site in conjunction with the next weekly image release. The names and home towns of respondents who answer all questions correctly by the deadline will also be published in the order responses were received. The first 3 people on this list who are not affiliated with NASA, JPL, or MISR and who did not win a prize in the last quiz will be sent a print of the image. A new 'Where on Earth...?' mystery appears as the MISR 'image of the week' approximately once per month. A new image of the week is released every Wednesday at noon Pacific time on the MISR home page http://www-misr.jpl.nasa.gov. The image also appears on the Atmospheric Sciences Data Center home page, http://eosweb.larc.nasa.gov, though usually with a several-hour delay. Image courtesy NASA/GSFC/LaRC/JPL, MISR Team.

2002-01-01

368

Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.  

PubMed

Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and research approaches that can be used for monitoring the geographical distribution and diversity of Beta populations. It has recently been shown that a century of gene flow from Beta vulgaris ssp. vulgaris has not altered the genetic diversity of wild Beta vulgaris L. ssp. maritima (L.) Arcang. in the Italian sugar beet seed production area. Future research should focus on the potential evolution of transgenic wild beet populations in comparison to these baseline data. Two monitoring models are presented describing how endpoints can be measured: (1) "Pre-post" crop commercialization against today's baseline and (2) "Parallel" to crop commercialization against GMP free reference areas/ populations. Model 2 has the advantage of taking ongoing changes in genetic diversity and population dynamics into account. Model 1 is more applicable if gene flow is so strong that most areas/populations contain GMPs. Important traits that may change the ecology of populations are genes that confer tolerance to biotic and abiotic stress. An assessment of environmental effects can realistically only be based on endpoints and consequences of gene introgression, which may include economic values of biodiversity in littoral and other ecosystems containing wild beet. In general, there is still a great need to harmonize worldwide monitoring systems by the development of appropriate methods to evaluate the environmental impact of introgressed transgenes. PMID:15612276

Bartsch, Detlef; Cuguen, Joel; Biancardi, Enrico; Sweet, Jeremy

2003-01-01

369

Construction of an in vitro bypassed pyruvate decarboxylation pathway using thermostable enzyme modules and its application to N-acetylglutamate production  

PubMed Central

Background Metabolic engineering has emerged as a practical alternative to conventional chemical conversion particularly in biocommodity production processes. However, this approach is often hampered by as yet unidentified inherent mechanisms of natural metabolism. One of the possible solutions for the elimination of the negative effects of natural regulatory mechanisms on artificially engineered metabolic pathway is to construct an in vitro pathway using a limited number of enzymes. Employment of thermostable enzymes as biocatalytic modules for pathway construction enables the one-step preparation of catalytic units with excellent selectivity and operational stability. Acetyl-CoA is a central precursor involved in the biosynthesis of various metabolites. In this study, an in vitro pathway to convert pyruvate to acetyl-CoA was constructed and applied to N-acetylglutamate production. Results A bypassed pyruvate decarboxylation pathway, through which pyruvate can be converted to acetyl-CoA, was constructed by using a coupled enzyme system consisting of pyruvate decarboxylase from Acetobacter pasteurianus and the CoA-acylating aldehyde dehydrogenase from Thermus thermophilus. To demonstrate the applicability of the bypassed pathway for chemical production, a cofactor-balanced and CoA-recycling synthetic pathway for N-acetylglutamate production was designed by coupling the bypassed pathway with the glutamate dehydrogenase from T. thermophilus and N-acetylglutamate synthase from Thermotoga maritima. N-Acetylglutamate could be produced from an equimolar mixture of pyruvate and ?-ketoglutarate with a molar yield of 55% through the synthetic pathway consisting of a mixture of four recombinant E. coli strains having either one of the thermostable enzymes. The overall recycling number of CoA was calculated to be 27. Conclusions Assembly of thermostable enzymes enables the flexible design and construction of an in vitro metabolic pathway specialized for chemical manufacture. We herein report the in vitro construction of a bypassed pathway capable of an almost stoichiometric conversion of pyruvate to acetyl-CoA. This pathway is potentially applicable not only to N-acetylglutamate production but also to the production of a wide range of acetyl-CoA-derived metabolites.

