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1

Provisioning Mass by Females of the Maritime Earwig, Anisolabis maritima, is not Adjusted Based on the Number of Young  

PubMed Central

The amount of parental provisioning is thought to reflect the need of offspring. This hypothesis was tested in the case of provisioning food mass to young with controlled clutch size using the maritime earwig, Anisolabis maritima Bonelli (Dermaptera: Anisolabididae). The female provisioned a constant mass of food to the young irrespective of the number of nymphs and the distance of food carrying. In addition, the survival rate of young did not change with adjusted clutch size. This study showed that A. maritima females appear to provide food mass to their nymphs independent of their number.

Suzuki, Seizi

2011-01-01

2

Progressive Provisioning by the Females of the Earwig, Anisolabis maritima, Increases the Survival Rate of the Young  

PubMed Central

Provisioning the young is an important form of insect parental care and is believed to improve the survival and growth of the young. Anisolabis maritima Bonelli (Dermaptera: Anisolabididae) is a cosmopolitan species of earwig that shows sub-social behavior in which the females tend clutches of eggs in soil burrows. The defensive and provisioning behaviors of these females were examined in this study. When disturbed, maternal individuals abandoned the nest less than non-maternal individuals. Females brought food to the nest after their eggs hatched, and the survival of the nymphs was increased by provisioning. Even when mothers were removed, providing food to the nymphs increased survival as well as when the nymphs were provisioned by the mother. These results show that A. maritima mothers provision the nymphs and that this provisioning improves their survival.

Suzuki, Seizi

2010-01-01

3

Morphological characterization of the antennal sensilla of t he earwig Anisolabis maritima (Dermaptera: Carcinophoridae) with reference to their probable functions  

PubMed Central

The earwig, Anisolabis maritima (Dermaptera: Carcinophoridae), is one of the most significant insects in KSA because, it was recorded in Saudi Arabia as a beneficial predator on eggs and newly hatched larvae of the red palm weevil, Rhyncophorus ferrugineus. We examined the external morphology of the antennal sensilla of males and females of A. maritima using scanning electron microscopy (SEM). The filiform antennae of A. maritima were of the conventional type comprising a basal scape, pedicle and a long, thread-like flagellum, which was composed of 12 flagellomeres of males and 16 flagellomeres of females. Six morphologically unique sensillar types were found and described on the antennae of males and females of A. maritima. Of those identified, there were three types of porous trichoid sensilla (long, curved and arcuate), and two types of basiconic sensilla (short and curved), and one type of aporous trichoid sensilla. The shape, external morphology and array of sensilla on the antennae of males and females of A. maritima were similar.

Al-Dosary, Mona Mohammed

2009-01-01

4

THE CAVERNICOLOUS FAUNA OF HAWAIIAN LAVA TUBES 12. A new species of blind troglobitic earwig (Dermaptera: Carcinophoridae), with a revision ofthe related surface-living earwigs of the Hawaiian Islands1  

Microsoft Academic Search

The first known species of blind troglobitic earwig, Anisolabis howarthi, is described from a pair found in caves on the island of Hawaii. The species is related to a complex of surface- living species hitherto knowrn under the name of Anisolabis perkinsi. This complex has been found to include, in addition to A. perkinsi, 4 new species, A. hawaiiensis, A.

A. Brindle

5

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

PubMed Central

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

Munoz, Nicole E.; Zink, Andrew G.

2012-01-01

6

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

7

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

PubMed Central

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

Engel, Michael S.

2011-01-01

8

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

9

Armament under direct sexual selection does not exhibit positive allometry in an earwig  

Microsoft Academic Search

The allometric scaling relationships of armaments and ornaments have been subject to extensive debate. A large body of empirical evidence suggests that sexually selected traits typically exhibit positive static allometry, where the large individuals express proportionally larger traits. Recent theory suggests that this need not be the case. We confirm this prediction using the earwig Euborellia brunneri as a model

Emile van Lieshout; Mark Adrian Elgar

2009-01-01

10

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

11

Side effects of plant protection products and biological interactions on the European earwig Forficula auricularia L.  

PubMed

Plant protection products are designed to control pests but can have negative side effects on non-target arthropods thus disturbing the important population of natural enemies required for biological control. Although the European earwig, Forficula auricularia L, (Dermaptera: Forficulidae) is not considered to be a key beneficial in pome fruit, it is an important predator of several pests, e.g. woolly apple aphid and pear sucker. The impact of non-selective plant protection products at crucial moments in their (univoltine) life cycle can be of significant relevance compared to insects with numerous generations. Foliar applications in spring when nymphs are migrating into the trees can reduce the number of adults in summer and subsequently affect the population size next year. Multiple and/or combined spraying during summer on adults may have a cumulative effect resulting in less over wintering females which possibly exhibit poor reproductive performance. Previous residual contact bioassays already revealed the harmful side effect of several formulated products on adults. Insects showing sub lethal symptoms recovered partially or died eventually. As spinosad caused significant toxicological effects it was subsequently tested in 3 different dose rates on adults and N4-nymphs. We noticed not only a clear dose-response relationship but N4-nymphs proved to be more susceptible than adults; even a dilution of 1/9-th of the registered dose rate still caused a mortality of 45.5 % after 20 days. Understanding the earwig's population dynamics is essential for efficient practical biocontrol. It proves difficult to increase population levels to sufficient high numbers for optimal pest control. Local biological factors might be limiting. Therefore, we tested two hypotheses that pertain to population limitation: 1. Bird predation during summer, 2. Small mammal nest predation during winter. Enclosure experiments showed no negative bird effect on earwig densities unless large bird flocks inhabited the area. Small mammals did not actively predate the over wintering nests, although other predatory arthropods may be important. PMID:20222599

Peusens, G; Moerkens, R; Beliën, T; Gobin, B

2009-01-01

12

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

13

Transglycosylation reactions of Thermotoga maritima ?-amylase  

Microsoft Academic Search

The capacity of Amy A, a ?-amylase from the hyperthermophilic bacteria Thermotoga maritima to carry out transfer reactions in addition to hydrolysis was investigated. Amy A is a saccharifying enzyme that catalyzes the hydrolysis of internal ?-1,4 linkages of glucose polymers generating low molecular weight products (G1–G7); however, in the long term it is capable of producing glucose and maltose

Alina Moreno; Juanita Yazmin Damian-Almazo; Alfonso Miranda; Gloria Saab-Rincon; Fernando Gonzalez; Agustin Lopez-Munguia

2010-01-01

14

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

PubMed Central

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.

Meunier, Joel; Kolliker, Mathias

2012-01-01

15

Identification of Methylation Sites in Thermotoga maritima Chemotaxis Receptors  

Microsoft Academic Search

Adaptation in bacterial chemotaxis involves reversible methylation of specific glutamate residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins. The specific sites of methylation in Salmonella enterica and Escherichia coli chemoreceptors, identified 2 decades ago, established a consensus sequence for methylation by methyltransferase CheR. Here we report the in vitro methylation of chemoreceptors from Thermotoga maritima, a hyperthermophile that has

Eduardo Perez; Haiyan Zheng; Ann M. Stock

2006-01-01

16

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

17

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

18

Trends in Codon and Amino Acid Usage in Thermotoga maritima  

Microsoft Academic Search

.   The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium\\u000a Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon\\u000a usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino

Alejandro Zavala; Hugo Naya; Héctor Romero; Héctor Musto

2002-01-01

19

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima  

PubMed Central

Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.

Rodionov, Dmitry A.; Rodionova, Irina A.; Li, Xiaoqing; Ravcheev, Dmitry A.; Tarasova, Yekaterina; Portnoy, Vasiliy A.; Zengler, Karsten; Osterman, Andrei L.

2013-01-01

20

Resistance to water stress of Alnus maritima: intraspecific variation and comparisons to other alders  

Microsoft Academic Search

Alnus maritima (seaside alder) is a rare and threatened woody species that occurs naturally as three disjunct subspecies. While its limited numbers and distribution have prompted investigations into the cause of its rarity, the aesthetic appeal and apparent flood resistance of A. maritima have led to a strong interest in its horticultural potential. The occurrence of all three subspecies of

James A. Schrader; Sarah J. Gardner; William R. Graves

2005-01-01

21

Complete mitochondrial genome of the free-living earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and phylogeny of Polyneoptera.  

PubMed

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

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

2012-08-06

22

Structure of a putative ?-phosphoglucomutase (TM1254) from Thermotoga maritima  

PubMed Central

The structure of TM1254, a putative ?-phosphoglucomutase from T. maritima, was determined to 1.74?Å resolution in a high-throughput structural genomics programme. Diffraction data were obtained from crystals belonging to space group P22121, with unit-cell parameters a = 48.16, b = 66.70, c = 83.80?Å, and were refined to an R factor of 19.2%. The asymmetric unit contained one protein molecule which is comprised of two domains. Structural homologues were found from protein databases that confirmed a strong resemblance between TM1254 and members of the haloacid dehalogenase (HAD) hydrolase family.

Strange, Richard W.; Antonyuk, Svetlana V.; Ellis, Mark J.; Bessho, Yoshitaka; Kuramitsu, Seiki; Shinkai, Akeo; Yokoyama, Shigeyuki; Hasnain, S. Samar

2009-01-01

23

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

24

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

25

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

2012-11-19

26

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

27

Do Conditions During Dormancy Influence Germination of Suaeda maritima?  

PubMed Central

Background and Aims Seeds of annual halophytes such as Suaeda maritima experience fluctuating salinity, hydration, hypoxia and temperature during dormancy. Germination then occurs in one flush of 2–3 weeks after about 5 months of winter dormancy during which time the seeds can remain in saline, often waterlogged soil. The aim of this study was to investigate the effect of simulated natural conditions during dormancy on germination and to compare this with germination following the usual conditions of storing seeds dry. The effects of hydration, salinity, hypoxia and temperature regimes imposed during dormancy on germination were investigated. Also looked at were the effects of seed size on germination and the interaction between salinity during dormancy and salinity at the time of germination. Methods Various pre-treatments were imposed on samples of seeds that had been stored dry or wet for different periods of time during the 5 months of natural dormancy. Subsequent germination tests were carried out in conditions that simulated those found in the spring when germination occurs naturally. Various salinities were imposed at germination for a test of interaction between storage salinity and salinity at germination. Key Results A temperature of about 15 °C was needed for germination and large seeds germinated earlier and better than small seeds. Cold seawater pre-treatment was necessary for good germination; the longer the saline pre-treatment during the natural dormancy period the better the germination. There appeared to be no effect of any specific ion of the seawater pre-treatment on germination and severe hypoxia did not prevent good germination. A short period of freezing stimulated early germination in dry-stored seed. Storage in cold saline or equivalent osmotic medium appeared to inhibit germination during the natural dormancy period and predispose the seed to germinate when the temperature rose and the salinity fell. Seeds that were stored in cold wet conditions germinated better in saline conditions than those stored dry. Conclusions The conditions under which seeds of S. maritima are stored affect their subsequent germination. Under natural conditions seeds remain dormant in highly saline, anoxic mud and then germinate when the temperature rises above about 15 °C and the salinity is reduced.

Wetson, Anne M.; Cassaniti, Carla; Flowers, Timothy J.

2008-01-01

28

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

29

Diversity and versatility of the Thermotoga maritima sugar kinome.  

PubMed

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

Rodionova, Irina A; Yang, Chen; Li, Xiaoqing; Kurnasov, Oleg V; Best, Aaron A; Osterman, Andrei L; Rodionov, Dmitry A

2012-08-10

30

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

PubMed

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

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

2008-08-05

31

Several Archaeal Homologs of Putative Oligopeptide-Binding Proteins Encoded by Thermotoga maritima Bind Sugars  

Microsoft Academic Search

The hyperthermophilic bacterium Thermotoga maritima has shared many genes with archaea through horizontal gene transfer. Several of these encode putative oligopeptide ATP binding cassette (ABC) transport- ers. We sought to test the hypothesis that these transporters actually transport sugars by measuring the substrate affinities of their encoded substrate-binding proteins (SBPs). This information will increase our understanding of the selective pressures

Dhaval M. Nanavati; K. Thirangoon; K. M. Noll

2006-01-01

32

Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

Co-cultivation of the hyperthermophiles Thermotoga maritima and Methanococcus jannaschii resulted in fivefold higher T. maritima cell densities when compared with monoculture as well as concomitant formation of exopolysaccharide and flocculation of heterotroph-methanogen cellular aggregates. Transcriptional analysis of T. maritima cells from these aggregates using a whole genome cDNA microarray revealed the induction of a putative exopolysaccharide synthesis pathway, regulated by intracellular levels of cyclic diguanosine 3',5'-(cyclic)phosphate (cyclic di-GMP) and mediated by the action of several GGDEF proteins, including a putative diguanylate cyclase (TM1163) and a putative phosphodiesterase (TM1184). Transcriptional analysis also showed that TM0504, which encodes a polypeptide containing a motif common to known peptide-signalling molecules in mesophilic bacteria, was strongly upregulated in the co-culture. Indeed, when a synthetically produced peptide based on TM0504 was dosed into the culture at ecologically relevant levels, the production of exopolysaccharide was induced at significantly lower cell densities than was observed in cultures lacking added peptide. In addition to identifying a pathway for polysaccharide formation in T. maritima, these results point to the existence of peptide-based quorum sensing in hyperthermophilic bacteria and indicate that cellular communication should be considered as a component of the microbial ecology within hydrothermal habitats. PMID:15660994

Johnson, Matthew R; Montero, Clemente I; Conners, Shannon B; Shockley, Keith R; Bridger, Stephanie L; Kelly, Robert M

2005-02-01

33

Decomposition processes of Spartina maritima in a salt marsh of the Basque Country  

Microsoft Academic Search

Decomposition dynamics of aerial parts and root-rhizomes of Spartina maritima in a Basque Country salt marsh was studied, using litter bags placed on the soil surface and buried 10 cm below ground. Aerial parts of the plant in aboveground position showed higher breakdown rates than samples placed belowground. There was no significant difference found between aerial parts and root-rhizomes buried.

J. Pozo; R. Colino

1992-01-01

34

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

Microsoft Academic Search

This study investigated the effect of photodynamic antimicrobial chemotherapy (PACT) using extracts from Alternanthera maritima on the viability of Candida dubliniensis. Human infections constitute a great health problem. Several antifungal drugs are currently available, but their uses are limited by a number of factors, such as low potency, poor solubility, microbial resistance, and drug toxicity. Therefore, the search for new

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

2010-01-01

35

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

36

The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture.  

PubMed

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 beta-specific glycosyl hydrolases; the latter were presumably involved in hydrolysis of beta-linked EPS to release cells from aggregates. Detachment of aggregates may facilitate colonization of new locations in natural environments where T. maritima coexists with other organisms. Taken together, these results demonstrate that syntrophic interactions can impact the transcriptome of heterotrophs in methanogenic coculture, and this factor should be considered in examining the microbial ecology in anaerobic environments. PMID:16391122

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

2006-01-01

37

Differential transcript regulation in Arabidopsis thaliana and the halotolerant Lobularia maritima indicates genes with potential function in plant salt adaptation  

Microsoft Academic Search

Salt stress is an environmental factor that severely impairs plant growth and productivity. Salinity-induced transcript accumulation was monitored in the salt-sensitive Arabidopsis thaliana and the related salt-tolerant Lobularia maritima using cDNA-arrays with expressed sequence tags derived from a cDNA subtraction library of salt-stressed L. maritima. The expression profiles revealed differences of the steady state transcript regulation in A. thaliana and

Olga V. Popova; Oksoon Yang; Karl-Josef Dietz; Dortje Golldack

2008-01-01

38

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

39

Gene Transfer and Genome Plasticity in Thermotoga maritima, a Model Hyperthermophilic Species†  

PubMed Central

The genome sequence of the hyperthermophilic bacterium Thermotoga maritima MSB8 presents evidence for lateral gene transfer events between bacterial and archaeal species. To estimate the extent of genomic diversity across the order Thermotogales, a comparative genomic hybridization study was initiated to compare nine Thermotoga strains to the sequenced T. maritima MSB8. Many differences could be associated with substrate utilization patterns, which are most likely a reflection of the environmental niche that these individual species occupy. A detailed analysis of some of the predicted variable regions demonstrates many examples of the deletion/insertion of complete cassettes of genes and of gene rearrangements and insertions of DNA within genes, with the C or N terminus being retained. Although the mechanism for gene transfer in this lineage remains to be elucidated, this analysis suggests possible associations with repetitive elements and highlights the possible benefits of rampant genetic exchange to these species.

Mongodin, Emmanuel F.; Hance, Ioana R.; DeBoy, Robert T.; Gill, Steven R.; Daugherty, Sean; Huber, Robert; Fraser, Claire M.; Stetter, Karl; Nelson, Karen E.

2005-01-01

40

Photosynthesis and photosystem 2 efficiency of two salt-adapted halophytic seashore Cakile maritima ecotypes  

Microsoft Academic Search

The effects of salinity (0–400 mM NaCl, marked S0, S100, S200, and S400) on growth, photosynthesis, photosystem 2 (PS2) efficiency, ion relations, and pigment contents were studied in two seashore\\u000a Cakile maritima ecotypes (Tabarka and Jerba, respectively, sampled from humid and arid bioclimatic areas). Growth of Jerba plants was improved\\u000a at S100 as compared to S0. Tabarka growth was inhibited

W. Megdiche; K. Hessini; F. Gharbi; C. A. Jaleel; R. Ksouri; C. Abdelly

2008-01-01

41

Expression and characterization of a thermostable ?-xylosidase from the hyperthermophile, Thermotoga maritima  

Microsoft Academic Search

A thermostable ß-xylosidase from a hyperthermophilic bacterium, Thermotoga maritima, was over-expressed in Escherichia coli using the T7 polymerase expression system. The expressed ß-xylosidase was purified in two steps, heat treatment and immobilized metal affinity chromatography, and gave a single band on SDS-PAGE. The maximum activity on p-nitrophenyl ß-d-xylopyranoside was at 90 °C and pH 6.1. The purified enzyme had a half-life of

Yemin Xue; Weilan Shao

2005-01-01

42

Xylanase Attachment to the Cell Wall of the Hyperthermophilic Bacterium Thermotoga maritima?  

PubMed Central

The cellular localization and processing of the endo-xylanases (1,4-?-d-xylan-xylanohydrolase; EC 3.2.1.8) of the hyperthermophile Thermotoga maritima were investigated, in particular with respect to the unusual outer membrane (“toga”) of this gram-negative bacterium. XynB (40 kDa) was detected in the periplasmic fraction of T. maritima cells and in the culture supernatant. XynA (120 kDa) was partially released to the surrounding medium, but most XynA remained cell associated. Immunogold labeling of thin sections revealed that cell-bound XynA was localized mainly in the outer membranes of T. maritima cells. Amino-terminal sequencing of purified membrane-bound XynA revealed processing of the signal peptide after the eighth residue, thereby leaving the hydrophobic core of the signal peptide attached to the enzyme. This mode of processing is reminiscent of type IV prepilin signal peptide cleavage. Removal of the entire XynA signal peptide was necessary for release from the cell because enzyme purified from the culture supernatant lacked 44 residues at the N terminus, including the hydrophobic part of the signal peptide. We conclude that toga association of XynA is mediated by residues 9 to 44 of the signal peptide. The biochemical and electron microscopic localization studies together with the amino-terminal processing data indicate that XynA is held at the cell surface of T. maritima via a hydrophobic peptide anchor, which is highly unusual for an outer membrane protein.

Liebl, Wolfgang; Winterhalter, Christoph; Baumeister, Wolfgang; Armbrecht, Martin; Valdez, Michael

2008-01-01

43

Isolation and analysis of genes for amylolytic enzymes of the hyperthermophilic bacterium Thermotoga maritima  

Microsoft Academic Search

In addition to the previously identified 4-?-glucanotransferase gene mgtA and the ?-amylase gene amyA of Thermotoga maritima strain MSB8 we have now isolated three further genes encoding amylolytic enzymes from a gene library of this ancestral bacterium. The genes code for the extremely thermostable enzymes pullulanase (pulA), maltodextrin phosphorylase (agpA) and ?-glucosidase (aglA) and have the potential to encode polypeptides

Miriam Bibel; Cornelia Brettl; Uwe Gosslar; Gernot Kriegshäuser; Wolfgang Liebl

1998-01-01

44

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

Microsoft Academic Search

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 Angstroms resolution using MAD phasing and synchrotron radiation. The protein is composed

R.-G. Zhang; Y.-C. Kim; T. Skarina; S. Beasley; R. Laskowski; C. Arrowsmith; A. Edwards; A. Joachimiak; A. Savchenko; Birbeck Coll

2002-01-01

45

(Beta alpha)8-barrel proteins of tryptophan biosynthesis in the hyperthermophile Thermotoga maritima.  

PubMed Central

To better understand the evolution of a key metabolic pathway, we have sequenced the trpCFBA gene cluster of the hyperthermophilic bacterium Thermotoga maritima. The genes were cloned by complementation in vivo of trp deletion strains of Escherichia coli. The new sequences, together with earlier findings, establish that the trp operon of T.maritima has the order trpE(G.D)CFBA, which might represent the ancestral organization of the tryptophan operon. Heterologous expression of the trp(G.D) and trpC genes in E.coli and N-terminal sequencing of their polypeptide products showed that their translation is initiated at the rate start codons TTG and ATC, respectively. Consequently, the N-terminus of the trp(G.D) fusion protein is 43 residues shorter than previously postulated. Amino acid composition and sequence analyses of the protein products of T.maritima trpC (indoleglycerol phosphate synthase), trpF (phosphoribosyl anthranilate isomerase) and trpA (alpha-subunit of tryptophan synthase) suggest that these thermostable (beta alpha)8-barrel proteins may be stabilized by additional salt bridges, compared with the mesostable forms. Another notable feature is the predicted lack of the N-terminal helix alpha 0 in the alpha-subunit of tryptophan synthase.

Sterner, R; Dahm, A; Darimont, B; Ivens, A; Liebl, W; Kirschner, K

1995-01-01

46

Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways.  

PubMed

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 approximately 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. PMID:18156253

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

2007-12-21

47

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

48

Glucose fermentation to acetate, CO 2 and H 2 in the anaerobic hyperthermophilic eubacterium Thermotoga maritima : involvement of the Embden-Meyerhof pathway  

Microsoft Academic Search

The hyperthermophilic anaerobic eubacterium Thermotoga maritima was grown on glucose as carbon and energy source. During growth 1 mol glucose was fermented to 2 mol acetate, 2 mol CO2 and 4 mol H2. The molar growth yicld on glucose (Yglucose) was about 45 g cell dry mass\\/mol glucose. In the presence of elemental sulfur growing cultures of T. maritima converted

Catrin Schröder; Martina Selig; Peter Schönheit

1994-01-01

49

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

SciTech Connect

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

S Park; B Crane

2011-12-31

50

Structural insight into the low affinity between Thermotoga maritima CheA and CheB compared to their Escherichia coli / Salmonella typhimurium counterparts  

PubMed Central

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

Park, SangYoun; Crane, Brian R.

2011-01-01

51

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

PubMed

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

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

2011-12-06

52

Reaction Cycle of Thermotoga maritima Copper ATPase and Conformational Characterization of Catalytically Deficient Mutants†  

PubMed Central

Copper transport ATPases sustain important roles in homeostasis of heavy metals and delivery of copper to metalloenzymes. The copper transport ATPase from Thermotoga maritima (CopA) provides a useful system for mechanistic studies, due to its heterologous expression and stability. Its sequence comprises 726 amino acids, including the N-terminal metal binding domain (NMBD), three catalytic domains (A, N, and P), and a copper transport domain formed by eight helices, including the transmembrane metal binding site (TMBS). We performed functional characterization and conformational analysis by proteolytic digestion of WT and mutated (NMBD deletion or mutation) T. maritima CopA, comparing it with Archaeoglobus fulgidus CopA and Ca2+ ATPase. A specific feature of T. maritima CopA is ATP utilization in the absence of copper, to form a low-turnover phosphoenzyme intermediate, with a conformation similar to that obtained by phosphorylation with Pi or phosphate analogues. On the other hand, formation of an activated state requires copper binding to both NMBD and TMBS, with consequent conformational changes involving the NMBD and A domain. Proteolytic digestion analysis demonstrates A domain movements similar to those of other P-type ATPases to place the conserved TGES motif in the optimal position for catalytic assistance. We also studied an H479Q mutation (analogous to one of human copper ATPase ATP7B in Wilson disease) that inhibits ATPase activity. We found that, in spite of the H479Q mutation within the nucleotide binding domain, the mutant still binds ATP, yielding a phosphorylation transition state conformation. However, covalent phosphoryl transfer is not completed, and no catalytic turnover is observed.

2009-01-01

53

Chemical Composition of Essential Oils and Aromatic Waters from Different Italian Anthemis maritima Populations.  

PubMed

The chemical composition of the essential oils and aromatic waters isolated from six Italian Anthemis maritima populations was determined by GC-FID and GC/MS analyses. In total, 122 and 100 chemical compounds were identified in the essential oils and the aromatic waters, respectively. The main compound classes represented in the oils were monoterpene hydrocarbons, oxygenated monoterpenes, sesquiterpene hydrocarbons, oxygenated sesquiterpenes, and terpene esters. Multivariate chemometric techniques such as cluster analysis (CA) and principal coordinate analysis (PCO) were used to classify the samples according to the geographical origin. Statistical analysis allowed the attribution of the analyzed populations to different chemotype groups. PMID:24078600

Ciccarelli, Daniela; Noccioli, Cecilia; Pistelli, Luisa

2013-09-01

54

Crystallization and preliminary X-ray crystallographic studies on 4-alpha-glucanotransferase from Thermotoga maritima.  

PubMed

Thermotoga maritima 4-alpha-glucanotransferase (GTase), a 52 kDa molecular-weight amylolytic enzyme, has been crystallized by the hanging-drop vapour-diffusion method using PEG monomethylether 5000 as a precipitating agent. A complete data set has been collected to 2.6 A resolution using cryocooling conditions and synchrotron radiation. The crystals belong to space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 92.6, b = 180.3, c = 199.2 A. PMID:11418778

Roujeinikova, A; Raasch, C; Sedelnikova, S; Liebl, W; Rice, D W

2001-06-21

55

Isolation and analysis of genes for amylolytic enzymes of the hyperthermophilic bacterium Thermotoga maritima.  

PubMed

In addition to the previously identified 4-alpha-glucanotransferase gene mgtA and the alpha-amylase gene amyA of Thermotoga maritima strain MSB8 we have now isolated three further genes encoding amylolytic enzymes from a gene library of this ancestral bacterium. The genes code for the extremely thermostable enzymes pullulanase (pulA), maltodextrin phosphorylase (agpA) and alpha-glucosidase (aglA) and have the potential to encode polypeptides with calculated molecular masses of 96.3 kDa, 96.1 kDa and 52.5 kDa, respectively. Comparative amino acid sequence analysis revealed that PulA and AgpA are clearly related to other known enzymes with similar function. AglA, on the other hand, was not related to other alpha-glucosidases but appears to belong to an enzyme family containing alpha-galactosidases and 6-phospho-beta-glucosidases. Enzyme properties are reported which demonstrate the extreme thermostability of these T. maritima enzymes. PMID:9453151

Bibel, M; Brettl, C; Gosslar, U; Kriegshäuser, G; Liebl, W

1998-01-01

56

Carbon isotopic fractionations associated with thermophilic bacteria Thermotoga maritima and Persephonella marina.  

PubMed

Stable carbon isotopes can provide insight into carbon cycling pathways in natural environments. We examined carbon isotope fractionations associated with a hyperthermophilic fermentative bacterium, Thermotoga maritima, and a thermophilic chemolithoautotrophic bacterium Persephonella marina. In T. maritima, phospholipid fatty acids (PLFA) are slightly enriched in 13C relative to biomass (epsilon = 0.1-0.8 per thousand). However, PLFA and biomass are depleted in 13C relative to the substrate glucose by approximately 8 per thousand. In P. marina, PLFA are 1.8-14.5 per thousand enriched in 13C relative to biomass, which suggests that the reversed tricarboxylic acid (TCA) cycle or the 3-hydroxypropionate pathway may be used for CO2 fixation. This is supported by small fractionation between biomass and CO2 (epsilon = -3.8 per thousand to -5.0 per thousand), which is similar to fractionations reported for other organisms using similar CO2 fixation pathways. Identification of the exact pathway will require biochemical assay for specific enzymes associated with the reversed TCA cycle or the 3-hydroxypropionate pathway. PMID:11966826

Zhang, Chuanlun L; Ye, Qi; Reysenbach, Anna-Louise; Götz, Dorothee; Peacock, Aaron; White, David C; Horita, Juske; Cole, David R; Fong, Jon; Pratt, Lisa; Fang, Jiasong; Huang, Yongsong

2002-01-01

57

Allosteric inhibitor specificity of Thermotoga maritima 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase.  

PubMed

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first step of the shikimate pathway for the biosynthesis of aromatic amino acids. Allosteric regulation of Thermotoga maritima DAH7PS is mediated by L-Tyr binding to a discrete ACT regulatory domain appended to a core catalytic (?/?)8 barrel. Variants of T. maritima DAH7PS (TmaDAH7PS) were created to probe the role of key residues in inhibitor selection. Substitution Ser31Gly severely reduced inhibition by L-Tyr. In contrast both L-Tyr and L-Phe inhibited the TmaHis29Ala variant, while the variant where Ser31 and His29 were interchanged (His29Ser/Ser31His), was inhibited to a greater extent by L-Phe than L-Tyr. These studies highlight the role and importance of His29 and Ser31 for determining both inhibitory ligand selectivity and the potency of allosteric response by TmaDAH7PS. PMID:23916814

Cross, Penelope J; Parker, Emily J

2013-07-31

58

Quinone- and nitroreductase reactions of Thermotoga maritima peroxiredoxin-nitroreductase hybrid enzyme.  

PubMed

Thermotoga maritima peroxiredoxin-nitroreductase hybrid enzyme (Prx-NR) consists of a FMN-containing nitroreductase (NR) domain fused to a peroxiredoxin (Prx) domain. These domains seem to function independently as no electron transfer occurs between them. The reduction of quinones and nitroaromatics by NR proceeded in a two-electron manner, and follows a 'ping-pong' scheme with sometimes pronounced inhibition by quinone substrate. The comparison of steady- and presteady-state kinetic data shows that in most cases, the oxidative half-reaction may be rate-limiting in the catalytic cycle of NR. The enzyme was inhibited by dicumarol, a classical inhibitor of oxygen-insensitive nitroreductases. The reduction of quinones and nitroaromatic compounds by Prx-NR was characterized by the linear dependence of their reactivity (logk(cat)/K(m)) on their single-electron reduction potentials E(7)(1), while the reactivity of quinones markedly exceeded the one with nitroaromatics. It shows that NR lacks the specificity for the particular structure of these oxidants, except their single-electron accepting potency and the rate of electron self-exchange. It points to the possibility of a single-electron transfer step in a net two-electron reduction of quinones and nitroaromatics by T. maritima Prx-NR, and to a significant diversity of the structures of flavoenzymes which may perform the two-electron reduction of quinones and nitroaromatics. PMID:22982531

Anusevi?ius, Žilvinas; Misevi?ien?, Lina; Šarlauskas, Jonas; Rouhier, Nicolas; Jacquot, Jean-Pierre; ??nas, Narimantas

2012-09-12

59

The influence of rice rats Oryzomys palustris on the habitat use of the seaside sparrow Ammospiza maritima  

Microsoft Academic Search

The influence of rodent activity on the distribution of the seaside sparrow Ammospiza maritima was investigated.1.Seaside sparrows nest in Juncus less frequently than in shorter, sparser vegetation (Distichlis and Salicornia), where nests are more often subjected to flooding and predation by fish crows.2.The activity spaces of seaside sparrows and rice rats Oryzomys palustris overlap, and the two species use similar

William Post

1981-01-01

60

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

Microsoft Academic Search

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.

Fabio Virgili; George Pagana; Louise Bourne; Gerald Rimbach; Fausta Natella; Catherine Rice-Evans; Lester Packer

2000-01-01

61

Identification and Characterization of a Novel Intracellular Alkaline  Amylase from the Hyperthermophilic Bacterium Thermotoga maritima MSB8  

Microsoft Academic Search

The gene for a novel -amylase, designated AmyC, from the hyperthermophilic bacterium Thermotoga maritima was cloned and heterologously overexpressed in Escherichia coli. The putative intracellular enzyme had no amino acid sequence similarity to glycoside hydrolase family (GHF) 13 -amylases, yet the range of substrate hydrolysis and the product profile clearly define the protein as an -amylase. Based on sequence similarity

Meike Ballschmiter; Ole Futterer; Wolfgang Liebl

2006-01-01

62

FIRST RECORD AND CHARACTERIZATION OF A POWDERY MILDEW ON A MEMBER OF THE JUNCAGINACEAE: LEVEILLULA TAURICA ON TRIGLOCHIN MARITIMA.  

Technology Transfer Automated Retrieval System (TEKTRAN)

The powdery mildew fungus Leveillula taurica (Erysiphales) is reported for the first time from Triglochin maritima (Jungacinaceae), a widespread salt marsh plant that causes economic losses because of its high toxicity to young livestock. This is the first report of a powdery mildew fungus on a mem...

63

Permeability and reactivity of Thermotoga maritima in latex bimodal blend coatings at 80°C: a model high temperature biocatalytic coating  

Microsoft Academic Search

Thermostable polymers cast as thin, porous coatings or membranes may be useful for concentrating and stabilizing hyperthermophilic microorganisms as biocatalysts. Hydrogel matricies can be unstable above 65°C. Therefore a 55-µm thick, two layer (cell coat + polymer top coat) bimodal, adhesive latex coating of partially coalesced polystyrene particles was investigated at 80°C using Thermotoga maritima as a model hyperthermophile. Coating

Olav K. Lyngberg; Chris Solheid; Salim Charaniya; Yue Ma; Venkata Thiagarajan; L. E. Scriven; Michael C. Flickinger

2005-01-01

64

Recombinant S-adenosylhomocysteine hydrolase from Thermotoga maritima: cloning, overexpression, characterization, and thermal purification studies.  

PubMed

S-Adenosylhomocysteine hydrolase (SAHase) encoded by sahase gene is a determinant when catalyzing the reversible conversion of adenosine and homocysteine to S-adenosylhomocysteine in most living organisms. The sahase gene was isolated from the genome of the highly thermostable anaerobic bacteria Thermotoga maritima, and then it was cloned, characterized, overexpressed using Escherichia coli, and partially purified by thermal precipitation. The thermal purification of the recombinant SAHase resulted in changes in the circular dichroism spectra. As a result of this analysis, it was possible to determine the structural changes in the composition of the ?-helix and ?-sheet content of the recombinant enzyme after purification. Moreover, a predicted secondary structure and 3D structural model was rendered by comparative molecular modeling to further understand the molecular function of this protein including its attractive biotechnological use. PMID:23588970

Lozada-Ramírez, J D; Sánchez-Ferrer, A; García-Carmona, F

2013-04-16

65

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

PubMed Central

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

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

2005-01-01

66

Structure of an essential GTPase, YsxC, from Thermotoga maritima  

PubMed Central

YsxC belongs to the YihA family of TRAFAC class GTPases. The protein is involved in the biogenesis of ribosomes and is essential for the survival of a wide range of bacteria. Here, crystal structures of YsxC from Thermotoga maritima and its complex with GDP were determined at maximal resolutions of 2.3 and 1.9?Å, respectively. Major structural differences are observed in the switch I region, which is disordered in the apo form but exists in both an ‘open’ and a ‘closed’ conformation in the GDP-bound state. A comparison with the structure of the GMPPNP–YsxC complex from Bacillus subtilis provides insights into the mechanism of conformational change in the switch I and II regions upon hydrolysis of GTP.

Chan, Kwok-Ho; Wong, Kam-Bo

2011-01-01

67

Crystallization and preliminary X-ray crystallographic studies on maltosyltransferase from Thermotoga maritima.  

PubMed

Thermotoga maritima maltosyltransferase (MTase) is a 73.7 kDa molecular weight amylolytic enzyme which catalyzes the transfer of maltosyl units from maltodextrins or starch to suitable acceptors. Crystals of recombinant MTase have been obtained by the hanging-drop vapour-diffusion method using ammonium phosphate as a precipitating agent. The crystals belong to space group P4(1)22 or its enantiomorph P4(3)22, with unit-cell parameters a = b = 148.7, c = 106.7 A. The asymmetric unit appears to contain one subunit, corresponding to a very low packing density of 4.0 A(3) Da(-1). The crystals diffract X-rays to at least 2.4 A resolution on a synchrotron-radiation source. PMID:10944350

Burke, J; Roujeinikova, A; Baker, P J; Sedelnikova, S; Raasch, C; Liebl, W; Rice, D W

2000-08-01

68

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

PubMed

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. PMID:23192024

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

2012-11-19

69

Several archaeal homologs of putative oligopeptide-binding proteins encoded by Thermotoga maritima bind sugars.  

PubMed

The hyperthermophilic bacterium Thermotoga maritima has shared many genes with archaea through horizontal gene transfer. Several of these encode putative oligopeptide ATP binding cassette (ABC) transporters. We sought to test the hypothesis that these transporters actually transport sugars by measuring the substrate affinities of their encoded substrate-binding proteins (SBPs). This information will increase our understanding of the selective pressures that allowed this organism to retain these archaeal homologs. By measuring changes in intrinsic fluorescence of these SBPs in response to exposure to various sugars, we found that five of the eight proteins examined bind to sugars. We could not identify the ligands of the SBPs TM0460, TM1150, and TM1199. The ligands for the archaeal SBPs are TM0031 (BglE), the beta-glucosides cellobiose and laminaribiose; TM0071 (XloE), xylobiose and xylotriose; TM0300 (GloE), large glucose oligosaccharides represented by xyloglucans; TM1223 (ManE), beta-1,4-mannobiose; and TM1226 (ManD), beta-1,4-mannobiose, beta-1,4-mannotriose, beta-1,4-mannotetraose, beta-1,4-galactosyl mannobiose, and cellobiose. For comparison, seven bacterial putative sugar-binding proteins were examined and ligands for three (TM0595, TM0810, and TM1855) were not identified. The ligands for these bacterial SBPs are TM0114 (XylE), xylose; TM0418 (InoE), myo-inositol; TM0432 (AguE), alpha-1,4-digalactouronic acid; and TM0958 (RbsB), ribose. We found that T. maritima does not grow on several complex polypeptide mixtures as sole sources of carbon and nitrogen, so it is unlikely that these archaeal ABC transporters are used primarily for oligopeptide transport. Since these SBPs bind oligosaccharides with micromolar to nanomolar affinities, we propose that they are used primarily for oligosaccharide transport. PMID:16461685

Nanavati, Dhaval M; Thirangoon, Kamolwan; Noll, Kenneth M

2006-02-01

70

Structural Insights into the Mechanism of the PLP Synthase Holoenzyme from Thermotoga maritima†,‡  

PubMed Central

Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B6 and is an important cofactor for several of the enzymes involved in the metabolism of amine-containing natural products such as amino acids and amino-sugars. The PLP synthase holoenzyme consists of two subunits: YaaD catalyzes the condensation of ribulose 5-phosphate, glyceraldehyde-3-phosphate and ammonia and YaaE catalyzes the production of ammonia from glutamine. Here we describe the structure of the PLP synthase complex (YaaD-YaaE) from Thermotoga maritima at 2.9 Å resolution. This complex consists of a core of 12 YaaD monomers with 12 noninteracting YaaE monomers attached to the core. Compared to the previously published structure of PdxS (a YaaD ortholog in Geobacillus stearothermophilus), the N-terminus (1–18), which includes helix ?0, the ?2-?2 loop(46–56), which includes new helix ?2a, and the C-terminus (270–280) of YaaD, are ordered in the complex but disordered in PdxS. A ribulose 5-phosphate is bound to YaaD via an imine with Lys82. Previous studies have demonstrated a similar imine at Lys149 and not at Lys81 (equivalent to Lys150 and 82 in T. maritima) for the Bacillus subtilis enzyme suggesting the possibility that two separate sites on YaaD are involved in PLP formation. A phosphate from the crystallization solution is found bound to YaaD and also serves as a marker for a possible second active site. An ammonia channel that connects the active site of YaaE with the ribulose 5-phosphate binding site was identified. This channel is similar to one found in imidazole glycerol phosphate synthase; however, when the ?-barrels of the two complexes are superimposed, the glutaminase domains are rotated by about 180° with respect to each other.

Zein, Fairuz; Zhang, Yan; Kang, You-Na; Burns, Kristin; Begley, Tadhg P.; Ealick, Steven E.