2013-01-01

370

Crystal Structure of the Response Regulator 02 Receiver Domain, the Essential YycF Two-Component System of Streptococcus pneumoniae in both Complexed and Native States†  

PubMed Central

A variety of bacterial cellular responses to environmental signals are mediated by two-component signal transduction systems comprising a membrane-associated histidine protein kinase and a cytoplasmic response regulator (RR), which interpret specific stimuli and produce a measured physiological response. In RR activation, transient phosphorylation of a highly conserved aspartic acid residue drives the conformation changes needed for full activation of the protein. Sequence homology reveals that RR02 from Streptococcus pneumoniae belongs to the OmpR subfamily of RRs. The structures of the receiver domains from four members of this family, DrrB and DrrD from Thermotoga maritima, PhoB from Escherichia coli, and PhoP from Bacillus subtilis, have been elucidated. These domains are globally very similar in that they are composed of a doubly wound ?5?5; however, they differ remarkably in the fine detail of the ?4-?4 and ?4 regions. The structures presented here reveal a further difference of the geometry in this region. RR02 is has been shown to be the essential RR in the gram-positive bacterium S. pneumoniae R. Lange, C. Wagner, A. de Saizieu, N. Flint, J. Molnos, M. Stieger, P. Caspers, M. Kamber, W. Keck, and K. E. Amrein, Gene 237:223-234, 1999; J. P. Throup, K. K. Koretke, A. P. Bryant, K. A. Ingraham, A. F. Chalker, Y. Ge, A. Marra, N. G. Wallis, J. R. Brown, D. J. Holmes, M. Rosenberg, and M. K. Burnham, Mol. Microbiol. 35:566-576, 2000). RR02 functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. Here we report the native structure of the receiver domain of RR02 from serotype 4 S. pneumoniae (as well as acetate- and phosphate-bound forms) at different pH levels. Two native structures at 2.3 Å, phased by single-wavelength anomalous diffraction (xenon SAD), and 1.85 Å and a third structure at pH 5.9 revealed the presence of a phosphate ion outside the active site. The fourth structure revealed the presence of an acetate molecule in the active site.

Bent, Colin J.; Isaacs, Neil W.; Mitchell, Timothy J.; Riboldi-Tunnicliffe, Alan

2004-01-01

371

Vibrational Analysis of Mononitrosyl Complexes in Hemerythrin and Flavodiiron Proteins: Relevance to Detoxifying NO Reductase  

PubMed Central

Flavodiiron proteins (FDPs) play important roles in the microbial nitrosative stress response in low-oxygen environments by reductively scavenging nitric oxide (NO). Recently, we showed that FMN-free diferrous FDP from Thermotoga maritima exposed to 1 equiv NO forms a stable diiron-mononitrosyl complex (deflavo-FDP(NO)) that can react further with NO to form N2O [Hayashi, T.; Caranto, J. D.; Wampler, D. A.; Kurtz, D. M., Jr.; Moënne-Loccoz, P. Biochemistry 2010, 49, 7040–7049]. Here we report resonance Raman and low-temperature photolysis FTIR data that better define the structure of this diiron-mononitrosyl complex. We first validate this approach using the stable diiron-mononitrosyl complex of hemerythrin, Hr(NO), for which we observe a ?(NO) at 1658 cm?1, the lowest ?(NO) ever reported for a nonheme {FeNO}7 species. Both deflavo-FDP(NO) and the mononitrosyl adduct of the flavinated FPD (FDP(NO)) show ?(NO) at 1681 cm?1, which is also unusually low. These results indicate that, in Hr(NO) and FDP(NO), the coordinated NO is exceptionally electron rich, more closely approaching the Fe(III)(NO?) resonance structure. In the case of Hr(NO), this polarization may be promoted by steric enforcement of an unusually small FeNO angle, while in FDP(NO), the Fe(III)(NO?) structure may be due to a semi-bridging electrostatic interaction with the second Fe(II) ion. In Hr(NO), accessibility and steric constraints prevent further reaction of the diiron-mononitrosyl complex with NO, whereas in FDP(NO) the increased nucleophilicity of the nitrosyl group may promote attack by a second NO to produce N2O. This latter scenario is supported by theoretical modeling [Blomberg, L. M.; Blomberg, M. R.; Siegbahn, P. E. J. Biol. Inorg. Chem. 2007, 12, 79–89]. Published vibrational data on bioengineered models of denitrifying heme-nonheme NO reductases[Hayashi, T.; Miner, K. D.; Yeung, N.; Lin, Y.-W.; Lu, Y.; Moënne-Loccoz, P. Biochemistry 2011, 50, 5939–5947] support a similar mode of activation of a heme {FeNO}7 species by the nearby nonheme Fe(II).