2008-01-01

71

Ecology of beach wrack in northern New England with special reference to Orchestia platensis*1  

NASA Astrophysics Data System (ADS)

The northern New England beach wrack community with special reference to the cosmopolitan amphipod crustacean, Orchestia platensis, was examined at estuarine and open coastal habitats. Beach wrack was dominated by the plant genera Ascophyllum, Zostera, Spartina and Chondrus, and was most abundant during spring and late summer. Animal community numbers, biomass and frequency in fresh to moderately decomposed wrack were dominated by O. platensis throughout the year at all habitats; oligochaetes and Collembola were also important. The abundance of O. platensis showed high spatial and temporal variability, with low abundance generally associated with decreased amounts of wrack during colder months. An exception was the winter presence of the species at one estuarine habitat, in patchy aggregations within gravel-cobble refuges. The abundance of O. platensis averaged 1280 (0.04 m 2) -1, with a maximum of 7040 (0.04 m 2) -1. The life cycle of O. platensis is bivoltine, with summer-hatched young reaching maturity within 1 month. Laboratory studies indicate females with up to 4 broods (30 days) -1, averaging 18 eggs brood -1. Orchestia platensis is omnivorous, eating fresh plant tissue, live oligochaetes, Limulus eggs and diatom 'fuzz'. The rate of laboratory consumption of algae and Zostera was 0.05 mg plant mg -1 wet body weight day -1. Presumptive predators of O. platensis are juvenile green crab, Carcinus maenus, and the earwig. Anisolabis maritima. The mobility, aggregation and aggressiveness of O. platensis assist the species in establishing and maintaining populations in the rigorous wrack habitat. The general competitive superiority of O. platensis over its congener, O. gammarella, and the co-occurrence of these species on both eastern and western Atlantic shores is discussed.

Behbehani, Manaf I.; Croker, Robert A.

1982-12-01

72

Interacting infl uence of cold stratifi cation treatment and osmotic potential on seed germination of Triglochin maritima L  

Microsoft Academic Search

Th e eff ect of cold stratifi cation treatment and isoosmotic NaCl and polyethyleneglycol (PEG) concentrations on germination of Triglochin maritima seeds was assessed. Th e highest (400 mM) NaCl concentration caused a signifi cant decrease in germination percentage and no germination was observed at the two highest (64 and 128 mM) PEG concentrations. Th e large diff erence in

Gederts Ievinsh

2007-01-01

73

Effect of the thermostable xylanase B (XynB) from Thermotoga maritima on the quality of frozen partially baked bread  

Microsoft Academic Search

The effect of the recombinantly produced xylanase B (XynB) from Thermotoga maritima MSB8 on the quality of frozen partially baked bread (FPBB) was investigated. Addition of XynB to wheat flour dough resulted in a significant increase in dough extensibility (L), swelling (G), and a decrease in dough resistance to deformation (P), configuration. Bread crumb characteristics were studied by differential scanning

Zhengqiang Jiang; Alain Le Bail; Aimin Wu

2008-01-01

74

Spatial and temporal variations in aboveground and belowground biomass of Spartina maritima (small cordgrass) in created and natural marshes  

NASA Astrophysics Data System (ADS)

Spartina species are commonly used for salt marsh manipulative projects, where aboveground and belowground biomasses are functional traits that play important roles, showing high spatial and temporal variations. This work analyses variations in AGB and BGB of Spartina maritima and abiotic environmental parameters along a chronosequence of six marshes created from 1997 to 2003 with disparate sediment dynamics, and adjacent natural marshes and unvegetated tidal flats. S. maritima behaved as an autogenic engineer, as its colonization of bare sediments yielded abiotic environmental changes: specifically, bed level rise accompanied by higher oxygenation and salinity. These modifications of the environment were site-specific, depending mainly on sedimentary dynamics. At the same time, abiotic environmental changes determined biomass production rates of S. maritima that were higher in more-accreting marshes; however, AGB was kept constant from early in its development (2 years). The increase in BGB with elevation seemed to be related to the inhibition of subsurface tissue development in anoxic sediments. Biomass accumulation and production varied markedly, depending on the spatial scale, indicating the relevance of the plot size chosen for the analysis of biomass of cordgrasses. Our results show that managers of salt marshes should consider sedimentary dynamics carefully when setting realistic expectations for success criteria of created and restored wetlands.

Castillo, Jesús M.; Leira-Doce, Pablo; Rubio-Casal, Alfredo E.; Figueroa, Enrique

2008-07-01

75

Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase crystals from Thermotoga maritima and Escherichia coli.  

PubMed

Octaprenyl pyrophosphate synthase (OPPs) catalyzes the condensation of five isopentenyl pyrophosphates with farnesyl pyrophosphate to generate C(40) octaprenyl pyrophosphate. The enzymes from the hyperthermophilic bacterium Thermotoga maritima and from the mesophilic Escherichia coli were expressed in E. coli and the recombinant proteins were purified and crystallized. The T. maritima OPPs crystals belong to space group P42(1)2, with unit-cell parameters a = b = 151.53, c = 69.72 A. The E. coli OPPs crystals belong to space group C222(1), with unit-cell parameters a = 247.66, b = 266.10, c = 157.93 A. Diffraction data were collected at 100 K using synchrotron radiation and an in-house X-ray source. Structure determination of T. maritima OPPs has been carried out using MIR data sets at 2.8 A resolution. The asymmetric unit contains one dimer. An initial model with 280 residues per subunit has been built and refined to 2.28 A resolution. It shows mostly helical structure and resembles that of avian farnesyl pyrophosphate synthase. PMID:14646090

Guo, Rey-Ting; Ko, Tzu-Ping; Chou, Chia-Cheng; Shr, Hui-Lin; Chu, Hsing-Mao; Tsai, Yao-Hsien; Liang, Po-Huang; Wang, Andrew H J

2003-11-27

76

Morphological and genetic distinctiveness of metallicolous and non-metallicolous populations of Armeria maritima s.l. (Plumbaginaceae) in Poland.  

PubMed

Patterns of morphological, genetic and epigenetic variation (DNA methylation pattern) were investigated in metallicolous (M) and non-metallicolous (NM) populations of Armeria maritima. A morphological study was carried out using plants from six natural populations grown in a greenhouse. Morphological variation was assessed using seven traits. On the basis of this study, three representative populations were selected for molecular analyses using metAFLP to study sequence- and methylation-based DNA variation. Only one morphological trait (length of outer involucral bracts) was common to both metallicolous populations studied; however, the level of variation was sufficient to differentiate between M and NM populations. Molecular analyses showed the existence of naturally occurring epigenetic variation in A. maritima populations, as well as structuring into distinct between and within population components. We show that patterns of population genetic structure differed depending on the information used in the study. Analysis of sequence-based information data demonstrates the presence of three well-defined and genetically differentiated populations. Methylation-based data show that two major groups of individuals are present, corresponding to the division into M and NM populations. These results were confirmed using different analytical approaches, which suggest that the DNA methylation pattern is similar in both M populations. We hypothesise that epigenetic processes may be involved in microevolution leading to development of M populations in A. maritima. PMID:22243547

Abratowska, A; W?sowicz, P; Bednarek, P T; Telka, J; Wierzbicka, M

2012-01-13

77

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

PubMed

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

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

2010-03-20

78

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 BmMTP11as 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

2013-07-18

79

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

PubMed Central

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

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

2013-01-01

80

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

PubMed

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 now been determined as I17, I53, S129, S134, G144, S164, P165, S187, V190, S169, T196, and S202. Analysis of the structure indicated a dimer in the asymmetric unit, two metal binding sites per monomer, and loops involved in the molecular oligomerization. These confer 98% similarity between ConM and other previously described lectins, derived from Canavalia ensiformis and Canavalia brasiliensis. Our functional data indicate that ConM exerts a concentration-dependent relaxant action on isolated aortic rings that probably occurs via an interaction with a specific lectin-binding site on the endothelium, resulting in a release of nitric oxide. PMID:16337811

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

2005-11-14

81

Detection of the strand exchange reaction using DNAzyme and Thermotoga maritima recombinase A.  

PubMed

We have designed multiple detection systems for the DNA strand exchange process. Thermostable Thermotoga maritima recombinase A (TmRecA), a core protein in homologous recombination, and DNAzyme, a catalytic DNA that can cleave a specific DNA sequence, are introduced in this work. In a colorimetric method, gold nanoparticles (AuNPs) modified with complementary DNAs (cDNAs) were assembled by annealing. Aggregated AuNPs were then separated irreversibly by TmRecA and DNAzyme, leading to a distinct color change in the particles from purple to red. For the case of fluorometric detection, fluorescein isothiocyanate (FITC)-labeled DNA as a fluorophore and black hole quencher 1 (BHQ1)-labeled DNA as a quencher were used; successful strand exchange was clearly detected by variations in fluorescence intensity. In addition, alterations in the impedance of a gold electrode with immobilized DNA were employed to monitor the regular exchange of DNA strands. All three methods provided sufficient evidence of efficient strand exchange reactions and have great potential for applications in the monitoring of recombination, discovery of new DNAzymes, detection of DNAzymes, and measurement of other protein activities. PMID:22178915

Jo, Hunho; Lee, Seonghwan; Min, Kyoungin; Ban, Changill

2011-11-16

82

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

83

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

PubMed

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 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 and paraoxon were determined to 2.4 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 Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction. PMID:22411095

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

2012-03-13

84

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

SciTech Connect

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 Angstroms 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 Zn2+ 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.

Zhang, R.-G.; Kim, Y.-C.; Skarina, T.; Beasley, S.; Laskowski, R.; Arrowsmith, C.; Edwards, A.; Joachimiak, A.; Savchenko, A.; Univ. of Toronto; Univ. Health Network; Birbeck Coll.

2002-05-24

85

Crystal Structures of the Laminarinase Catalytic Domain from Thermotoga maritima MSB8 in Complex with Inhibitors  

PubMed Central

Laminarinases hydrolyzing the ?-1,3-linkage of glucans play essential roles in microbial saccharide degradation. Here we report the crystal structures at 1.65–1.82 ? resolution of the catalytic domain of laminarinase from the thermophile Thermotoga maritima with various space groups in the ligand-free form or in the presence of inhibitors gluconolactone and cetyltrimethylammonium. Ligands were bound at the cleft of the active site near an enclosure formed by Trp-232 and a flexible GASIG loop. A closed configuration at the active site cleft was observed in some molecules. The loop flexibility in the enzyme may contribute to the regulation of endo- or exo-activity of the enzyme and a preference to release laminaritrioses in long chain carbohydrate hydrolysis. Glu-137 and Glu-132 are proposed to serve as the proton donor and nucleophile, respectively, in the retaining catalysis of hydrolyzation. Calcium ions in the crystallization media are found to accelerate crystal growth. Comparison of laminarinase and endoglucanase structures revealed the subtle difference of key residues in the active site for the selection of ?-1,3-glucan and ?-1,4-glucan substrates, respectively. Arg-85 may be pivotal to ?-1,3-glucan substrate selection. The similarity of the structures between the laminarinase catalytic domain and its carbohydrate-binding modules may have evolutionary relevance because of the similarities in their folds.

Jeng, Wen-Yih; Wang, Nai-Chen; Lin, Cheng-Tse; Shyur, Lie-Fen; Wang, Andrew H.-J.

2011-01-01

86

Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination  

PubMed Central

Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be greatly facilitated by biophysical techniques that are capable of evaluating and assessing the fold and oligomeric state of these proteins solubilized in detergent micelles. In this study, an approach to the characterization of detergent-solubilized integral membrane proteins is presented. Eight Thermotoga maritima membrane proteins were screened for solubility in 11 detergents, and the resulting soluble protein–detergent complexes were characterized with small angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD) spectroscopy, and chemical cross-linking to evaluate the homogeneity, oligomeric state, radius of gyration, and overall fold. A new application of SAXS is presented, which does not require density matching, and NMR methods, typically used to evaluate soluble proteins, are successfully applied to detergent-solubilized membrane proteins. Although detergents with longer alkyl chains solubilized the most proteins, further characterization indicates that some of these protein–detergent complexes are not well suited for NMR structure determination due to conformational exchange and protein oligomerization. These results emphasize the need to screen several different detergents and to characterize the protein–detergent complex in order to pursue structural studies. Finally, the physical characterization of the protein–detergent complexes indicates optimal solution conditions for further structural studies for three of the eight overexpressed membrane proteins.

Columbus, Linda; Lipfert, Jan; Klock, Heath; Millett, Ian; Doniach, Sebastian; Lesley, Scott A.

2006-01-01

87

Enzymatic activity in the rhizosphere of Spartina maritima: potential contribution for phytoremediation of metals.  

PubMed

Extracellular enzymatic activity (EEA) of five enzymes (peroxidase, phenol oxidase, beta-glucosidase, beta-N-acetylglucosaminidase and acid phosphatase) was analysed in sediments colonised by Spartina maritima in two salt marshes (Rosário and Pancas) of the Tagus estuary (Portugal) with different characteristics such as sediment parameters and metal contaminant levels. Our aim was a better understanding of the influence of the halophyte on microbial activity in the rhizosphere under different site conditions, and its potential consequences for metal cycling and phytoremediation in salt marshes. Acid phosphatase and beta-N-acetylglucosaminidase presented significantly higher EEA in Rosário than in Pancas, whereas the opposite occurred for peroxidase. This was mainly attributed to differences in organic matter between the two sites. A positive correlation between root biomass and EEA of hydrolases (beta-glucosidase, beta-N-acetylglucosaminidase and acid phosphatase) was found, indicating a possible influence of the halophyte in sediment microbial function. This would potentially affect metal cycling in the rhizosphere through microbial reactions. PMID:17935772

Reboreda, Rosa; Caçador, Isabel

2007-09-11

88

Expression and characterization of a thermostable beta-xylosidase from the hyperthermophile, Thermotoga maritima.  

PubMed

A thermostable beta-xylosidase from a hyperthermophilic bacterium, Thermotoga maritima, was over-expressed in Escherichia coli using the T7 polymerase expression system. The expressed beta-xylosidase was purified in two steps, heat treatment and immobilized metal affinity chromatography, and gave a single band on SDS-PAGE. The maximum activity on p-nitrophenyl beta-D-xylopyranoside was at 90 degrees C and pH 6.1. The purified enzyme had a half-life of over 22-min at 95 degrees C, and retained over 57% of its activity after holding a pH ranging from 5.4 to 8.5 for 1 h at 80 degrees C. Among all tested substrates, the purified enzyme had specific activities of 275, 50 and 29 U mg(-1) on pNPX, pNPAF, and pNPG, respectively. The apparent Michaelis constant of the beta-xylosidase was 0.13 mM for p NPX with a V (max) of 280 U mg(-1). When the purified beta-xylosidase was added to xylanase, corncob xylan was hydrolized completely to xylose. PMID:15604789

Xue, Yemin; Shao, Weilan

2004-10-01

89

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

PubMed Central

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

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

1995-01-01

90

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

91

Substrate Specificities and Expression Patterns Reflect the Evolutionary Divergence of Maltose ABC Transporters in Thermotoga maritima  

PubMed Central

Duplication of transporter genes is apparent in the genome sequence of the hyperthermophilic bacterium Thermotoga maritima. The physiological impacts of these duplications are not well understood, so we used the bacterium's two putative maltose transporters to begin a study of the evolutionary relationship between a transporter's function and the control of expression of its genes. We show that the substrate binding proteins encoded by these operons, MalE1 and MalE2, have different substrate specificities and affinities and that they are expressed under different growth conditions. MalE1 binds maltose (dissociation constant [KD], 24 ± 1 ?M), maltotriose (KD, 8 ± 0.5 nM), and ?-(1?4)-mannotetraose (KD, 38 ± 1 ?M). In contrast, MalE2 binds maltose (KD, 8.4 ± 1 ?M), maltotriose (KD, 11.5 ± 1.5 ?M), and trehalose (KD, 9.5 ± 1.0 ?M) confirming the findings of Wassenberg et al. (J. Mol. Biol. 295:279-288, 2000). Neither protein binds lactose. We examined the expression of these operons at both the transcriptional and translational levels and found that MalE1 is expressed in cells grown on lactose or guar gum and that MalE2 is highly expressed in starch- and trehalose-grown cells. Evidence is provided that malE1, malF1, and perhaps malG1 are cotranscribed and so constitute an operon. An open reading frame encoding a putative transcriptional regulatory protein adjacent to this operon (TM1200) is also up-regulated in response to growth on lactose. These evolutionarily related transporter operons have diverged both in function and expression to assume apparently different physiological roles.

Nanavati, Dhaval M.; Nguyen, Tu N.; Noll, Kenneth M.

2005-01-01

92

Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.  

PubMed

A Gram-negative, aerobic, short rod-shaped bacterium, designated strain YC6898(T), was isolated from the surface-sterilized root of a halophyte (Suaeda maritima) inhabiting tidal flat of Namhae Island, Korea. Strain YC6898(T) grew optimally at 30-37 °C and pH 6.5-7.5. The strain inhibited mycelial growth of Pythium ultimum and Phytophthora capsici. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YC6898(T) belongs to the genus Hoeflea in the family Phyllobacteriaceae. Its closest relatives were Hoeflea alexandrii AM1V30(T) (96.7% 16S rRNA gene sequence similarity), Hoeflea anabaenae WH2K(T) (95.7%), Hoeflea phototrophica DFL-43(T) (95.5%) and Hoeflea marina LMG 128(T) (94.8%). Strain YC6898(T) contained Q-10 as the major ubiquinone. The major fatty acids of strain YC6898(T) were C18:1?7c (61.1%), C16:0 (11.9%), 11-methyl C18:1?7c (9.6%) and C19:0 cyclo ?8c (8.0%). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unknown lipids and an unknown glycolipid. The total genomic DNA G+C content was 53.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain YC6898(T) represents a novel species of the genus Hoeflea, for which the name Hoeflea suaedae sp. nov. is proposed. The type strain is YC6898(T) (=KACC 14911(T)=NBRC 107700(T)). PMID:23159752

Chung, Eu Jin; Park, Jeong Ae; Pramanik, Prabhat; Bibi, Fehmida; Jeon, Che Ok; Chung, Young Ryun

2012-11-16

93

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

SciTech Connect

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

Morar, Mariya; Anand, Ruchi; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E. (MIT); (Cornell)

2008-09-11

94

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

SciTech Connect

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

Morar, Mariya; Hoskins, Aaron A.; Stubbe, JoAnne; Ealick, Steven E. (MIT); (Cornell)

2008-10-02

95

Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia?  

PubMed Central

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

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

2010-01-01

96

Glucose fermentation of acetate, CO 2 and H 2 in the anaerobic hyperthermophilic eubacterium Thermotoga maritima : involvement of the Embden-Meyerhof pathway  

Microsoft Academic Search

The hyperthermophilic anaerobic eubacterium Thermotoga maritima was grown on glucose as carbon and energy source. During growth 1 mol glucose was fermented to 2 mol acetate, 2 mol CO 2 and 4 mol H 2. The molar growth yield on glucose (Y glucose) was about 45 g cell dry mass\\/mol glucose. In the presence of elemental sulfur growing cultures of

C. Schröder; M. Selig; P. Schönheit

1994-01-01

97

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

Microsoft Academic Search

The genome sequence of the hyperthermophilic bacterium Thermotoga maritima encodes a number of glycosyl hydrolases. Many of these enzymes have been shown in vitro to degrade specific glycosides that presumably serve as carbon and energy sources for the organism. However, because of the broad substrate specificity of many glycosyl hydrolases, it is difficult to determine the physiological substrate preferences for

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

2002-01-01

98

Genetic evidence for hybridization between the native Spartina maritima and the introduced Spartina alterniflora (Poaceae) in South-West France: Spartina × neyrautii re-examined  

Microsoft Academic Search

.  ?Spartina alterniflora, a perennial grass native to the North American Atlantic coast, was introduced during the 19th century in western Europe\\u000a (Southern England and western France) where it hybridized with the native Spartina maritima. In England, the sterile hybrid S. ? townsendii gave rise by chromosome doubling to the highly fertile allopolyploid Spartina anglica, which has now invaded many salt

A. Baumel; M. L. Ainouche; M. T. Misset; J. P. Gourret; R. J. Bayer

2003-01-01

99

Draft Genome Sequence of Thermotoga maritima A7A Reconstructed from Metagenomic Sequencing Analysis of a Hydrocarbon Reservoir in the Bass Strait, Australia  

PubMed Central

The draft genome sequence of Thermotoga maritima A7A was obtained from a metagenomic assembly obtained from a high-temperature hydrocarbon reservoir in the Gippsland Basin, Australia. The organism is predicted to be a motile anaerobe with an array of catabolic enzymes for the degradation of numerous carbohydrates.

Sutcliffe, Brodie; Rosewarne, Carly P.; Greenfield, Paul; Li, Dongmei

2013-01-01

100

Properties and gene structure of the Thermotoga maritima alpha-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium.  

PubMed

Thermotoga maritima MSB8 has a chromosomal alpha-amylase gene, designated amyA, that is predicted to code for a 553-amino-acid preprotein with significant amino acid sequence similarity to the 4-alpha-glucanotransferase of the same strain and to alpha-amylase primary structures of other organisms. Upstream of the amylase gene, a divergently oriented open reading frame which can be translated into a polypeptide with similarity to the maltose-binding protein MalE of Escherichia coli was found. The T. maritima alpha-amylase appears to be the first known example of a lipoprotein alpha-amylase. This is in agreement with observations pointing to the membrane localization of this enzyme in T. maritima. Following the signal peptide, a 25-residue putative linker sequence rich in serine and threonine was found. The amylase gene was expressed in E. coli, and the recombinant enzyme was purified and characterized. The molecular mass of the recombinant enzyme was estimated at 61 kDa by denaturing gel electrophoresis (63 kDa by gel permeation chromatography). In a 10-min assay at the optimum pH of 7.0, the optimum temperature of amylase activity was 85 to 90 degrees C. Like the alpha-amylases of many other organisms, the activity of the T. maritima alpha-amylase was dependent on Ca2+. The final products of hydrolysis of soluble starch and amylose were mainly glucose and maltose. The extraordinarily high specific activity of the T. maritima alpha-amylase (about 5.6 x 10(3) U/mg of protein at 80 degrees C, pH 7, with amylose as the substrate) together with its extreme thermal stability makes this enzyme an interesting candidate for biotechnological applications in the starch processing industry. PMID:9006052

Liebl, W; Stemplinger, I; Ruile, P

1997-02-01

101

Properties and gene structure of the Thermotoga maritima alpha-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium.  

PubMed Central

Thermotoga maritima MSB8 has a chromosomal alpha-amylase gene, designated amyA, that is predicted to code for a 553-amino-acid preprotein with significant amino acid sequence similarity to the 4-alpha-glucanotransferase of the same strain and to alpha-amylase primary structures of other organisms. Upstream of the amylase gene, a divergently oriented open reading frame which can be translated into a polypeptide with similarity to the maltose-binding protein MalE of Escherichia coli was found. The T. maritima alpha-amylase appears to be the first known example of a lipoprotein alpha-amylase. This is in agreement with observations pointing to the membrane localization of this enzyme in T. maritima. Following the signal peptide, a 25-residue putative linker sequence rich in serine and threonine was found. The amylase gene was expressed in E. coli, and the recombinant enzyme was purified and characterized. The molecular mass of the recombinant enzyme was estimated at 61 kDa by denaturing gel electrophoresis (63 kDa by gel permeation chromatography). In a 10-min assay at the optimum pH of 7.0, the optimum temperature of amylase activity was 85 to 90 degrees C. Like the alpha-amylases of many other organisms, the activity of the T. maritima alpha-amylase was dependent on Ca2+. The final products of hydrolysis of soluble starch and amylose were mainly glucose and maltose. The extraordinarily high specific activity of the T. maritima alpha-amylase (about 5.6 x 10(3) U/mg of protein at 80 degrees C, pH 7, with amylose as the substrate) together with its extreme thermal stability makes this enzyme an interesting candidate for biotechnological applications in the starch processing industry.

Liebl, W; Stemplinger, I; Ruile, P

1997-01-01

102

ATP-dependent glucokinase from the hyperthermophilic bacterium Thermotoga maritima represents an extremely thermophilic ROK glucokinase with high substrate specificity.  

PubMed

The gene (open reading frame (ORF) Tm1469, glk) encoding ATP-dependent ROK (repressors, ORFs, sugar kinases) glucokinase (ATP-GLK, EC 2.7.1.2) of the hyperthermophilic bacterium Thermotoga maritima was cloned and functionally expressed in Escherichia coli. The purified recombinant enzyme is a homodimer with an apparent molecular mass of 80 kDa composed of 36-kDa subunits. Rate dependence (at 80 degrees C) on glucose and ATP followed Michaelis-Menten kinetics with apparent Km values of 1.0 and 0.36 mM, respectively; apparent Vmax values were about 370 U mg(-1). The enzyme was highly specific for glucose as phosphoryl acceptor. Besides glucose only 2-deoxyglucose was phosphorylated to some extent, whereas mannose and fructose were not used. With a temperature optimum of 93 degrees C the enzyme is the most thermoactive bacterial ATP-GLK described. PMID:14553940

Hansen, Thomas; Schönheit, Peter

2003-09-26

103

Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634  

PubMed Central

As a part of the Joint Center for Structural Genomics (JCSG) biological targets, the structures of soluble domains of membrane proteins from Thermotoga maritima were pursued. Here, we report the crystal structure of the soluble domain of TM1634, a putative membrane protein of 128 residues (15.1 kDa) and unknown function. The soluble domain of TM1634 is an ?-helical dimer that contains a single tetratrico peptide repeat (TPR) motif in each monomer where each motif is similar to that found in Tom20. The overall fold, however, is unique and a DALI search does not identify similar folds beyond the 38-residue TPR motif. Two different putative ligand binding sites, in which PEG200 and Co2+ were located, were identified using crystallography and NMR, respectively.

McCleverty, Clare J.; Columbus, Linda; Kreusch, Andreas; Lesley, Scott A.

2008-01-01

104

Whole-Genome Expression Profiling of Thermotoga maritima in Response to Growth on Sugars in a Chemostat  

PubMed Central

To provide data necessary to study catabolite-linked transcriptional networks in Thermotoga maritima, we used full-genome DNA microarray analysis of global transcriptional responses to growth on glucose, lactose, and maltose in a chemostat. A much larger number of genes changed expression in cells grown on lactose than on maltose, each relative to genes expressed in cells grown on glucose. Genes encoding putative oligopeptide transporters were often coregulated with adjacent glycosidase-encoding genes. Genes encoding enzymes catalyzing NADH oxidation were up-regulated on both lactose and maltose. Genes involved in iron and sulfur metabolism were differentially expressed in response to lactose. These data help define the sets of coregulated genes and suggest possible functions for their encoded products.

Nguyen, Tu N.; Ejaz, Arvin D.; Brancieri, Mark A.; Mikula, Amy M.; Nelson, Karen E.; Gill, Steven R.; Noll, Kenneth M.

2004-01-01

105

Identification and Characterization of a Novel Intracellular Alkaline ?-Amylase from the Hyperthermophilic Bacterium Thermotoga maritima MSB8  

PubMed Central

The gene for a novel ?-amylase, designated AmyC, from the hyperthermophilic bacterium Thermotoga maritima was cloned and heterologously overexpressed in Escherichia coli. The putative intracellular enzyme had no amino acid sequence similarity to glycoside hydrolase family (GHF) 13 ?-amylases, yet the range of substrate hydrolysis and the product profile clearly define the protein as an ?-amylase. Based on sequence similarity AmyC belongs to a subgroup within GHF 57. On the basis of amino acid sequence similarity, Glu185 and Asp349 could be identified as the catalytic residues of AmyC. Using a 60-min assay, the maximum hydrolytic activity of the purified enzyme, which was dithiothreitol dependent, was found to be at 90°C. AmyC displayed a remarkably high pH optimum of pH 8.5 and an unusual sensitivity towards both ATP and EDTA.

Ballschmiter, Meike; Futterer, Ole; Liebl, Wolfgang

2006-01-01

106

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

107

The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production.  

PubMed

The hyperthermophilic and anaerobic bacterium Thermotoga maritima ferments a wide variety of carbohydrates, producing acetate, CO(2), and H(2). Glucose is degraded through a classical Embden-Meyerhof pathway, and both NADH and reduced ferredoxin are generated. The oxidation of these electron carriers must be coupled to H(2) production, but the mechanism by which this occurs is unknown. The trimeric [FeFe]-type hydrogenase that was previously purified from T. maritima does not use either reduced ferredoxin or NADH as a sole electron donor. This problem has now been resolved by the demonstration that this hydrogenase requires the presence of both electron carriers for catalysis of H(2) production. The enzyme oxidizes NADH and ferredoxin simultaneously in an approximately 1:1 ratio and in a synergistic fashion to produce H(2). It is proposed that the enzyme represents a new class of bifurcating [FeFe] hydrogenase in which the exergonic oxidation of ferredoxin (midpoint potential, -453 mV) is used to drive the unfavorable oxidation of NADH (E(0)' = -320 mV) to produce H(2) (E(0)' = -420 mV). From genome sequence analysis, it is now clear that there are two major types of [FeFe] hydrogenases: the trimeric bifurcating enzyme and the more well-studied monomeric ferredoxin-dependent [FeFe] hydrogenase. Almost one-third of the known H(2)-producing anaerobes appear to contain homologs of the trimeric bifurcating enzyme, although many of them also harbor one or more homologs of the simpler ferredoxin-dependent hydrogenase. The discovery of the bifurcating hydrogenase gives a new perspective on our understanding of the bioenergetics and mechanism of H(2) production and of anaerobic metabolism in general. PMID:19411328

Schut, Gerrit J; Adams, Michael W W

2009-05-01

108

The elucidation of the structure of Thermotoga maritima peptidoglycan reveals two novel types of cross-link.  

PubMed

Thermotoga maritima is a Gram-negative, hyperthermophilic bacterium whose peptidoglycan contains comparable amounts of L- and D-lysine. We have determined the fine structure of this cell-wall polymer. The muropeptides resulting from the digestion of peptidoglycan by mutanolysin were separated by high-performance liquid chromatography and identified by amino acid analysis after acid hydrolysis, dinitrophenylation, enzymatic determination of the configuration of the chiral amino acids, and mass spectrometry. The high-performance liquid chromatography profile contained four main peaks, two monomers, and two dimers, plus a few minor peaks corresponding to anhydro forms. The first monomer was the d-lysine-containing disaccharide-tripeptide in which the D-Glu-D-Lys bond had the unusual gamma-->epsilon arrangement (GlcNAc-MurNAc-L-Ala-gamma-D-Glu-epsilon-D-Lys). The second monomer was the conventional disaccharide-tetrapeptide (GlcNAc-MurNAc-L-Ala-gamma-D-Glu-L-Lys-D-Ala). The first dimer contained a disaccharide-L-Ala as the acyl donor cross-linked to the alpha-amine of D-Lys in a tripeptide acceptor stem with the sequence of the first monomer. In the second dimer, donor and acceptor stems with the sequences of the second and first monomers, respectively, were connected by a D-Ala4-alpha-D-Lys3 cross-link. The cross-linking index was 10 with an average chain length of 30 disaccharide units. The structure of the peptidoglycan of T. maritima revealed for the first time the key role of D-Lys in peptidoglycan synthesis, both as a surrogate of L-Lys or meso-diaminopimelic acid at the third position of peptide stems and in the formation of novel cross-links of the L-Ala1(alpha-->alpha)D-Lys3 and D-Ala4(alpha-->alpha)D-Lys3 types. PMID:19542229

Boniface, Audrey; Parquet, Claudine; Arthur, Michel; Mengin-Lecreulx, Dominique; Blanot, Didier

2009-06-19

109

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

110

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

111

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

112

Batis maritima (Saltwort\\/Beachwort): a nutritious, halophytic, seed bearings, perennial shrub for cultivation and recovery of otherwise unproductive agricultural land affected by salinity  

Microsoft Academic Search

To date, this study constitutes the first scientific investigation into the elucidation of the chemical\\/physical and nutritional composition and characteristics of the seed of Batis maritima (Saltwort or Beachwort) a C3 perennial, dioecious, high seed bearing, halophytic succulent shrub commonly habitating salt-marshes and salt-flats worldwide. It was found that the small (<1.00 mm and <0.5 mg) lenticular shaped oil seed

Massimo F Marcone

2003-01-01

113

Determination of the sodium, potassium and chloride ion concentrations in the chloroplasts of the halophyte Suaeda maritima by non-aqueous cell fractionation  

Microsoft Academic Search

Summary Leaf material from the halophyteSuaeda maritima L. Dum. grown under both saline and non-saline conditions was fractionated under non-aqueous conditions in order to determine the ion content of various subcellular compartments. Fractions containing cell walls, nuclei and chloroplasts were successfully prepared and contents of DNA, chlorophyll, protein and Na+, K+, and Cl- determined. The cell wall fraction was not

Diana M. R. Harvey; T. J. Flowers

1978-01-01

114

The HU protein from Thermotoga maritima: recombinant expression, purification and physicochemical characterization of an extremely hyperthermophilic DNA-binding protein 1 1 Edited by T. Richmond  

Microsoft Academic Search

The histone-like protein TmHU from the hyperthermophilic eubacterium Thermotoga maritima was cloned, expressed to high levels in Escherichia coli, and purified to homogeneity by heat precipitation and cation exchange chromatography. CD spectroscopical studies with secondary structure analysis as well as comparative modeling demonstrate that the dimeric TmHU has a tertiary structure similar to other homologous HU proteins. The Tm of

Dirk Esser; Rainer Rudolph; Rainer Jaenicke; Gerald Böhm

1999-01-01

115

Identification of residues important for NAD + binding by the Thermotoga maritima ?-glucosidase AglA, a member of glycoside hydrolase family 4  

Microsoft Academic Search

The NAD+-requiring enzymes of glycoside hydrolase family 4 (GHF4) contain a region with a conserved Gly-XXX-Gly-Ser (GXGS) motif near their N-termini that is reminiscent of the fingerprint region of the Rossmann fold, a conserved structural motif of classical nicotinamide nucleotide-binding proteins. The function of this putative NAD+-binding motif in the ?-glucosidase AglA of Thermotoga maritima was probed by directed mutagenesis.

Carsten Raasch; Martin Armbrecht; Wolfgang Streit; Birte Höcker; Norbert Sträter; Wolfgang Liebl

2002-01-01

116

The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity 1 1 Edited by R. Huber  

Microsoft Academic Search

Maltosyltransferase (MTase) from the hyperthermophile Thermotoga maritima represents a novel maltodextrin glycosyltransferase acting on starch and malto-oligosaccharides. It catalyzes the transfer of maltosyl units from ?-1,4-linked glucans or malto-oligosaccharides to other ?-1,4-linked glucans, malto-oligosaccharides or glucose. It belongs to the glycoside hydrolase family 13, which represents a large group of (?\\/?)8 barrel proteins sharing a similar active site structure. The

Anna Roujeinikova; Carsten Raasch; Jacky Burke; Patrick J Baker; Wolfgang Liebl; David W Rice

2001-01-01

117

Thermostable continuous coupled assay for measuring glucose using glucokinase and glucose-6-phosphate dehydrogenase from the marine hyperthermophile Thermotoga maritima.  

PubMed

A novel, thermostable adaptation of the coupled-enzyme assay for monitoring glucose concentrations was developed for an optimal temperature of 85 degrees C. This is the first report of a thermostable glucostat from a marine hyperthermophile. The continuous assay, using glucokinase (Glk) and glucose-6-phosphate dehydrogenase (Gpd) from Thermotoga maritima, demonstrated robust activity over a range of temperatures (75-90 degrees C) and pH values (6.8- 8.5). Purified glucokinase had a monomeric molecular mass of 33.8kDa while that of glucose-6-phosphate dehydrogenase (D-glucose 6-phosphate:NADP oxidoreductase) was 57.5kDa. The high-temperature assay provided a method for directly assaying the activity of another hyperthermophilic enzyme, 1,4-beta-D-glucan glucohydrolase (GghA) from Thermotoga neapolitana. To provide a benchmark for protein-engineering experiments involving GghA, a three-enzyme continuous assay (performed at 85 degrees C), linking wild-type GghA, Glk, and Gpd, measured glucose produced from GghA's hydrolysis of cellobiose, one of GghA's secondary substrates. The assay established the kinetic behavior of wild-type GghA toward cellobiose and was used to screen for changes in the catalytic efficiency of variant GghA(s) induced by random mutagenesis. The assay's development will allow high-throughput screening of other thermostable glucose-producing enzymes, including those applicable to commercial biomass conversion. PMID:12814622

McCarthy, James K; O'Brien, Charles E; Eveleigh, Douglas E

2003-07-15

118

A novel alpha-D-galactosynthase from Thermotoga maritima converts beta-D-galactopyranosyl azide to alpha-galacto-oligosaccharides.  

PubMed

The large-scale production of oligosaccharides is a daunting task, hampering the study of the role of glycans in vivo and the testing of the efficacy of novel glycan-based drugs. Glycosynthases, mutated glycosidases that synthesize oligosaccharides in high yields, are becoming important chemo-enzymatic tools for the production of oligosaccharides. However, while ?-glycosynthase can be produced with a rather well-established technology, examples of ?-glycosynthases are thus far limited only to enzymes from glycoside hydrolase 29 (GH29), GH31 and GH95 families. ?-L-Fucosynthases from GH29 use convenient glycosyl azide derivatives as a strategic alternative to glycosyl fluoride donors. However, the general applicability of this method to other ?-glycosynthases is not trivial and remains to be confirmed. Here, ?-D-galactopyranosyl azide was converted to ?-galacto-oligosaccharides with good yields and high regioselectivity, catalyzed by a novel ?-galactosynthase based on the GH36 ?-galactosidase from the hyperthermophilic bacterium Thermotoga maritima. These results open a new avenue to the practical synthesis of biologically interesting ?-galacto-oligosaccharides and demonstrate more widespread use of ?-glycosyl-azide as donors, confirming their utility to expand the repertoire of glycosynthases. PMID:21084405

Cobucci-Ponzano, Beatrice; Zorzetti, Carmela; Strazzulli, Andrea; Carillo, Sara; Bedini, Emiliano; Corsaro, Maria Michela; Comfort, Donald A; Kelly, Robert M; Rossi, Mosè; Moracci, Marco

2010-11-17

119

Cytotoxic and antimicrobial constituents of the bark of Diospyros maritima collected in two geographical locations in Indonesia.  

PubMed

Bioactivity-directed fractionation of extracts of two Diospyros maritima bark samples from Indonesia,one collected at sea level in a beach forest in Java and the other collected at a slight elevation away from the sea shore on the island of Lombok, yielded a diverse set of secondary metabolites. The naphthoquinone plumbagin (1), although found in extracts of both specimens, constituted a much larger percentage of the former sample, which also yielded a series of plumbagin dimers, maritinone (2), chitranone (3), and zeylanone (4). The latter sample yielded a new naphthoquinone derivative, (4S)-shinanolone (5), and a new natural product coumarin, 7,8-dimethoxy-6-hydroxycoumarin (6), along with three other analogues of plumbagin, 2-methoxy-7-methyljuglone (7), 3-methoxy-7-methyljuglone (8), and 7-methyljuglone (9). The structures of compounds 5 and 6 were elaborated by physical, spectral, and chemical methods. All of the isolates were evaluated in both cytotoxicity and antimicrobial assays, and structure-activity relationships of these naphthoquinones are proposed. Plumbagin (1) and maritinone (2) were evaluated also for in vivo antitumor activity in the hollow fiber assay, but both were found to be inactive. PMID:15270571

Gu, Jian-Qiao; Graf, Tyler N; Lee, Dongho; Chai, Hee-Byung; Mi, Qiuwen; Kardono, Leonardus B S; Setyowati, Fransisca M; Ismail, Rachman; Riswan, Soedarsono; Farnsworth, Norman R; Cordell, Geoffrey A; Pezzuto, John M; Swanson, Steven M; Kroll, David J; Falkinham, Joseph O; Wall, Monroe E; Wani, Mansukh C; Kinghorn, A Douglas; Oberlies, Nicholas H

2004-07-01

120

In planta differential targeting analysis of Thermotoga maritima Cel5A and CBM6-engineered Cel5A for autohydrolysis.  