Hayashi, Takahiro; Caranto, Jonathan D.; Matsumura, Hirotoshi; Kurtz, Donald M.; Moenne-Loccoz, Pierre

2012-01-01

372

Selenium removal and mass balance in a constructed flow-through wetland system.  

PubMed

A field study on the removal of Se from agricultural subsurface drainage was conducted from May 1997 to February 2001 in the Tulare Lake Drainage District (TLDD) of San Joaquin Valley, California. A flow-through wetland system was constructed consisting of ten 15- x 76-m unlined cells that were continuously flooded and planted with either a monotype or combination of plants, including sturdy bulrush [Schoenoplectus robustus (Pursh) M.T. Strong], baltic rush (Juncus balticus Willd.), smooth cordgrass (Spartina alterniflora Loisel.), rabbitsfoot grass [Polypogon monspeliensis (L.) Desf.], salt-grass lDistichlis spicata (L.) Greene], cattail (Typha latifolia L.), tule [Schoenoplectus acutus (Muhl. ex Bigelow) A. Löve & D. Löve], and widgeon grass (Ruppia maritima L.). One cell had no vegetation planted. The objectives of this research were to evaluate Se removal efficiency of each wetland cell and to carry out a mass balance on Se. The inflow drainage water to the cells had average annual Se concentrations of 19 to 22 microg L(-1) dominated by selenate [Se(VI), 95%]. Average weekly water residence time varied from about 3 to 15 d for Cells 1 through 7 (target 7 d), 19 to 33 d for Cells 8 and 9 (target 21 d), and 13 to 18 d for Cell 10 (target 14 d). Average weekly Se concentration ratios of outflow to inflow ranged from 0.45 to 0.79 and mass ratio (concentration x water volume) from 0.24 to 0.52 for year 2000, that is, 21 to 55% reduction in Se concentration and 48 to 76% Se removal in mass by the wetland, respectively. The nonvegetated cell showed the least Se removal both in concentration and in mass. The global mass balance showed that on the average about 59% of the total inflow Se was retained within the cells and Se outputs were outflow (35%), seepage (4%), and volatilization (2%). Independent measurements of the Se retained in the cells totaled 53% of the total Se inflow: 33% in the surface (0-20 cm) sediment, 18% in the organic detrital layer above the sediment, 2% in the fallen litter, < 1% in the standing plants, and < 1% in the surface water. Thus, about 6% of the total Se inflow was unaccounted for in the internal compartments. PMID:12931913

Gao, S; Tanji, K K; Lin, Z Q; Terry, N; Peters, D W

2003-01-01

373

Response of biotic communities to salinity changes in a Mediterranean hypersaline stream  

PubMed Central

Background This study investigates the relationship between salinity and biotic communities (primary producers and macroinvertebrates) in Rambla Salada, a Mediterranean hypersaline stream in SE Spain. Since the 1980's, the mean salinity of the stream has fallen from about 100 g L-1 to 35.5 g L-1, due to intensive irrigated agriculture in the watershed. Furthermore, large dilutions occur occasionally when the water irrigation channel suffers cracks. Results Along the salinity gradient studied (3.5 – 76.4 g L-1) Cladophora glomerata and Ruppia maritima biomass decreased with increasing salinity, while the biomass of epipelic algae increased. Diptera and Coleoptera species dominated the community both in disturbed as in re-established conditions. Most macroinvertebrates species found in Rambla Salada stream are euryhaline species with a broad range of salinity tolerance. Eight of them were recorded in natural hypersaline conditions (~100 g L-1) prior to important change in land use of the watershed: Ephydra flavipes, Stratyomis longicornis, Nebrioporus ceresyi, N. baeticus, Berosus hispanicus, Enochrus falcarius, Ochthebius cuprescens and Sigara selecta. However, other species recorded in the past, such as Ochthebius glaber, O. notabilis and Enochrus politus, were restricted to a hypersaline source or absent from Rambla Salada. The dilution of salinity to 3.5 – 6.8 gL-1 allowed the colonization of species with low salininty tolerance, such as Melanopsis praemorsa, Anax sp., Simulidae, Ceratopogonidae and Tanypodinae. The abundance of Ephydra flavipes and Ochthebius corrugatus showed a positive significant response to salinity, while Anax sp., Simulidae, S. selecta, N. ceresyi, N. baeticus, and B. hispanicus showed significant negative correlations. The number of total macroinvertebrate taxa, Diptera and Coleoptera species, number of families, Margalef's index and Shannon's diversity index decreased with increasing salinity. However, the rest of community parameters, such as the abundance of individuals, evenness and Simpson's index, showed no significant response to changes in salinity. Classification and ordination analysis revealed major differences in macroinvertebrate community structure between hypersaline conditions (76.4 g L-1) and the rest of the communities observed at the lower salinity levels, and revealed that below ~75 g L-1, dissimilarities in the communities were greater between the two habitats studied (runs and pools) than between salinity levels. Conclusion Salinity was the first factor determining community composition and structure in Rambla Salada stream followed by the type of habitat.