PubMed

The heterologous expression of glycosyl hydrolases in bioenergy crops can improve the lignocellulosic conversion process for ethanol production. We attempted to obtain high-level expression of an intact Thermotoga maritima endoglucanase, Cel5A, and CBM6-engineered Cel5A in transgenic tobacco plants for the mass production and autohydrolysis of endoglucanase. Cel5A expression was targeted to different subcellular compartments, namely, the cytosol, apoplast, and chloroplast, using the native form of the pathogenesis-related protein 1a (PR1a) and Rubisco activase (RA) transit peptides. Cel5A transgenic tobacco plants with the chloroplast transit peptide showed the highest average endoglucanase activity and protein accumulation up to 4.5% total soluble protein. Cel5A-CBM6 was targeted to the chloroplast and accumulated up to 5.2% total soluble protein. In terms of the direct conversion of plant tissue into free sugar, the Cel5A-CBM6 transgenic plant was 33% more efficient than the Cel5A transgenic plant. The protein stability of Cel5A and Cel5A-CBM6 in lyophilized leaf material is an additional advantage in the bioconversion process. PMID:21152978

Mahadevan, Shobana Arumugam; Wi, Seung Gon; Kim, Yeon Ok; Lee, Kwang Ho; Bae, Hyeun-Jong

2010-12-09

121

Amino acid transport in thermophiles: characterization of an arginine-binding protein from Thermotoga maritima. 3. Conformational dynamics and stability.  

PubMed

Arginine-binding protein from Thermotoga maritima (TmArgBP) is a 27.7 kDa protein possessing the typical two domain structure of the periplasmic binding protein family. The protein is characterized by high specificity and affinity for binding a single molecule of l-arginine. In this work, the effect of temperature and/or guanidine hydrochloride on structure and stability of the protein in the absence and in the presence of l-arginine has been investigated by differential scanning calorimetry, far-UV circular dichroism and intrinsic tryptophan phosphorescence and fluorescence. The results revealed that TmArgBP undergoes an irreversible one-step thermal unfolding process in a cooperative mode. The TmArgBP melting temperature was recorded at 115 °C. The presence of l-arginine did not change the protein secondary structure content as well as the intrinsic phosphorescence and fluorescence protein properties, even if it increases the structural stability of the protein. The obtained results are discussed in combination with a detailed inspection of the three-dimensional structure of the protein. PMID:23232322

Ausili, A; Pennacchio, A; Staiano, M; Dattelbaum, J D; Fessas, D; Schiraldi, A; D'Auria, S

2012-11-29

122

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

123

Analgesic effects and mechanisms of anti-inflammation of taraxeren-3-one from Diospyros maritima in mice.  

PubMed

This study investigated the analgesic effects of taraxeren-3-one, which is an ingredient from Diospyros maritima (DM), using the models of acetic acid-induced writhing response and the formalin test, and its anti-inflammatory effects using the model of ?-carrageenan (Carr)-induced paw edema. Treatment of male ICR mice with taraxeren-3-one inhibited the numbers of writhing response and formalin-induced pain in the late phase, significantly. In the anti-inflammatory test, taraxeren-3-one decreased paw edema at 4 and 5 h after Carr administration and increased the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and glutathione (GSH) in the liver tissue at 5 h after Carr injection. Taraxeren-3-one affects malondialdehyde (MDA), nitric oxide (NO), and tumor necrosis factor-? (TNF-?) levels from both the edema paw and serum at 5 h after Carr injection. Western blotting revealed that taraxeren-3-one decreased Carr-induced inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) expressions. These anti-inflammatory mechanisms of taraxeren-3-one might be related to the decrease in the level of MDA in the edema paw via increasing the activities of SOD, CAT, GPx, and GSH in the liver. Also, taraxeren-3-one could affect the production of NO and TNF-? and, therefore, affect the anti-inflammatory effects. PMID:21732622

Chang, Tien-Ning; Huang, Shyh-Shyun; Chang, Yuan-Shiun; Chang, Chi-I; Yang, Hsin-Ling; Deng, Jeng-Shyan; Kuo, Yueh-Hsiung; Huang, Guan-Jhong

2011-08-05

124

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

125

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

126

Reaction kinetic pathway of the recombinant octaprenyl pyrophosphate synthase from Thermotoga maritima: how is it different from that of the mesophilic enzyme.  

PubMed

Octaprenyl pyrophosphate synthase (OPPs) catalyzes the chain elongation of farnesyl pyrophosphate (FPP) via consecutive condensation reactions with five molecules of isopentenyl pyrophosphate (IPP) to generate all-trans C40-octaprenyl pyrophosphate. The polymer forms the side chain of ubiquinone that is involved in electron transport system to produce ATP. Our previous study has demonstrated that Escherichia coli OPPs catalyzes IPP condensation with a rate of 2 s(-1) but product release limits the steady-state rate at 0.02 s(-1) [Biochim. Biophys. Acta 1594 (2002) 64]. In the present studies, a putative gene encoding for OPPs from Thermotoga maritima, an anaerobic and thermophilic bacterium, was expressed, purified, and its kinetic pathway was determined. The enzyme activity at 25 degrees C was 0.005 s(-1) under steady-state condition and was exponentially increased with elevated temperature. In contrast to E. coli OPPs, IPP condensation rather than product release was rate limiting in enzyme reaction. The product of chain elongation catalyzed by T. maritima OPPs was C40 and the rate of its conversion to C45 was negligible. Under single-turnover condition with 10 microM OPPs-FPP complex and 1 microM IPP, only the C20 was formed rather than C20-C40 observed for E. coli enzyme. Together, our data suggest that the thermophilic OPPs from T. maritima has lower enzyme activity at 25 degrees C, higher product specificity, higher thermal stability and lower structural flexibility than its mesophilic counterpart from E. coli. PMID:12479413

Kuo, Tun-Hsun; Liang, Po-Huang

2002-09-23

127

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

2013-08-23

128

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

PubMed Central

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

Kletzin, A; Adams, M W

1996-01-01

129

Crystallization and preliminary X-ray crystallographic analysis of CheW from Thermotoga maritima: a coupling protein of CheA and the chemotaxis receptor  

PubMed Central

The CheW protein plays a key role in bacterial chemotaxis signal transduction by coupling CheA to chemotaxis receptors. CheW from Thermotoga maritima has been overexpressed in Escherichia coli and crystallized at 298?K using ammonium sulfate as a salt precipitant. X-ray diffraction data have been collected to 3.10?Å resolution at 100?K using synchrotron radiation. The crystal belonged to space group P63, with unit-cell parameters a = b = 61.265, c = 361.045?Å. The asymmetric unit may contain four to six CheW molecules.

Park, SangYoun; Crane, Brian R.

2011-01-01

130

Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination.  

PubMed

Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to generate C40 octaprenyl pyrophosphate (OPP), which constitutes the side chain of bacterial ubiquinone or menaquinone. In this study, the first structure of long chain C40-OPPs from Thermotoga maritima has been determined to 2.28-A resolution. OPPs is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity. An elongated hydrophobic tunnel between D and F alpha-helices contains two DDXXD motifs on the top for substrate binding and is occupied at the bottom with two large residues Phe-52 and Phe-132. The products of the mutant F132A OPPs are predominantly C50, longer than the C40 synthesized by the wild-type and F52A mutant OPPs, suggesting that Phe-132 is the key residue for determining the product chain length. Ala-76 and Ser-77 located close to the FPP binding site and Val-73 positioned further down the tunnel were individually mutated to larger amino acids. A76Y and S77F mainly produce C20 indicating that the mutated large residues in the vicinity of the FPP site limit the substrate chain elongation. Ala-76 is the fifth amino acid upstream from the first DDXXD motif on helix D of OPPs, and its corresponding amino acid in FPPs is Tyr. In contrast, V73Y mutation led to additional accumulation of C30 intermediate. The new structure of the trans-type OPPs, together with the recently determined cis-type UPPs, significantly extends our understanding on the biosynthesis of long chain polyprenyl molecules. PMID:14617622

Guo, Rey-Ting; Kuo, Chih-Jung; Chou, Chia-Cheng; Ko, Tzu-Ping; Shr, Hui-Lin; Liang, Po-Huang; Wang, Andrew H-J

2003-11-15

131

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

132

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

PubMed Central

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

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

2008-01-01

133

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

2012-07-21

134

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

135

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

PubMed

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

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

2000-11-01

136

The characterization of Thermotoga maritima ferritin reveals an unusual subunit dissociation behavior and efficient DNA protection from iron-mediated oxidative stress.  

PubMed

Ferritin from the hyperthermophilic anaerobe Thermotoga maritima, a bacterium of ancient phylogenetic origin, is structurally similar to known bacterial and eukaryotic ferritins: 24 identical subunits assemble into a shell having octahedral symmetry and a Mr of about 460 kDa. T. maritima ferritin (TmFtn), purified to homogeneity as a recombinant protein, contains approximately 2-3 iron atoms and can incorporate efficiently up to 3,500 atoms in the form of a ferric oxy-hydroxide mineral at 80°C, the optimal growth temperature of the bacterium. The 24-mer unexpectedly dissociates reversibly into dimers at low ionic strengths. In turn, dimers re-associate into the native 24-mer assembly at high protein concentrations and upon incorporation of iron micelles containing at least 500 Fe(III). TmFtn uses O(2) as efficient iron oxidant. The reaction stoichiometry is 3-4 O(2):Fe(II) as in all bacterial ferritins. Accordingly no H(2)O(2) is released into solution, a feature reflected in the in vitro ability of TmFtn to reduce significantly iron-mediated oxidative damage to DNA at 80°C. A similar TmFtn-mediated ROS detoxifying role likely occurs in the bacterium which lacks the SOD/catalase defense systems of the aerobic world. PMID:21487935

Ceci, Pierpaolo; Forte, Elena; Di Cecca, Gisa; Fornara, Manuela; Chiancone, Emilia

2011-04-13

137

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

PubMed Central

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

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

2002-01-01

138

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

PubMed Central

Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6422, with unit-cell parameters a = b = 148.49, c = 106.96?Å, ? = 120.0°. Assuming the presence of two molecules in the asymmetric unit, the calculated V M is 2.84?Å3?Da?1, which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3?Å resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan.

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

2008-01-01

139

Crystallization and preliminary X-ray crystallographic analysis of Thermotoga maritima CheA P3-P4-P5 domains in complex with CheW  

PubMed Central

The CheA–CheW complex plays a key role in bacterial chemotaxis signal transduction by initiating phosphotransfer to response regulators via coupling to the chemoreceptors. CheA (P3-P4-P5 domains) and CheW from Thermotoga maritima were overexpressed in Escherichia coli and crystallized as a complex at 298?K using ammonium dihydrogen phosphate as a precipitant. X-ray diffraction data were collected to ?8?Å resolution at 100?K using synchrotron radiation. The crystal belonged to space group I222 or I212121, with unit-cell parameters a = 184.2, b = 286.4, c = 327.7?Å. The asymmetric unit may contain six to ten CheA–CheW molecules.

Park, SangYoun; Kim, Keon Young; Kim, Sunmin; Crane, Brian R.

2012-01-01

140

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

141

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

PubMed

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

Nadwodnik, Jan; Lohaus, Gertrud

2008-01-09

142

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

PubMed

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

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

2008-06-13

143

Enhancement of the Alcoholytic Activity of ?-Amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by Site-Directed Mutagenesis?  

PubMed Central

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

Damian-Almazo, Juanita Yazmin; Moreno, Alina; Lopez-Munguia, Agustin; Soberon, Xavier; Gonzalez-Munoz, Fernando; Saab-Rincon, Gloria

2008-01-01

144

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

145

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

PubMed

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, a strong amylase and glucosidase inhibitor, to acarviosine and glucose. Also, TMG initially hydrolyzes p-nitrophenyl-alpha-pentaoside to give maltopentaose and p-nitrophenol, implying that the enzyme specifically cleaves a glucose unit from the reducing end of maltooligosaccharides unlike to other glucosidases. Since its enzymatic activity is negligible if alpha-methylglucoside is present in the reducing end, the type of the residue at the reducing end of the substrate is important for the TMG activity. These results support the fact that TMG is a novel exo-acting glucosidase possessing the characteristics of both CD-/pullulan hydrolyzing enzyme and alpha-glucosidase. PMID:12127967

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

2002-07-26

146

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

147

Effect of dietary supplementation with Suaeda maritima on blood physiology, innate immune response, and disease resistance in olive flounder against Miamiensis avidus.  

PubMed

The effect of Suaeda maritima enriched diet on blood physiology, innate immune response, and disease resistance in olive flounder Paralichythys olivaceus against Miamiensis avidus on weeks 1, 2, and 4 was investigated. Feeding with any enriched diet and then challenging with M. avidus significantly increased white blood cells (WBC) on weeks 2 and 4; the red blood cells (RBC) significantly increased with 0.1% and 1.0% enriched diets on week 4. The hemoglobin (Hb) and hematocrit (Ht) levels significantly increased when fed with 0.1% and 1.0% supplementation diets on weeks 2 and 4. The mean corpuscular volume (MCV) did not significantly vary with any diet and time; however the mean corpuscular hemoglobin (MCH) and mean corpuscular hemoglobin concentration (MCHC) significantly increased with 0.1% and 1.0% supplementation diets on weeks 2 and 4. The leukocytes such as lymphocytes (Lym), monocytes (Mon), neutrophils (Neu) and biochemical parameters such as total protein (TP), glucose (GLU), and calcium (CAL) levels significantly increased in 0.1% and 1.0% supplementation diet fed groups on weeks 2 and 4. The serum lysozyme activity was significantly enhanced in 0.1% and 1.0% supplementation diet fed groups from weeks 1 to 4 when compared to the control (0% herbal extract enriched diet). The scuticocidal activity and respiratory burst activity were significantly enhanced when fish were fed with 0.1% and 1.0% supplementation diets from weeks 2 and 4. The protective effect in terms of cumulative mortality (50% and 40%) was low in groups on being fed with 0.1% and 1.0% supplemented diet. Therefore the present study suggested that 0.1% and 1.0% S. maritime-supplemented diets protect the hematological and biochemical parameters, improving the innate immunity, affording protection disease from M. avidus infection in olive flounder. PMID:22490817

Harikrishnan, Ramasamy; Kim, Ju-Sang; Kim, Man-Chul; Dharaneedharan, Subramanian; Kim, Dong-Hwi; Hong, Seung-Hyun; Song, Chang-Young; Balasundaram, Chellam; Heo, Moon-Soo

2012-04-03

148

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

149

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

150

Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov.  

PubMed

A novel thermophilic, chemoheterotrophic, Gram-negative-staining, multicellular filamentous bacterium, designated strain 110S(T), was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequences nested strain 110S(T) in a novel class-level clone cluster of the phylum 'Chloroflexi'. The isolate grows by dissimilatory iron- and nitrate-reduction under anaerobic conditions, which is the first report of these abilities in the phylum 'Chloroflexi'. The organism is capable of growth with oxygen, ferric iron and nitrate as a possible electron acceptor, has a wide range of growth temperatures, and tolerates higher NaCl concentrations for growth compared to the other isolates in the phylum. Using phenotypic and phylogenetic data, strain 110S(T) (= JCM 17282(T) = NBRC 107679(T) = DSM 23922(T) = KCTC 23289(T) = ATCC BAA-2145(T)) is proposed as the type strain of a novel species in a new genus, Ardenticatena maritima gen. nov., sp. nov. In addition, as strain 110S(T) apparently constitutes a new class of the phylum 'Chloroflexi' with other related uncultivated clone sequences, we propose Ardenticatenia classis nov. and the subordinate taxa Ardenticatenales ord. nov. and Ardenticatenaceae fam. nov. PMID:23378114

Kawaichi, Satoshi; Ito, Norihiro; Kamikawa, Ryoma; Sugawara, Tatsuya; Yoshida, Takashi; Sako, Yoshihiko

2013-02-01

151

Kinetic and mechanistic analyses of new classes of inhibitors of two-component signal transduction systems using a coupled assay containing HpkA-DrrA from Thermotoga maritima.  

PubMed

Two-component signal transduction systems (TCSs) play fundamental roles in bacterial survival and pathogenesis and have been proposed as targets for the development of novel classes of antibiotics. A new coupled assay was developed and applied to analyse the kinetic mechanisms of three new kinds of inhibitors of TCS function. The assay exploits the biochemical properties of the cognate HpkA-DrrA histidine kinase-response regulator pair from Thermotoga maritima and allows multiple turnovers of HpkA, linear formation of phosphorylated DrrA, and Michaelis-Menten analysis of inhibitors. The assay was validated in several ways, including confirmation of competitive inhibition by adenosine 5'-beta,gamma-imidotriphosphate (AMP-PNP). The coupled assay, autophosphorylation and chemical cross-linking were used to determine the mechanisms by which several compounds inhibit TCS function. A cyanoacetoacetamide showed non-competitive inhibition with respect to ATP concentration in the coupled assay. The cyanoacetoacetamide also inhibited autophosphorylation of histidine kinases from other bacteria, indicating that the coupled assay could detect general inhibitors of histidine kinase function. Inhibition of HpkA autophosphorylation by this compound was probably caused by aggregation of HpkA, consistent with a previous model for other hydrophobic compounds. In contrast, ethodin was a potent inhibitor of the combined assay, did not inhibit HpkA autophosphorylation, but still led to aggregation of HpkA. These data suggest that ethodin bound to the HpkA kinase and inhibited transfer of the phosphoryl group to DrrA. A peptide corresponding to the phosphorylation site of DrrA appeared to inhibit TCS function by a mechanism similar to that of ethodin, except that autophosphorylation was inhibited at high peptide concentrations. The latter mechanism of inhibition of TCS function is unusual and its analysis demonstrates the utility of these approaches to the kinetic analyses of additional new classes of inhibitors of TCS function. PMID:15073298

Foster, J Estelle; Sheng, Qin; McClain, Jonathan R; Bures, Mark; Nicas, Thalia I; Henry, Kenneth; Winkler, Malcolm E; Gilmour, Raymond

2004-04-01

152

Effects of bisphenol A in the ring-legged earwig, Euborellia annulipes  

Microsoft Academic Search

Bisphenol A is a known endocrine disruptor in vertebrates that mimics the action of estrogens by interacting with hormone\\u000a receptors. It also affects reproduction and development in many invertebrate animals, though mechanisms of action are unclear.\\u000a Terrestrial insects, despite their abundance and profound ecological significance, have been largely overlooked as a group\\u000a that might be affected by vertebrate endocrine disrupting

Susan M. RankinEvan; Evan M. Grosjean

2010-01-01

153

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

Federal Register 2010, 2011, 2012, 2013

...including chemical, physical, spatial, and temporal factors) as all the rest of the world's...increased substrate homogeneity, increased temporal water velocity (increased water flow...Disease or Predation The geographic isolation of the Hawaiian Islands restricted...

2010-06-24

154

Bredin-Archbold-Smithsonian Biological Survey of Dominica: The Dermaptera (Earwigs) of Dominica. Smithsonian Contributions to Zoology, Number 63.  

National Technical Information Service (NTIS)

An account of the known Dermaptera of Dominica is presented, largely based on material collected during the Bredin-Archbold-Smithsonian Biological Survey of Dominica. This material is now in the United States National Museum. Of the nine species of the or...

A. Brindle

1971-01-01

155

Effects of the concurrent exclusion of ants and earwigs on aphid abundance in an organic citrus grove  

Microsoft Academic Search

Based on the well-known mutualism between ants (Hymenoptera: Formicidae) and aphids (Homoptera: Aphididae), we conducted a\\u000a five-year experiment of ant-exclusion from the canopies of citrus trees as a possible method of biological control of aphids.\\u000a However, our results showed that the exclusion of ants from the canopies increased, instead of reducing, aphid abundance.\\u000a To explain this unexpected result, we reasoned

Josep Piñol; Xavier Espadaler; Núria Cañellas; Nicolás Pérez

2009-01-01

156

Magnetic imaging of a submerged Roman harbour, Caesarea Maritima, Israel  

NASA Astrophysics Data System (ADS)

The harbour built by King Herod's engineers at Caesarea represented a major advance in Roman harbour construction that incorporated the use of large (390 m^3), form-filled hydraulic concrete blocks to build an extensive foundation for the harbour moles and breakwater barriers. Marine geophysical surveys were recently conducted across the submerged harbour in an attempt to map the configuration of the buried concrete foundation. A total of 107 line km of high-resolution marine magnetic surveys (nominal 15 m line separations) and bathymetry data were acquired over a 1 km^2 area of the submerged harbour using an Overhauser marine magnetometer, integrated DGPS and single-beam (200 KHz) echosounder. The feasibility of magnetic detection of the concrete was established before the survey by magnetic susceptibility testing of concrete core samples. All concrete samples contained appreciable amounts of fe-oxide-rich volcanic ash ('pozzolana') and showed uniformly high susceptibility values (k > 10^-^4 cgs) when compared to harbour bottom sediments and building stones (k < 10 ^-^6 cgs). Magnetic surveys of the harbour identify a localized increase in magnetic intensity (ca. 1-7 nT) that is attributed to the presence of hydraulic concrete within the buried harbour structure. The mapped anomaly patterns are distinctly rectilinear, indicating that the concrete foundation was laid out in header fashion in dominantly N-S and W-E trending segments. Magnetic lows identify 'cells' within the concrete foundation framework that were likely filled with harbour sediments prior to construction of the harbour moles and quays.

Boyce, J. I.; Reinhardt, E. G.; Raban, A.; Pozza, M. R.

2003-04-01

157

Millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from Thermotoga maritima.  

PubMed

IGPS is a 51 kDa heterodimeric enzyme comprised of two proteins, HisH and HisF, that catalyze the hydrolysis of glutamine to produce NH(3) in the HisH active site and the cyclization of ammonia with N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) in HisF to produce imidazole glycerol phosphate (IGP) and 5-aminoimidazole-4-carboxamide ribotide (AICAR). Binding of PRFAR and IGP stimulates glutaminase activity in the HisH enzyme over 5,000 and 100-fold, respectively, despite the active sites being >25 A apart. The details of this long-range protein communication process were investigated by solution NMR spectroscopy and CPMG relaxation dispersion experiments. Formation of the heterodimer enzyme results in a reduction in millisecond motions in HisF that extend throughout the protein. Binding of lGP results in an increase in protein-wide millisecond dynamics evidenced as severe NMR line broadening and elevated R (ex) values. Together, these data demonstrate a grouping of flexible residues that link the HisF active site with the protein interface to which HisH binds and provide a model for the path of communication between the IGPS active sites. PMID:19565337

Lipchock, James; Loria, J Patrick

2009-06-30

158

Outstanding appearance of Ruppia maritima along Baja California Sur, México and its influence in trophic networks  

Microsoft Academic Search

Human impact and global warming are driving major modifications to the world’s ecosystems, the coastal zone being one of the\\u000a most damaged. Seagrass meadows constitute coastal communities that have experienced great losses worldwide. The dominant seagrass\\u000a in the meadows of the Pacific coast of North America is Zostera marina. There is evidence that Z. marina has been replaced in some

Jorge Lopez-Calderon; Rafael Riosmena-Rodríguez; Juan M. Rodríguez-Baron; Javier Carrión-Cortez; Jorge Torre; Alf Meling-López; Gustavo Hinojosa-Arango; Gustavo Hernández-Carmona; Jaqueline García-Hernández

2010-01-01

159

Cloning, expression, purification and crystallization of the Rho transcription termination factor from Thermotoga maritima  

Microsoft Academic Search

Rho is an essential ATP-dependant homohexameric helicase that is found in the vast majority of bacterial species. It is responsible for transcription termination at factor-dependent terminators. Rho binds to a specific region of the newly-synthesised mRNA and translocates along the chain until it reaches and disassembles the transcription complex. Basically, two crystallographic structures of Rho hexamer from Escherichia coli have

Albert Canals; Miquel Coll

2009-01-01

160

Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C  

Microsoft Academic Search

A novel type of bacterium has been isolated from various geothermally heated locales on the sea floor. The organisms are strictly anaerobic, rod-shaped, fermentative, extremely thermophilic and grow between 55 and 90°C with an optimum of around 80°C. Cells show a unique sheath-like structure and monotrichous flagellation. By 16S rRNA sequencing they clearly belong to the eubacteria, although no close

Robert Huber; Thomas A. Langworthy; Helmut König; Michael Thomm; Carl R. Woese; Uwe B. Sleytr; Karl O. Stetter

1986-01-01

161

A Highly Active Protein Repair Enzyme from an Extreme Thermophile: The l-Isoaspartyl Methyltransferase from Thermotoga maritima  

Microsoft Academic Search

We show that the open reading frame in theThermotoga maritimagenome tentatively identified as thepcmgene (R. V. Swansonet al., J. Bacteriol.178, 484–489, 1996) does indeed encode a proteinl-isoaspartate (d-aspartate)O-methyltransferase (EC 2.1.1.77) and that this protein repair enzyme displays several novel features. We expressed the 317 amino acid pcm gene product of this thermophilic bacterium inEscherichia colias a fusion protein with an

Jeffrey K. Ichikawa; Steven Clarke

1998-01-01

162

Arabidopsis thaliana Rubisco small subunit transit peptide increases the accumulation of Thermotoga maritima endoglucanase Cel5A in chloroplasts of transgenic tobacco plants.  

PubMed

Over the past decade various approaches have been used to increase the expression level of recombinant proteins in plants. One successful approach has been to target proteins to specific subcellular sites/compartments of plant cells, such as the chloroplast. In the study reported here, hyperthermostable endoglucanase Cel5A was targeted into the chloroplasts of tobacco plants via the N-terminal transit peptide of nuclear-encoded plastid proteins. The expression levels of Cel5A transgenic lines were then determined using three distinct transit peptides, namely, the light-harvesting chlorophyll a/b-binding protein (CAB), Rubisco small subunit (RS), and Rubisco activase (RA). RS:Cel5A transgenic lines produced highly stable active enzymes, and the protein accumulation of these transgenic lines was up to 5.2% of the total soluble protein in the crude leaf extract, remaining stable throughout the life cycle of the tobacco plant. Transmission election microscopy analysis showed that efficient targeting of Cel5A protein was under the control of the transit peptide. PMID:19851881

Kim, Suyeon; Lee, Dae-Seok; Choi, In Seong; Ahn, Sung-Ju; Kim, Yong-Hwan; Bae, Hyeun-Jong

2009-10-23

163

Biosynthesis of animal and plant bufadienolides. Parallel experiments with pregn-5-en-3-ß-ol-20-one-20- 14 C in Scilla maritima and Bufo paracnemis  

Microsoft Academic Search

Zusammenfassung Pregnenolon-20-14C wird von roten Meerzwiebeln als Vorstufe für herzwirksame Glykoside verwendet, dagegen kannBufo paracnemis diese Produkte, subkutan appliziert, nicht in die üblichen Krötengifte überführen.

Ana M. Porto; E. G. Gros

1970-01-01

164

Role of the phenylalanine 260 residue in defining product profile and alcoholytic activity of the ? -amylase AmyA from Thermotoga maritima  

Microsoft Academic Search

Some ?-amylases besides catalyzing the hydrolysis of ?-1,4 glycosidic bonds in starch are also capable of carrying out some transglycosylation activity. The importance of aromatic\\u000a residues near the catalytic site in determining the ratio of these two competing activities has been remarked in the past.\\u000a In the present work we investigated the role of residue 260 in the product profile

Juanita Y. Damián-Almazo; Agustin López-Munguía; Xavier Soberón-Mainero; Gloria Saab-Rincón

2008-01-01

165

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

166

Effect of Azadirachtin on vitellogenesis of Labidura riparia (Insect Dermaptera)  

Microsoft Academic Search

This study investigates the effects of the insect growth regulator Azadirachtin (AZA) on the ultrastructure of ovaries and fat body of the earwig Labidura riparia. Ovarian development is severely reduced in AZA-injected females in a dose-dependent manner. Follicles exhibit degenerative changes, separation of follicle cells from the oocyte, and lack of pinocytotic vesicles as of yolk spheres in cortical ooplasm.

F. Sayah; C. Fayet; M. Idaomar; A. Karlinsky

1996-01-01

167

Geographical Distribution of the Dermaptera and the Continental Drift Hypothesis  

Microsoft Academic Search

THE Dermaptera (earwigs) are a group of insects which live in litter, under bark, in soil, compact vegetation, hollow plant stems and have retiring habits. Many of the primitive subfamilies are wingless, and only a few of the winged species are known to fly. Popham and Brindle1,2 have given details of the geographical distribution of each species. The Dermaptera seem

E. J. Popham; B. F. J. Manly

1969-01-01

168

Behaviour in Lizards  

Microsoft Academic Search

WE kept here this summer two common lizards (Lacerta vivipara), one a very active male, the other a female which was much less active because she was soon to give birth to a litter of young. One day I turned a batch of earwigs into the lizards' bowl, and a vigorous hunt ensued. When a lizard seizes any sort of

E. Leonard Gill

1921-01-01

169

Mulch and Moisture Pests and Occasional Invaders  

NSDL National Science Digital Library

Tutorials on houshold pests. Each tutorial has 50 questions; incorrect answers lead to additional information. Covers booklice, plaster beetles, centipedes, millipedes, amphipods, earwigs, pillbugs, sowbugs, fungus gnats, springtails, silverfish, scorpions, thrips, crickets and plaster bagworm. Requires Windows. $15. Easy to use once loaded on hard drive. Some of the pests depicted are largely restricted to the Deep South. Part number SW 161.

0002-11-30

170

Comparative costs of promiscuity and monogramy: A test of reproductive effort theory  

Microsoft Academic Search

Sharp-tailed sparrows Ammospiza caudacuta and seaside sparrows A. maritima co-occupy salt marshes in northeastern North America and are ecologically similar. Female caudacuta care for their young unaided, in comparison to martima's dual parental behavior. The annual reproductive effort of female caudacuta is higher than that of female maritima. Under reproductive effort theory, as both species' reproductive output is the same,

William Post; Jon S. Greenlaw

1982-01-01

171

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

2013-02-13

172

MONITOR FOR FRUIT-EATING INSECTS TO PROTECT BERRY HARVEST  

Microsoft Academic Search

Just as berry fruits approach maturity and are ready to pick, there are fruit-eating insects that can re- duce the harvestable crop and contaminate the berry product. Some of the common fruit-eating insects ob- served in Utah include the stink bug, lygus bug, earwig, grasshopper, and several species of fruit-eating wasps. These insects suck or chew into the individual drupelets

Diane Alston; USU Entomologist

173

76 FR 2114 - Notice of Agreements Filed  

Federal Register 2010, 2011, 2012, 2013

...Ltd.; Mitsui O.S.K. Lines, Ltd.; Montemar Maritima, S.A.; Norasia Container Lines Limited; Senator Lines GmbH; Wan Hai Lines Ltd.; Yangming Marine Transport Corp.; Zim Integrated Shipping Services, Ltd. Filing Party: Eric C....

2011-01-12

174

Seasonal Patterns of CO2 and Water Vapor Exchange of Three Salt Marsh Succulents.  

National Technical Information Service (NTIS)

Diurnal carbon dioxide exchange patterns of three salt marsh succulents, Borrichia frutescens, Batis maritima and Salicornia virginica, were determined on a seasonal basis in the marsh at Sapelo Island, Georgia. Year-round photosynthetic activity was obse...

A. E. Antlfinger E. L. Dunn

1979-01-01

175

Effect of some insecticides on acetylcholinesterase from beneficial insects: Coccinella septempunctata, Chrysoperla carnea and Forficula auricularia.  

PubMed

In vitro enzyme activity of head homogenates from adults of Coccinella septempunctata, Chrysoperla carnea and Forficula auricularia originated from different habitats in Belgium (wheat, barley, rye, set-aside fields and experimental orchard, uncultivated area) were investigated in presence of insecticide active ingredients. Using the procedure of Ellman, I50 (M) and Ki (M-1 min-1) values were established. The beneficial insects showed the least susceptibility to diazinon and the differences between their measured values were not remarkable. Paraoxon was extremely toxic to the AChE of F. auricularia but Ch. carnea and C. septempunctata were similarly more tolerant to this organophosphate. In the case of malaoxon earwig and green lacewing AChEs were much more sensitive than AChE of the ladybird beetle. Measuring the carbaryl inhibition, F. auricularia was the least tolerant. The susceptibility of ladybird AChE differed highly from that of both species. According to the measured values, the green lacewing was less tolerant than the ladybird beetle but more tolerant compared with the common earwig. Summarizing our biochemical results, the order of susceptibility of beneficial insects to insecticides investigated was the following F. auricularia > Ch. carnea > C. septempunctata. PMID:12696436

Bozsik, Andras; Francis, Frédéric; Gaspar, Charles; Haubruge, Eric

2002-01-01

176

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

177

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

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. PMID:9882656

Gribaldo, S; Lumia, V; Creti, R; Conway de Macario, E; Sanangelantoni, A; Cammarano, P

1999-01-01

178

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

179

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

PubMed Central

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.; DiPippo, Jonathan L.; Bruce, David C.; Detter, Christopher; Tapia, Roxanne; Han, Shunsheng; Saunders, Elizabeth; Goodwin, Lynne A.; Han, James; Woyke, Tanja; Pitluck, Sam; Pennacchio, Len; Nolan, Matthew; Mikhailova, Natalia; Lykidis, Athanasios; Land, Miriam L.; Brettin, Thomas; Stetter, Karl O.; Nelson, Karen E.; Gogarten, J. Peter; Noll, Kenneth M.

2011-01-01

180

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

181

Photoprotective role of inflorescence and UV-radiation effects on pollen viability of different freshwater plants  

Microsoft Academic Search

.  The possible protective role against ultraviolet (UV) radiation of the sheathing leaves that wrap the young flowers of Ruppia drepanensis and Althenia orientalis was assessed. The effects of UV radiation on the viability of their pollen grains and those of R. maritima were also analysed. The absorption of the sheathing leaves of R. depranensis for visible and UV wavelengths was

Rafael M. Conde-Álvarez; Félix L. Figueroa; Elena Bañares-España; José M. Nieto-Caldera

2008-01-01

182

Why don't female purple sandpipers perform brood care? A removal experiment  

Microsoft Academic Search

In most monogamous sandpiper species, females share parental care but leave the brood earlier than males, a feature unusual among birds in general. In the purple sandpiper (Calidris maritima), females almost always leave the brood at hatching and never share brood care. Males perform uniparental brood care from hatching until well after fledging. In this paper, we report the results

Elin P. Pierce; Lewis W. Oring; Eivin Røskaft; Jan T. Lifjeld

2010-01-01

183

Microbial Modification of Red Squill as a Rodenticide.  

National Technical Information Service (NTIS)

The purpose of the study was to develop a basis for a new palatable, lethal, and emetic red squill rodenticide. Red squill, Urginea maritima (Liliaceae) is an onion-like plant whose bulbs and roots contain bufadienolides such as scilliroside, a bitter gly...

A. J. Verbiscar T. F. Banigan R. E. Marsh A. D. Tunberg

1985-01-01

184

Increasing vineyard floral resources may not enhance localised biological control of the leafroller Epiphyas postvittana (Lepidoptera: Tortricidae) by Dolichogenidea spp. (Hymenoptera: Braconidae) parasitoids  

Microsoft Academic Search

In agroecosystems, the efficacy of biological control exerted by many parasitoids is predicted to be enhanced where the availability of floral resources is increased. Such resources may attract parasitoids and enhance their longevity and fecundity. In Hawke's Bay, New Zealand, this prediction was tested by adding varying quantities of potted flowering alyssum (Lobularia maritima) (Brassicaceae) to plots containing apple plants

V. A. Bell; R. J. Brightwell; P. J. Lester

2006-01-01

185

Submerged versus air-exposed intertidal macrophyte productivity: from physiological to community-level assessments  

Microsoft Academic Search

The photosynthetic productivity of the intertidal communities dominated by the seagrass Zostera noltii and the cordgrass Spartina maritima was assessed in two contrasting situations during a tidal cycle, i.e., air exposure and water immersion. Two complementary methods were used: infra red gas analysis of CO2 flux measurements in whole communities and chlorophyll a fluorescence measurements of individual plants photosynthetic activity.

João Silva; Rui Santos; Maria Ll. Calleja; Carlos M. Duarte

2005-01-01

186

PYCNOGENOL DOES NOT IMPACT THE ANTIOXIDANT OR VITAMIN C STATUS OF HEALTHY YOUNG ADULTS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The objectives of this study were to determine if Pycnogenol (PYC), a water-processed extract made from the bark of Pinus maritima, interacts with vitamin C to increase its concentration and to increase total antioxidant capacity of serum and urine. Design The study design was a nonrandom interventi...

187

Arbuscular mycorrhizas in coastal sand dunes of the Paraguaná Peninsula, Venezuela  

Microsoft Academic Search

Arbuscular mycorrhizal colonization was measured in the most abundant plant species of the Paraguaná Peninsula, northwestern Venezuela. These plant species included: Acacia tortuosa, Argusia gnaphalodes, Croton punctatus, Croton rhamnifolius, Egletes prostrata, Melochia tomentosa, Panicum vaginatum, Scaevola plumieri, Sporobolus virginicus, Suriana maritima, Leptothrium rigidum, and Fimbristylis cymosa. Mycorrhizal colonization was assessed using the Trouvelot et al. (1986) method that allows for

C. Alarcón; G. Cuenca

2005-01-01

188

Heavy metal uptake by marsh plants in hydroponic solution cultures  

Microsoft Academic Search

Eight marsh plants were grown in chemically controlled hydroponic solutions containing three concentrations of heavy metals to evaluate the ability of each plant species to take up and accumulate heavy metals. The marsh plants studited were Cyperus esculentus, Scirpus validus, Spartina patens, Scirpus robustus, Distichiis spicata, Triglochin maritima, Spartina alterniflora, and Spartina foliosa. These species represented freshwater, brackish water, and

C. R. Lee; T. C. Sturgis; M. C. Landin

1981-01-01

189

Suitability of some farmscaping plants as nectar sources for the parasitoid wasp, Microplitis croceipes (Hymenoptera: Braconidae): Effects on longevity and body nutrients  

Microsoft Academic Search

In support of an ongoing study to evaluate potential farmscaping plants for utilization in organic vegetable production systems, we examined the effects of the nectar of three flowering plant species, sweet alyssum (Lobularia maritima), buckwheat (Fagopyrum sagittatum), and licorice mint (Agastache foeniculum), on the lifespan and body nutrient levels of the wasp, Microplitis croceipes (Cresson) (Hymenoptera: Braconidae), a key parasitoid

Timothy D. Nafziger; Henry Y. Fadamiro

2011-01-01

190

Do Spalax ehrenbergi blind mole rats use food odours in searching for and selecting food?  

Microsoft Academic Search

This laboratory study examined responses of Israeli blind subterranean mole rats (of the Spalax ehrenbergi superspecies) to food odours (Narcissus tazetta and Urginea maritima bulbs) and assessed to what extent mole rats’ odour preferences are indicative of their food preferences and whether these preferences influence their foraging behaviour. Prior to odour testing, mole rats ate Narcissus bulbs preferentially and avoided

G. Heth; J. Todrank; E. Nevo

2000-01-01

191

A study on the bio-hydro mechanical effects of the tree roots on the Agacl? coal reclaimed – forested land  

Microsoft Academic Search

The research area that is in the north of Istanbul (Turkey) and it is a land of open pit coal mining residuals reclaimed and turned to forest in 1988–1989. The materials that are open pit mine spoils are formed by sandy loam, sandy clay loam, heavy loam and clay (noncalcareous Pliocene I sediments). Pseudoacacia (Robinia pseudoacacia), Maritima Pine (Pinus pinaster)

Nuray Tokgöz

2005-01-01

192

Flower color affects tri-trophic-level biocontrol interactions  

Microsoft Academic Search

The adults of many parasitoid species require nectar for optimal fitness, but very little is known of flower recognition. Flight cage experiments showed that the adults of an egg parasitoid (Trichogramma carverae Oatman and Pinto) benefited from alyssum (Lobularia maritima L.) bearing white flowers to a greater extent than was the case for light pink, dark pink or purple flowered

Mahmuda Begum; Geoff M. Gurr; Steve D. Wratten; Helen I. Nicola

2004-01-01

193

The importance of salt-marsh wetness for seed exploitation by dabbling ducks Anas sp  

Microsoft Academic Search

The relationship between the inundation of a salt marsh in southeast Denmark not subject to lunar tides and the availability and predation of seeds of the annuals Salicornia spp. and Suada maritima by autumn staging dabbling ducks was studied by carrying out exclosure experiments over the course of 2 years. There was a marked difference in the wetness of the salt

Ole R. Therkildsen; Thomas Bregnballe

2006-01-01

194

Strategies of heavy metal uptake by three plant species growing near a metal smelter  

Microsoft Academic Search

Some higher plant species have developed heavy metal tolerance strategies which enable them to survive and reproduce in highly metal-contaminated soils. We have investigated such heavy metal uptake and accumulation strategies of two absolute metallophyte species (Armeria maritima ssp. halleri and Cardaminopsis halleri) and one pseudometallophyte (Agrostis tenuis) growing near a former metal smelter. Samples of plant parts and soil

H Dahmani-Muller; F van Oort; B Gélie; M Balabane

2000-01-01

195

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

196

Acoustic detection of Oryctes rhinoceros (Coleoptera: Scarabaeidae: Dynastinae) and Nasutitermes luzonicus (Isoptera: Termitidae) in palm trees in urban Guam.  