Velasco, Josefa; Millan, Andres; Hernandez, Juan; Gutierrez, Cayetano; Abellan, Pedro; Sanchez, David; Ruiz, Mar

2006-01-01

374

Brazil The Duck Lagoon  

NASA Technical Reports Server (NTRS)

This Multi-angle Imaging SpectroRadiometer (MISR) image of Brazil covers an area of about 298 kilometers x 358 kilometers, and was captured by the instrument's vertical-viewing (nadir) camera on December 27, 2001. The 'Lagoa dos Patos', in the Brazilian state of Rio Grande do Sul, translates to 'the Duck Lagoon'. It was named by 16th century Jesuit settlers, who asked the King of Spain to grant them title to the lagoon so that they could breed ducks. The King consented, but revoked his edict when he discovered that the 'duck-pond' (measuring about 14,000 square kilometers) was one of the largest lagoonal systems in the world. Note the sediment plume emanating from the southern end of the lagoon. Sailors in the 16th century imagined this outlet to be the mouth of a large river. Early Portuguese explorers mistook the entrance to the lagoon for the mouth of a great river and called it the Rio Grande. A series of wave-like points and curls form 'cusps' on the inner shores of the lagoon. The lagoon's characteristics change with short-term tide-induced cyclic perturbations, and with longer term large scale meteorological conditions. The distinctive wavelike 'cusps' along the inner shores result from the circulation, erosion and accumulation of sediments driven by wind and tidal action. The El Nino Southern Oscillation (ENSO) circulation affects precipitation amount and continental runoff, thereby changing the contents of the lagoon waters. High rainfall and increased freshwater discharge during El Nino events correspond with elevated dissolved nutrient concentrations and increased phytoplankton growth. La Nina years are dry and the associated low rainfall reduces the freshwater recharge to the lagoon, causing an increase in salinity. Occasional blooms of toxic cyanobacteria (Microcystis aeruginosa), have been registered in the lagoon when nutrient concentrations are elevated. A number of reeds and grasses are important to the lagoon estuary, including widgeon grass (Ruppia maritima) which reaches peak production during summer. Sea turtles (Chelonia mydas) can be found in the lagoon during spring and summer. Although the lowland tapir (Tapirus terrestris) is found in some parts of Rio Grande do Sul, the Baird's tapir (Tapirus bairdii), is not distributed within the image area (it is restricted to Central America). MISR was built and is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Earth Science, Washington, DC. The Terra satellite is managed by NASA's Goddard Space Flight Center, Greenbelt, MD. JPL is a division of the California Institute of Technology. Image credit: NASA/GSFC/LaRC/JPL, MISR Team.

2002-01-01

375

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation.  