PubMed

Adult and larval Oryctes rhinoceros (L.) (Coleoptera: Scarabaeidae: Dynastinae) were acoustically detected in live and dead palm trees and logs in recently invaded areas of Guam, along with Nasutitermes luzonicus Oshima (Isoptera: Termitidae), and other small, sound-producing invertebrates and invertebrates. The low-frequency, long-duration sound-impulse trains produced by large, active O. rhinoceros and the higher frequency, shorter impulse trains produced by feeding N. luzonicus had distinctive spectral and temporal patterns that facilitated their identification and discrimination from background noise, as well as from roaches, earwigs, and other small sound-producing organisms present in the trees and logs. The distinctiveness of the O. rhinoceros sounds enables current usage of acoustic detection as a tactic in Guam's ongoing O. rhinoceros eradication program. PMID:20857720

Mankin, R W; Moore, A

2010-08-01

197

Effect of Azadirachtin on vitellogenesis of Labidura riparia (Insect Dermaptera).  

PubMed

This study investigates the effects of the insect growth regulator Azadirachtin (AZA) on the ultrastructure of ovaries and fat body of the earwig Labidura riparia. Ovarian development is severely reduced in AZA-injected females in a dose-dependent manner. Follicles exhibit degenerative changes, separation of follicle cells from the oocyte, and lack of pinocytotic vesicles as of yolk spheres in cortical ooplasm. Adipocytes show fragmented rough endoplasmic reticulum (RER), numerous autophagic vacuoles, multivesicular bodies, osmiophilic lipid droplets, and many large glycogen areas. Gel electrophoresis reveals that vitellogenin is absent from both fat body and hemolymph, and that vitellin is not deposited in the ovary. These pathological effects are not linked to an absence of feeding. The effect of AZA on vitellogenesis is rescuable by Juvenile hormone (JH) treatment. The inhibition of vitellogenesis by AZA is discussed on the basis of its direct cytotoxic effect as well as its interference with the neuroendocrine system. PMID:18621345

Sayah, F; Fayet, C; Idaomar, M; Karlinsky, A

1996-12-01

198

Tagus estuary and Ria de Aveiro salt marsh dynamics and the impact of sea level rise  

NASA Astrophysics Data System (ADS)

Different characteristics of Spartina maritima found in two distinct salt marshes located in different estuaries were analysed through interpretation of their local hydrodynamic patterns, as well as the impact of sea level rise on physical processes and consequently on plant dynamics and salt marshes stability. These salt marshes are situated in two of the most important Portuguese coastal systems, Tagus estuary (Rosário salt marsh) and Ria de Aveiro lagoon (Barra salt marsh), which are dominated by physical processes that induce strong tidal currents. They were monitored during one year and plant and sediment samples of S. maritima were collected quarterly in order to determine the vegetation coverage, above and belowground biomass, organic matter and sediment moisture. Residual circulation, tidal asymmetry and tidal dissipation were determined from numerical modelling results of the MOHID 2D model that was applied to each coastal system, considering the actual sea level and a sea level rise (SLR) scenario.

Valentim, J. M.; Vaz, N.; Silva, H.; Duarte, B.; Caçador, I.; Dias, J. M.

2013-09-01

199

Drought, but not salinity, determines the apparent effectiveness of halophytes colonized by arbuscular mycorrhizal fungi.  

PubMed

The halophytes Plantago maritima, Aster tripolium, Artemisia santonicum, Puccinellia limosa, Festuca pseudovina and Lepidium crassifolium from two different saline soils of the Hungarian steppe were examined for colonization by arbuscular mycorrhizal fungi (AMF). The salt aster (A. tripolium) and the sea plantain (P. maritima) were examined more thoroughly by recording root colonization parameters, the salt content in the soil and monthly precipitations in 2001 and 2002. Mycorrhizal colonization was maximal in late spring to early summer and had a second peak later in the autumn. Arbuscule formation and overall mycorrhizal colonization appeared to be inversely correlated with the intensity of rainfall at the investigated sites. The results suggest that, in addition to seasonality, drought may play an important role in governing mycorrhizal activity in saline habitats. In greenhouse experiments, conditions in which AMF could overcome the inhibitory effects of sodium chloride on establishing plant-mycorrhizal symbiosis were not met. PMID:18155803

Füzy, Anna; Biró, Borbála; Tóth, Tibor; Hildebrandt, Ulrich; Bothe, Hermann

2007-12-26

200

Directed Evolution of a Pyruvate Aldolase to Recognize A Long Chain Acyl Substrate  

PubMed Central

The use of biological catalysts for industrial scale synthetic chemistry is highly attractive, given their cost effectiveness, high specificity that obviates the need for protecting group chemistry, and the environmentally benign nature of enzymatic procedures. Here we evolve the naturally occurring 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolases from Thermatoga maritima and Escherichia coli, into enzymes that recognize a non-functionalized electrophilic substrate, 2-keto-4-hydroxyoctonoate (KHO). Using an in vivo selection based on pyruvate auxotrophy, mutations were identified that lower the KM value up to 100-fold in E. coli KDPG aldolase, and that enhance the efficiency of retro-aldol cleavage of KHO by increasing the value of kcat/KM up to 25-fold in T. maritima KDPG aldolase. These data indicate that numerous mutations distal from the active site contribute to enhanced “uniform binding” of the substrates, which is the first step in the evolution of novel catalytic activity.

Cheriyan, Manoj; Walters, Matthew J.; Kang, Brian D.; Anzaldi, Laura L.; Toone, Eric J.; Fierke, Carol A.

2011-01-01

201

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

PubMed

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

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

2007-03-01

202

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

Microsoft Academic Search

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

Osigwe Esue; Denis Wirtz; Yiider Tseng

2006-01-01

203

Effects of Monospecific Banks of Salt Marsh Vegetation on Sediment Bacterial Communities  

Microsoft Academic Search

The aim of this study was to understand if two species of salt marsh plants, widely distributed in European estuaries (Spartina maritima and Halimione portulacoides) differently influence the distribution, activity, and metabolic physiology of sediment bacterial communities in monospecific\\u000a banks, in comparison with uncolonized sediment (control). Microbiological descriptors of abundance and activity were assessed\\u000a along vertical profiles of sediments. Rates

Vanessa Oliveira; Ana L. Santos; Francisco Coelho; Newton C. M. Gomes; Helena Silva; Adelaide Almeida; Ângela Cunha

2010-01-01

204

H 2 synthesis from pentoses and biomass in Thermotoga spp  

Microsoft Academic Search

We have investigated H2 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,\\u000a while glycerol was not metabolised by either species. Glycerol was also not metabolised by

Niels T. EriksenMartin; Martin Leegaard Riis; Nikolaj Kyndby Holm; Niels Iversen

2011-01-01

205

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

206

Management of Meloidogyne incognita , the root-knot nematode, on soybean as affected by marigold and sea ambrosia (damsisa) plants  

Microsoft Academic Search

Marigolds (Tagetes erecta and T. patula) or sea ambrosia (Ambrosia maritima) as intercropped plants with soybean (Glycine max) cv. Giza 21 infected with Meloidogyne incognita, the root-knot nematode, significantly (P0.05 and 0.01) reduced nematode numbers on soybean as indicated by the percentage reduction of galls, developmental stages and egg masses in roots and juveniles (J2) in soil. Marigolds significantly (P0.05

M. H. El-Hamawi; M. M. A. Youssef; Hanaa S. Zawam

2004-01-01

207

Stratigraphic and Ecophysical Characterizations of Salt Pools: Dynamic Landforms of the Webhannet Salt Marsh, Wells, ME, USA  

Microsoft Academic Search

Salt pools are water-filled depressions common to north-temperate salt marshes. In Wells, ME, USA, cores reveal a unique salt\\u000a pool signature consisting of water-saturated dark-gray mud often containing fragments of Ruppia maritima. Cores through pool sediment reenter salt marsh peat, not tidal flat sediment, demonstrating that most pools are of secondary\\u000a origin. A principal component analysis of attribute data collected

Kristin R. Wilson; Joseph T. Kelley; Arie Croitoru; Michele Dionne; Daniel F. Belknap; Robert Steneck

2009-01-01

208

Abundance of wigeongrass during winter and use by herbivorous waterbirds in a texas coastal marsh  

Microsoft Academic Search

Wigeongrass (Ruppia maritima), a submerged aquatic plant inhabiting estuarine wetlands, is an important winter food for waterbirds along the Texas Gulf\\u000a Coast. We examined availability of wigeongrass at Mad Island Wildlife Management Area, Texas, USA by estimating aboveground\\u000a biomass from October through January, 1998–1999 and 2001–2002. We also used an exclosure experiment to determine the extent\\u000a to which herbivory by

Kevin M. Hartke; Kevin H. Kriegel; G. Matt Nelson; M. Todd Merendino

2009-01-01

209

Enhancement of transglycosylation activity by construction of chimeras between mesophilic and thermophilic ?-glucosidase  

Microsoft Academic Search

The family 3 ?-glucosidase from Thermotoga maritima is a highly thermostable enzyme (85°C) that displays transglycosylation activity. In contrast, the ?-glucosidase from Cellvibrio gilvus is mesophilic (35°C) and displays no such transglycosylation activity. Both enzymes consist of two domains, an N-terminal and a C-terminal domain, and the amino acid identities between the two enzymes in these domains are 32.4 and

Kshamata Goyal; Bong Jo Kim; Jong-Deog Kim; Yeon-Kye Kim; Motomitsu Kitaoka; Kiyoshi Hayashi

2002-01-01

210

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

Microsoft Academic Search

The applicability of mitochondrial DNA (mtDNA) sequencing was investigated for the identification of the following forensically important species of blowflies from southeastern Australia: Calliphoraalbifrontalis, C.augur, C.dubia, C.hillihilli, C.maritima, C.stygia, C.vicina, Chrysomyarufifacies, Ch.varipes and Onesiatibialis. 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

J. F. Wallman; S. C. Donnellan

2001-01-01

211

The eVect of resource provisioning and sugar composition of foods on longevity of three Gonatocerus spp., egg parasitoids of Homalodisca vitripennis  

Microsoft Academic Search

The eVect of dietary supplements on the longevity of male and female Gonatocerus ashmeadi, G. triguttatus and G. fasciatus (Hyme- noptera: Mymaridae), was determined in the laboratory. Treatments included: water only, 3:1 honey-water solution, Xoral and extra- Xoral nectars from Wve diVerent plants (excised stems from Fagopyrum esculentum, Lobularia maritima, Phacelia tanacetifolia, Anethum graveolens and Vicia faba), honeydew from Coccus

Nicola A. Irvin; Mark S. Hoddle; Steven J. Castle

2007-01-01

212

Heavy metal uptake by selected marsh plant species grown in hydroponic cultures  

Microsoft Academic Search

Eight marsh plant species (Cyperus esculentus, Scirpus validus, Spartina patens, Scirpus robustus, Triglochin maritima, Distichlis spicata, Spartina alterniflora, and Spartina foliosa) were grown under greenhouse conditions in chemically controlled nutrient solutions. Heavy metals (zinc, cadmium, nickel, chromium, and lead) were added to the nutrient solutions at levels of 0, 0.5, and 1.0 mg\\/l. Plant parts (leaves, rhizomes, tubers, and roots)

C. R. Lee; T. C. Sturgis; M. C. Landin

1975-01-01

213

Age-specific, density-dependent and environment-based mortality of a short-lived perennial herb  

Microsoft Academic Search

Density-independent and density-dependent processes affect plant mortality. Although less well understood, age-specific mortality can also play an important role in plant mortality. The goal of this study was to analyse sev- eral factors accounting for mortality in the Mediterranean short-lived peren- nial herb Lobularia maritima. We followed three cohorts of plants (from emergence to death) during 4 years in field

F. X. Pico ´; J. Retana

2008-01-01

214

A Cluster of Thermotoga neapolitana Genes Involved in the Degradation of Starch and Maltodextrins: the Molecular Structure of the Locus  

Microsoft Academic Search

A 5451-bp genome fragment of the hyperthermophilic anaerobic eubacterium Thermotoga neapolitana has been cloned and sequenced. The fragment contains one truncated and three complete open reading frames highly homologous to the starch\\/maltodextrin utilization gene cluster from T. maritima whose genome sequence is known. The incomplete product of the first frame is highly homologous to MalG, the Escherichia coli protein of

O. V. Berezina; N. A. Lunina; V. V. Zverlov; D. G. Naumoff; W. Liebl; G. A. Velikodvorskaya

2003-01-01

215

Use of drift substrates to characterize marine fungal communities from the west coast of Portugal.  

PubMed

This survey reports the occurrence, diversity and similarity of marine fungi associated with five categories of drift substrates (Arundo donax, Phragmites australis, Spartina maritima, "other stems" and driftwood) collected on four sandy beaches of the western coast of Portugal. "Other stems" and driftwood are composite samples with a variety of identified and unidentified pieces of non-woody and woody substrates respectively. Fifty-six taxa were identified, including 38 Ascomycota and 18 anamorphic fungi. Twenty-six taxa were generalists; however several cases of "substrate recurrence" were identified. The very frequent fungi differed among the categories of studied substrates, with the exception of Corollospora maritima, very frequent on four categories. Except for S. maritima, P. australis and driftwood, cases of multiple fungal colonization were rare. S. maritima was the single substrate with five different marine fungi on one sample, as well as with the highest number of very frequent fungi, highest percentage of colonization and average number of fungi per sample. Driftwood presented the highest value of fungal richness (37 taxa) and A. donax the lowest (22 taxa). ANOSIM analysis of similarity showed that all substrates supported different fungal communities with the exception of the pair P. australis/"other stems". The effect of sample size on estimated fungal richness was tested, and the results let us conclude that, although most of the sporadic fungi (<1% occurrence) will be detected only in a very large number of samples, 60 samples of A. donax and "other stems" and 70 samples of all the other substrates may suffice to assess their respective representative marine mycota. PMID:22241614

Azevedo, Egidia; Rebelo, Rui; Caeiro, Maria Filomena; Barata, Margarida

2012-01-12

216

The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor  

Microsoft Academic Search

Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 Angstroms resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an

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

2001-01-01

217

Cloning, expression and characterization of L-arabinose isomerase from Thermotoga neapolitana: bioconversion of D-galactose to D-tagatose using the enzyme  

Microsoft Academic Search

Gene araA encoding an L-arabinose isomerase (AraA) from the hyperthermophile, Thermotoga neapolitana 5068 was cloned, sequenced, and expressed in Escherichia coli. The gene encoded a polypeptide of 496 residues with a calculated molecular mass of 56?677 Da. The deduced amino acid sequence has 94.8% identical amino acids compared with the residues in a putative L-arabinose isomerase of Thermotoga maritima. The

Byoung-Chan Kim; Yoon-Hee Lee; Han-Seung Lee; Dong-Woo Lee; Eun-Ah Choe; Yu-Ryang Pyun

2002-01-01

218

Selenium Levels in Biota from Irrigation Drainwater Impoundments in the San Joaquin Valley, California  

Microsoft Academic Search

Waterfowl, fish, invertebrates, and plants were collected from impoundments used for evaporating subsurface irrigation drainwater in Kings and Kern counties, California. Specimens were analyzed for trace elements with emphasis on selenium. Dry weight concentrations of total selenium ranged from 2.5 to 17 ?g\\/g in wigeongrass, Ruppia maritima; 7.6 to 30 ?g\\/g in water boatmen, Corixidae; 12 to 40 ?\\/g in

Douglas A. Barnum; David S. Gilmer

1988-01-01

219

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

Microsoft Academic Search

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 Ther- motoga 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

SIMONETTA GRIBALDO; VALENTINA LUMIA; ROBERTA CRETI; EVERLY CONWAY DE MACARIO; ANNAMARIA SANANGELANTONI; PIERO CAMMARANO

1999-01-01

220

Role of Entropy in Protein Thermostability:  Folding Kinetics of a Hyperthermophilic Cold Shock Protein at High Temperatures Using 19 F NMR †  

Microsoft Academic Search

We used 19F NMR to extend the temperature range accessible to detailed kinetic and equilibrium studies of a hyperthermophilic protein. Employing an optimized incorporation strategy, the small cold shock protein from the bacterium Thermotoga maritima(TmCsp) was labeled with 5-fluorotryptophan. Although chaotropically induced unfolding transitions revealed a significant decrease in the stabilization free energy upon fluorine labeling, the protein's kinetic folding

Benjamin Schuler; Werner Kremer; Hans Robert Kalbitzer; Rainer Jaenicke

2002-01-01

221

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

222

A comparison of Hox3 and Zen protein coding sequences in taxa that span the Hox3 \\/ zen divergence  

Microsoft Academic Search

The class 3 Hox genes of insects have diverged—in expression domain and functional role during embryogenesis—compared to those\\u000a of other bilaterians. Whereas the canonical ortholog (Hox3) is involved in axial patterning of the embryonic body, the insect ortholog (zen) is involved in extraembryonic development. In this paper, we present sequence data from the centipede Strigamia maritima, the collembolan Folsomia candida,

Kristen Anne Panfilio; Michael Akam

2007-01-01

223

Metal-rich concretions on the roots of salt marsh plants: Mechanism and rate of formation  

Microsoft Academic Search

The roots of the vascular plant Spartina maritima, growing in the saltmarshes of the Tagus Estuary, Portugal, are surrounded by tubular concretions whose diameter can reach >0.2 cm. Concretions are also found scattered within the sediment matrix in and below the root zone. The concretions comprise 4% (DW) of the sediment and contain 11.7 2 1.6% iron compared to 4.9

Bjørn Sundby; Carlos Vale; Isabel Caçador; Fernando Catarino; Maria-João Madureira; Miguel Caetano

1998-01-01

224

Reactions of various plant species to inoculation with potato aucuba mosaic virus  

Microsoft Academic Search

Inoculation with PAMV produced local lesions inGomphrena globosa andPhaseolus vulgaris cv. Bruine stam.Browallia americana, B. viscosa, Cyphomandra betacea, Melilotus indicus, Lycopersicon pimpinellifolium, Nicotiana amplexicaulis, N. clevelandii, N. maritima, N. nudicaulis, N. setchellii andN. solanifolia were symptomless hosts.Melilotus sulcatus was not susceptible. Sugar pea cultivars included in our experiments were better local-lesion hosts than the common pea cultivars. Although severity of

J. A. de Bokx

1975-01-01

225

Pullulanase Type I from Fervidobacterium pennavorans Ven5: Cloning, Sequencing, and Expression of the Gene and Biochemical Characterization of the Recombinant Enzyme  

Microsoft Academic Search

The gene encoding the type I pullulanase from the extremely thermophilic anaerobic bacterium Fervidobac- terium pennavorans Ven5 was cloned and sequenced in Escherichia coli. The pulA gene from F. pennavorans Ven5 had 50.1% pairwise amino acid identity with pulA from the anaerobic hyperthermophile Thermotoga maritima and contained the four regions conserved among all amylolytic enzymes. The pullulanase gene (pulA) encodes

COSTANZO BERTOLDO; FIONA DUFFNER; PER L. JORGENSEN; GARABED ANTRANIKIAN; Screening Biotechnology; Novo Nordisk

1999-01-01

226

Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences  

Microsoft Academic Search

In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and\\/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same

Robert T. DeBoy; Emmanuel F. Mongodin; Joanne B. Emerson; Karen E. Nelson

2006-01-01

227

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

228

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

PubMed

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

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

2010-01-01

229

Liposome-mediated DNA uptake and transient expression in Thermotoga.  

PubMed

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

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

2001-02-01

230

Hidden diversity in wild Beta taxa from Portugal: insights from genome size and ploidy level estimations using flow cytometry.  