PubMed

The review describes four flavin-containing cytoplasmatic multienzyme complexes from anaerobic bacteria and archaea that catalyze the reduction of the low potential ferredoxin by electron donors with higher potentials, such as NAD(P)H or H(2) at ? 100 kPa. These endergonic reactions are driven by concomitant oxidation of the same donor with higher potential acceptors such as crotonyl-CoA, NAD(+) or heterodisulfide (CoM-S-S-CoB). The process called flavin-based electron bifurcation (FBEB) can be regarded as a third mode of energy conservation in addition to substrate level phosphorylation (SLP) and electron transport phosphorylation (ETP). FBEB has been detected in the clostridial butyryl-CoA dehydrogenase/electron transferring flavoprotein complex (BcdA-EtfBC), the multisubunit [FeFe]hydrogenase from Thermotoga maritima (HydABC) and from acetogenic bacteria, the [NiFe]hydrogenase/heterodisulfide reductase (MvhADG-HdrABC) from methanogenic archaea, and the transhydrogenase (NfnAB) from many Gram positive and Gram negative bacteria and from anaerobic archaea. The Bcd/EtfBC complex that catalyzes electron bifurcation from NADH to the low potential ferredoxin and to the high potential crotonyl-CoA has already been studied in some detail. The bifurcating protein most likely is EtfBC, which in each subunit (??) contains one FAD. In analogy to the bifurcating complex III of the mitochondrial respiratory chain and with the help of the structure of the human ETF, we propose a conformational change by which ?-FADH(-) in EtfBC approaches ?-FAD to enable the bifurcating one-electron transfer. The ferredoxin reduced in one of the four electron bifurcating reactions can regenerate H(2) or NADPH, reduce CO(2) in acetogenic bacteria and methanogenic archaea, or is converted to ??H(+)/Na(+) by the membrane-associated enzyme complexes Rnf and Ech, whereby NADH and H(2) are recycled, respectively. The mainly bacterial Rnf complexes couple ferredoxin oxidation by NAD(+) with proton/sodium ion translocation and the more diverse energy converting [NiFe]hydrogenases (Ech) do the same, whereby NAD(+) is replaced by H(+). Many organisms also use Rnf and Ech in the reverse direction to reduce ferredoxin driven by ??H(+)/Na(+). Finally examples are shown, in which the four bifurcating multienzyme complexes alone or together with Rnf and Ech are integrated into energy metabolisms of nine anaerobes. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. PMID:22800682

Buckel, Wolfgang; Thauer, Rudolf K

2013-02-01

376

Cloning, Sequencing, and Characterization of a Heat- and Alkali-Stable Type I Pullulanase from Anaerobranca gottschalkii  

PubMed Central

The gene encoding a type I pullulanase was identified from the genome sequence of the anaerobic thermoalkaliphilic bacterium Anaerobranca gottschalkii. In addition, the homologous gene was isolated from a gene library of Anaerobranca horikoshii and sequenced. The proteins encoded by these two genes showed 39% amino acid sequence identity to the pullulanases from the thermophilic anaerobic bacteria Fervidobacterium pennivorans and Thermotoga maritima. The pullulanase gene from A. gottschalkii (encoding 865 amino acids with a predicted molecular mass of 98 kDa) was cloned and expressed in Escherichia coli strain BL21(DE3) so that the protein did not have the signal peptide. Accordingly, the molecular mass of the purified recombinant pullulanase (rPulAg) was 96 kDa. Pullulan hydrolysis activity was optimal at pH 8.0 and 70°C, and under these physicochemical conditions the half-life of rPulAg was 22 h. By using an alternative expression strategy in E. coli Tuner(DE3)(pLysS), the pullulanase gene from A. gottschalkii, including its signal peptide-encoding sequence, was cloned. In this case, the purified recombinant enzyme was a truncated 70-kDa form (rPulAg?). The N-terminal sequence of purified rPulAg? was found 252 amino acids downstream from the start site, presumably indicating that there was alternative translation initiation or N-terminal protease cleavage by E. coli. Interestingly, most of the physicochemical properties of rPulAg? were identical to those of rPulAg. Both enzymes degraded pullulan via an endo-type mechanism, yielding maltotriose as the final product, and hydrolytic activity was also detected with amylopectin, starch, ?-limited dextrins, and glycogen but not with amylose. This substrate specificity is typical of type I pullulanases. rPulAg was inhibited by cyclodextrins, whereas addition of mono- or bivalent cations did not have a stimulating effect. In addition, rPulAg? was stable in the presence of 0.5% sodium dodecyl sulfate, 20% Tween, and 50% Triton X-100. The pullulanase from A. gottschalkii is the first thermoalkalistable type I pullulanase that has been described.

Bertoldo, Costanzo; Armbrecht, Martin; Becker, Fiona; Schafer, Thomas; Antranikian, Garabed; Liebl, Wolfgang

2004-01-01

377

Genetic and biochemical dissection of a HisKA domain identifies residues required exclusively for kinase and phosphatase activities.  

PubMed

Two-component signal transduction systems, composed of histidine kinases (HK) and response regulators (RR), allow bacteria to respond to diverse environmental stimuli. The HK can control both phosphorylation and subsequent dephosphorylation of its cognate RR. The majority of HKs utilize the HisKA subfamily of dimerization and histidine phosphotransfer (DHp) domains, which contain the phospho-accepting histidine and directly contact the RR. Extensive genetics, biochemistry, and structural biology on several prototypical TCS systems including NtrB-NtrC and EnvZ-OmpR have provided a solid basis for understanding the function of HK-RR signaling. Recently, work on NarX, a HisKA_3 subfamily protein, indicated that two residues in the highly conserved region of the DHp domain are responsible for phosphatase activity. In this study we have carried out both genetic and biochemical analyses on Myxococcus xanthus CrdS, a member of the HisKA subfamily of bacterial HKs. CrdS is required for the regulation of spore formation in response to environmental stress. Following alanine-scanning mutagenesis of the ?1 helix of the DHp domain of CrdS, we determined the role for each mutant protein for both kinase and phosphatase activity. Our results indicate that the conserved acidic residue (E372) immediately adjacent to the site of autophosphorylation (H371) is specifically required for kinase activity but not for phosphatase activity. Conversely, we found that the conserved Thr/Asn residue (N375) was required for phosphatase activity but not for kinase activity. We extended our biochemical analyses to two CrdS homologs from M. xanthus, HK1190 and HK4262, as well as Thermotoga maritima HK853. The results were similar for each HisKA family protein where the conserved acidic residue is required for kinase activity while the conserved Thr/Asn residue is required for phosphatase activity. These data are consistent with conserved mechanisms for kinase and phosphatase activities in the broadly occurring HisKA family of sensor kinases in bacteria. PMID:23226719

Willett, Jonathan W; Kirby, John R

2012-01-01

378

Topsoil morphology indicates bio-effective redox conditions in Venice salt marshes  

NASA Astrophysics Data System (ADS)

Visual traces of iron reduction and oxidation are linked to the redox status of soils and have been used to characterise the quality of agricultural soils. We tested whether this feature could also be used to explain the spatial pattern of the natural vegetation of tidal habitats. If so, an easy assessment of the effect of rising sea level on tidal ecosystems would be possible. Our study was conducted at the salt marshes of the northern lagoon of Venice, which are strongly threatened by erosion and rising sea level and are part of the world heritage "Venice and its lagoon". We analysed the abundance of plant species at 255 sampling points along a land-sea gradient. In addition, we surveyed the redox morphology (presence/absence of red iron oxide mottles in the greyish topsoil horizons) of the soils and the presence of disturbances. We used indicator species analysis, correlation trees and multivariate regression trees to analyse relations between soil properties and plant species distribution. Plant species with known sensitivity to anaerobic conditions (e.g. Halimione portulacoides) were identified as indicators for oxic soils (showing iron oxide mottles within a greyish soil matrix). Plant species that tolerate a low redox potential (e.g. Spartina maritima) were identified as indicators for anoxic soils (greyish matrix without oxide mottles). Correlation trees and multivariate regression trees indicate the dominant role of the redox morphology of the soils in plant species distribution. In addition, the distance from the mainland and the presence of disturbances were identified as tree-splitting variables. The small-scale variation of oxygen availability plays a key role for the biodiversity of salt marsh ecosystems. Our results suggest that the redox morphology of salt marsh soils indicates the plant availability of oxygen. Thus, the consideration of this indicator may enable an understanding of the heterogeneity of biological processes in oxygen-limited systems and may be a sensitive and easy-to-use tool to assess human impacts on salt marsh ecosystems.

Lang, Friederike; von der Lippe, Moritz; Schimpel, Susanne; Scozzafava-Jaeger, Tiberio; Straub, Wolfgang

2010-03-01

379

Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction  

NASA Astrophysics Data System (ADS)

A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene reconstruction studies in astrobiology and also be applicable to the study of point mutation in conformational thermostabilization research with Synchrotron based X-ray data for drug applications such as Parkinson's disease.

Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

2013-09-01

380

Post-translational Modification of Ribosomal Proteins  

PubMed Central

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 ? 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.

Arragain, Simon; Garcia-Serres, Ricardo; Blondin, Genevieve; Douki, Thierry; Clemancey, Martin; Latour, Jean-Marc; Forouhar, Farhad; Neely, Helen; Montelione, Gaetano T.; Hunt, John F.; Mulliez, Etienne; Fontecave, Marc; Atta, Mohamed

2010-01-01