PubMed

Crop wild relatives constitute a broad pool of potentially useful genetic resources for plant breeders. The genus Beta L. (Amaranthaceae) is an important source of crops, primarily for sugar production. Until recently, species within Section Beta were mostly cytogenetically uniform, with diploidy being prevalent. Still, with the discovery of tetraploid individuals of the wild B. macrocarpa in the Canary Islands, a large-scale study was necessary to evaluate the cytogenetic diversity within the wild Beta. For that, genome size and ploidy level of B. vulgaris subsp. maritima and B. macrocarpa from 21 populations across Portugal mainland and islands, including all know populations of the later taxon, were estimated using propidium iodide flow cytometry. This work revealed a cytogenetically diverse scenario. The analyzed populations were mostly diploid, except for one population of B. vulgaris subsp. maritima that presented both diploid and tetraploid individuals, and for two populations of B. macrocarpa where two or three cytotypes (diploids, tetraploids and/or hexaploids) were found. The nuclear DNA content of diploid individuals was estimated as 1.44±0.035 and 1.41±0.027 pg/2C for B. vulgaris subsp. maritima and B. macrocarpa, respectively. Also, leaves of both species presented variable levels of endopolyploidy. The obtained results are discussed within the context of interspecific hybridization and cryptic diversity and constitute significant data for the conservation of these wild Beta crop relatives. PMID:23602101

Castro, Sílvia; Romeiras, Maria M; Castro, Mariana; Duarte, Maria Cristina; Loureiro, João

2013-03-05

231

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

PubMed

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

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

2009-09-01

232

Spectral reflectance properties of mangrove species of the Muthupettai mangrove environment, Tamil Nadu.  

PubMed

In the Muthupettai mangrove environment, spectral properties of six mangrove species viz. Avicennia marina, Aegiceras corniculatum, Excoecaria agallocha, Acanthus ilicifolius, Suaeda monoica and S. maritima was studied using Multi band Ground Truth Radiometer (Model-041). The study found that the chlorophyll concentration of different mangrove leaves varies between 0.05 and 0.36 mg g(-1), registering the minimum in S. maritima and maximum in E. agallocha. Interestingly species with higher chlorophyll concentration showed lower reflectance values alteast in the spectral bands 1 and 2. E. agallocha registered 0.36 mg g(-1) of chlorophyll while it recorded only 2.18 and 2.43% reflectance where as S. maritima recorded 3.16 and 3.27% of reflectance in bands 1 and 2. This indicates chlorophyll concentration is one of major factors responsible in determining the reflectance pattern of the pant communities. The spectral properties of mangroves were largely differed with that of the water and soil samples collected from the same locations, these results favourd the utilization of remotely sensed data for depicting various water and soil quality parameters from that of mangrove species in the mangrove environment. This study also found that the difference in reflectance of mangroves at canopy level is not only influenced by the chlorophyll content of species but also by the prevailing environmental condition and background reflectance of soil and water as well. PMID:19295083

Ajithkumar, T T; Thangaradjou, T; Kannan, L

2008-09-01

233

Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales  

PubMed Central

Background The mal genes that encode maltose transporters have undergone extensive lateral transfer among ancestors of the archaea Thermococcus litoralis and Pyrococcus furiosus. Bacterial hyperthermophiles of the order Thermotogales live among these archaea and so may have shared in these transfers. The genome sequence of Thermotoga maritima bears evidence of extensive acquisition of archaeal genes, so its ancestors clearly had the capacity to do so. We examined deep phylogenetic relationships among the mal genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry. Results We demonstrate that the two maltose ATP binding cassette (ABC) transporter operons now found in Tc. litoralis and P. furiosus (termed mal and mdx genes, respectively) are not closely related to one another. The Tc. litoralis and P. furiosus mal genes are most closely related to bacterial mal genes while their respective mdx genes are archaeal. The genes of the two mal operons in Tt. maritima are not related to genes in either of these archaeal operons. They are highly similar to one another and belong to a phylogenetic lineage that includes mal genes from the enteric bacteria. A unique domain of the enteric MalF membrane spanning proteins found also in these Thermotogales MalF homologs supports their relatively close relationship with these enteric proteins. Analyses of genome sequence data from other Thermotogales species, Fervidobacterium nodosum, Thermosipho melanesiensis, Thermotoga petrophila, Thermotoga lettingae, and Thermotoga neapolitana, revealed a third apparent mal operon, absent from the published genome sequence of Tt. maritima strain MSB8. This third operon, mal3, is more closely related to the Thermococcales' bacteria-derived mal genes than are mal1 and mal2. F. nodosum, Ts. melanesiensis, and Tt. lettingae have only one of the mal1-mal2 paralogs. The mal2 operon from an unknown species of Thermotoga appears to have been horizontally acquired by a Thermotoga species that had only mal1. Conclusion These data demonstrate that the Tc. litoralis and P. furiosus mdx maltodextrin transporter operons arose in the Archaea while their mal maltose transporter operons arose in a bacterial lineage, but not the same lineage as the two maltose transporter operons found in the published Tt. maritima genome sequence. These Tt. maritima maltose transporters are phylogenetically and structurally similar to those found in enteric bacteria and the mal2 operon was horizontally transferred within the Thermotoga lineage. Other Thermotogales species have a third mal operon that is more closely related to the bacterial Thermococcales mal operons, but the data do not support a recent horizontal sharing of that operon between these groups.

2008-01-01

234

Diet of western Burrowing Owls wintering in southern Texas  

USGS Publications Warehouse

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

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

2007-01-01

235

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

PubMed

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

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

2007-10-16

236

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

237

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

USGS Publications Warehouse

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

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

2001-01-01

238

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

239

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

2007-02-23

240

Structural biology of S -adenosylmethionine decarboxylase  

Microsoft Academic Search

S-adenosylmethionine decarboxylase (AdoMetDC) is a critical enzyme in the polyamine biosynthetic pathway and a subject of many\\u000a structural and biochemical investigations for anti-cancer and anti-parasitic therapy. The enzyme undergoes an internal serinolysis\\u000a reaction as a post-translational modification to generate the active site pyruvoyl group for the decarboxylation process.\\u000a The crystal structures of AdoMetDC from Homo sapiens, Solanum tuberosum, Thermotoga maritima,

Shridhar BaleSteven; Steven E. Ealick

2010-01-01

241

On salt marsh vegetation in North Korea  

Microsoft Academic Search

The salt marsh vegetation on the west coast of North Korea was studied by the method of the Zürich-Montpellier school. The\\u000a following communities were distinguished:Suaedetum japonicae, Scirpetum iseensis, Artemisietum fukudo, and the following were described as new:Triglochini maritimae-Phragmitetum communis, Artemisio capillaris-Salsoletum komarovii andSalsolo komarovii-Rosetum rugosae. The phytocoenological material was also analysed by means of numerical techniques.\\u000a \\u000a The population density ofSuaeda

Ji?í Kolbek; Ji?í Dostálek; Ivan Jarolímek; Ivan Ostrý; Li Sek-Ha

1989-01-01

242

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

PubMed

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

Chandrasekaran, Manivachagam; Kannathasan, Krishnan; Venkatesalu, Venugopalan

243

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

PubMed

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

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

2009-10-14

244

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

245

Responses of halophytes to high salinities and low water potentials.  

PubMed

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

Jefferies, R L; Rudmik, T; Dillon, E M

1979-12-01

246

Hydrogen transfer between methanogens and fermentative heterotrophs in hyperthermophilic cocultures  

SciTech Connect

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

Muralidharan, V.; Hirsh, I.S.; Bouwer, E.J. [Johns Hopkins Univ., Baltimore, MD (United States); Rinker, K.D.; Kelly, R.M. [North Carolina State Univ., Raleigh, NC (United States). Dept. of Chemical Engineering

1997-11-05

247

Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme.  

PubMed

The CCA-adding enzyme synthesizes the CCA sequence at the 3' end of tRNA without a nucleic acid template. The crystal structures of class II Thermotoga maritima CCA-adding enzyme and its complexes with CTP or ATP were determined. The structure-based replacement of both the catalytic heads and nucleobase-interacting neck domains of the phylogenetically closely related Aquifex aeolicus A-adding enzyme by the corresponding domains of the T. maritima CCA-adding enzyme allowed the A-adding enzyme to add CCA in vivo and in vitro. However, the replacement of only the catalytic head domain did not allow the A-adding enzyme to add CCA, and the enzyme exhibited (A, C)-adding activity. We identified the region in the neck domain that prevents (A, C)-adding activity and defines the number of nucleotide incorporations and the specificity for correct CCA addition. We also identified the region in the head domain that defines the terminal A addition after CC addition. The results collectively suggest that, in the class II CCA-adding enzyme, the head and neck domains collaboratively and dynamically define the number of nucleotide additions and the specificity of nucleotide selection. PMID:19745807

Toh, Yukimatsu; Takeshita, Daijiro; Numata, Tomoyuki; Fukai, Shuya; Nureki, Osamu; Tomita, Kozo

2009-09-10

248

Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme  

PubMed Central

The CCA-adding enzyme synthesizes the CCA sequence at the 3? end of tRNA without a nucleic acid template. The crystal structures of class II Thermotoga maritima CCA-adding enzyme and its complexes with CTP or ATP were determined. The structure-based replacement of both the catalytic heads and nucleobase-interacting neck domains of the phylogenetically closely related Aquifex aeolicus A-adding enzyme by the corresponding domains of the T. maritima CCA-adding enzyme allowed the A-adding enzyme to add CCA in vivo and in vitro. However, the replacement of only the catalytic head domain did not allow the A-adding enzyme to add CCA, and the enzyme exhibited (A, C)-adding activity. We identified the region in the neck domain that prevents (A, C)-adding activity and defines the number of nucleotide incorporations and the specificity for correct CCA addition. We also identified the region in the head domain that defines the terminal A addition after CC addition. The results collectively suggest that, in the class II CCA-adding enzyme, the head and neck domains collaboratively and dynamically define the number of nucleotide additions and the specificity of nucleotide selection.

Toh, Yukimatsu; Takeshita, Daijiro; Numata, Tomoyuki; Fukai, Shuya; Nureki, Osamu; Tomita, Kozo

2009-01-01

249

Structure-Based Activity Prediction for an Enzyme of Unknown Function  

SciTech Connect

With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10{sup 5} M{sup -1} s{sup -1}). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.

Hermann,J.; Marti-Arbona, R.; Fedorov, A.; Fedorov, E.; Almo, S.; Shoichet, B.; Raushel, F.

2007-01-01

250

Vasodilator effects of Diocleinae lectins from the Canavalia genus.  

PubMed

This study investigated and compared vascular actions of leguminous lectins obtained from the Canavalia genus (Canavalia brasiliensis, Canavalia gladiata, and Canavalia maritima) in the rat models of paw edema and isolated aorta. Paw edema was induced by subcutaneous injection of lectins (0.01-1 mg/kg) in animals pre-treated or not with indomethacin or L-NAME. In isolated aorta, cumulative concentration curves of C. gladiata or C. brasiliensis (1-100 microg/ml) were performed at the contraction plateau induced by phenylephrine or at tissue basal tonus. The mechanism of the lectin relaxant action was investigated by previous addition of L-NAME, indomethacin, or tetraethylammonium. In both models, the lectin domain involvement was evaluated by incubation of lectins with their ligand and non-ligand sugars. The lectins induced paw edema paralleled by protein leakage. The edematogenic activity elicited by C. gladiata and C. brasiliensis involves prostaglandins and nitric oxide (NO), while that of C. maritima occurs without NO interference. C. gladiata and C. brasiliensis elicited aorta relaxation involving NO and prostacyclin, while that of C. gladiata included EDHF. All lectin effects were prevented by their binding sugars. The present study demonstrated important vasodilator effects of different degrees and mechanisms in vivo and in vitro of Canavalia lectins. In vivo, the edematogenic activity was paralleled by plasma exudation, and in vitro, aorta relaxation was strictly dependent on intact endothelium. All effects occurred via interaction with lectin domains and participation of NO and/or prostanoids. PMID:19855960

Assreuy, Ana Maria Sampaio; Fontenele, Sabrina Rodrigues; Pires, Alana de Freitas; Fernandes, Débora Costa; Rodrigues, Natália Velloso Fontenelle C; Bezerra, Eduardo Henrique Salviano; Moura, Tales Rocha; do Nascimento, Kyria Santiago; Cavada, Benildo Sousa

2009-10-24

251

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

2011-07-20

252

The functional exchangeability of pk- and k-turns in RNA structure  

PubMed Central

Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase P of Thermotoga maritima is globally very similar to a k-turn, but lacks all the standard features of that structure, including long-range hydrogen bonds between the two helical arms. We show here that in an isolated RNA duplex, the pk-turn fails to adopt a tightly kinked structure, but rather is a flexible element. This suggests that the tertiary contacts of RNase P assist its folding into the required kinked structure. We find that we can replace the k-turn of the SAM-I riboswitch with the pk-turn, such that the resulting RNA retains its ability to bind SAM, although with lower affinity. We also find that we can replace the pk-turn of T. maritima RNase P with a standard k-turn (in either orientation) with retention of ribozyme activity. Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another.

Daldrop, Peter; Masquida, Benoit; Lilley, David M.J.

2013-01-01

253

The functional exchangeability of pk- and k-turns in RNA structure.  

PubMed

Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase P of Thermotoga maritima is globally very similar to a k-turn, but lacks all the standard features of that structure, including long-range hydrogen bonds between the two helical arms. We show here that in an isolated RNA duplex, the pk-turn fails to adopt a tightly kinked structure, but rather is a flexible element. This suggests that the tertiary contacts of RNase P assist its folding into the required kinked structure. We find that we can replace the k-turn of the SAM-I riboswitch with the pk-turn, such that the resulting RNA retains its ability to bind SAM, although with lower affinity. We also find that we can replace the pk-turn of T. maritima RNase P with a standard k-turn (in either orientation) with retention of ribozyme activity. Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another. PMID:23364423

Daldrop, Peter; Masquida, Benoît; Lilley, David M J

2013-01-30

254

Arbuscular mycorrhizas in coastal sand dunes of the Paraguaná Peninsula, Venezuela.  

PubMed

Arbuscular mycorrhizal colonization was measured in the most abundant plant species of the Paraguaná Peninsula, northwestern Venezuela. These plant species included: Acacia tortuosa, Argusia gnaphalodes, Croton punctatus, Croton rhamnifolius, Egletes prostrata, Melochia tomentosa, Panicum vaginatum, Scaevola plumieri, Sporobolus virginicus, Suriana maritima, Leptothrium rigidum, and Fimbristylis cymosa. Mycorrhizal colonization was assessed using the Trouvelot et al. (1986) method that allows for simultaneous evaluation of frequency of colonization (%F), intensity of colonization (%M), and the proportion of arbuscules (%A) and vesicles (%V) present in the roots. Average frequency of colonization was 69%. The highest frequency of colonization was around 92% in C. rhamnifolius and A. tortuosa; in the other species, it varied from 49 to 86%. L. rigidum and F. cymosa were considered nonmycorrhizal because its colonization was very scarce and at all times appeared without arbuscules. Average intensity of colonization was 7%. The highest intensity of colonization was 18% in C. rhamnifolius. In the other species, it varied from 3 to 15%. Paspalum vaginatum, A. gnaphalodes, M. tomentosa, and S. maritima had their fungal structures tightly packed in modified little ovoid roots. In general, frequency of AM colonization was high and similar to those reported for other tropical ecosystems, whereas the intensity of AM colonization was low and similar to values obtained in analogous studies in disturbed ecosystems. PMID:16007471

Alarcón, C; Cuenca, G

2005-11-11

255

Structural Insights into the Catalytic Mechanism of Bacterial Guanosine-diphospho-d-mannose Pyrophosphorylase and Its Regulation by Divalent Ions*  

PubMed Central

GMP catalyzes the formation of GDP-Man, a fundamental precursor for protein glycosylation and bacterial cell wall and capsular polysaccharide biosynthesis. Crystal structures of GMP from the thermophilic bacterium Thermotoga maritima in the apo form, in complex with the substrates mannose-1-phosphate or GTP and bound with the end product GDP-Man in the presence of the essential divalent cation Mg2+, were solved in the 2.1–2.8 ? resolution range. The T. maritima GMP molecule is organized in two separate domains: a N-terminal Rossman fold-like domain and a C-terminal left-handed ?-helix domain. Two molecules associate into a dimer through a tail-to-tail arrangement of the C-terminal domains. Comparative analysis of the structures along with characterization of enzymatic parameters reveals the bases of substrate specificity of this class of sugar nucleotidyltransferases. In particular, substrate and product binding are associated with significant changes in the conformation of loop regions lining the active center and in the relative orientation of the two domains. Involvement of both the N- and C-terminal domains, coupled to the catalytic role of a bivalent metal ion, highlights the catalytic features of bacterial GMPs compared with other members of the pyrophosphorylase superfamily.

Pelissier, Marie-Cecile; Lesley, Scott A.; Kuhn, Peter; Bourne, Yves

2010-01-01

256

Conformational Flexibility and Peptide Interaction of the Translocation ATPase SecA  

SciTech Connect

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

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

2010-09-21

257

Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.  

PubMed

In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both the T. maritima and T. neapolitana lineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains of T. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in the Thermotogales likely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations. PMID:16547022

DeBoy, Robert T; Mongodin, Emmanuel F; Emerson, Joanne B; Nelson, Karen E

2006-04-01

258

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

PubMed Central

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

Meunier, Joel; Kolliker, Mathias

2012-01-01

259

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

PubMed Central

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 Omp?) and the porin OmpB (or Omp?). 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 ?-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 ?-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; Wu, Si; Brewer, Heather M.; Gogarten, J. Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

2012-01-01

260

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

261

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

262

New crystal forms of Diocleinae lectins in the presence of different dimannosides  

PubMed Central

Studying the interactions between lectins and sugars is important in order to explain the differences observed in the biological activities presented by the highly similar proteins of the Diocleinae subtribe. Here, the crystallization and preliminary X-­ray data of Canavalia gladiata lectin (CGL) and C. maritima lectin (CML) complexed with Man(?1-2)Man(?1)OMe, Man(?1-3)Man(?1)OMe and Man(?1-4)Man(?1)OMe in two crystal forms [the complexes with Man(?1-3)Man(?1)OMe and Man(?1-4)Man(?1)OMe crystallized in space group P32 and those with Man(?1-2)Man(?1)OMe crystallized in space group I222], which differed from those of the native proteins (P21212 for CML and C222 for CGL), are reported. The crystal complexes of ConA-like lectins with Man(?1-4)Man(?1)OMe are reported here for the first time.

Moreno, Frederico Bruno Mendes Batista; Bezerra, Gustavo Arruda; de Oliveira, Taiana Maia; de Souza, Emmanuel Prata; da Rocha, Bruno Anderson Matias; Benevides, Raquel Guimaraes; Delatorre, Plinio; Cavada, Benildo Sousa; de Azevedo, Walter Filgueira

2006-01-01

263

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

PubMed Central

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

Martinez-Hackert, Erik; Hendrickson, Wayne A.

2009-01-01

264

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

265

[A new approach for study of structural and functional properties of proteins with unknown functions].  

PubMed

Selected proteins were produced in Escherichia coli bacterial expression system--three proteins from extremophil bacteria: a putative monooxygenase from Deinococcus radiodurans, a putative nucleotidyltransferase from Thermotoga maritima, a putative oxidoreductase from Exiguobacterium sibiricum; and a shaperon from Homo sapiens DJ-1. The protocol of isolation & purification of recombinant proteins were developed that allowed to obtain expression products with the purity of no less than 96%. Conditions for the crystallization have been selected that allowed a stable growth of crystals. Preliminary x-ray experiments were conducted in order to confirm the quality of produced crystals; the resolution of obtained structural data was from 1.2 to 1.8 angstrom. PMID:22792712

Gorbacheva, M A; Iarosh, A G; Dorovatovski?, P V; Rakitina, T V; Bo?ko, K M; Korzhenevski?, D A; Lipkin, A V; Popov, V O; Shumilin, I A

266

A Continuous Assay of Acetate-Kinase Activity: Measurement of Inorganic Phosphate Release Generated by Hydroxylaminolysis of Acetyl Phosphate  

PubMed Central

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 Km for acetate than previously published.

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

2008-01-01

267

Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada  

PubMed Central

Abstract Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves.

Saarela, Jeffery M.

2012-01-01

268

Feeding ecology of waterfowl wintering on evaporation ponds in California  

USGS Publications Warehouse

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

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

1991-01-01

269

Inorganic pyrophosphatases: one substrate, three mechanisms.  

PubMed

Soluble inorganic pyrophosphatases (PPases) catalyse an essential reaction, the hydrolysis of pyrophosphate to inorganic phosphate. In addition, an evolutionarily ancient family of membrane-integral pyrophosphatases couple this hydrolysis to Na(+) and/or H(+) pumping, and so recycle some of the free energy from the pyrophosphate. The structures of the H(+)-pumping mung bean PPase and the Na(+)-pumping Thermotoga maritima PPase solved last year revealed an entirely novel membrane protein containing 16 transmembrane helices. The hydrolytic centre, well above the membrane, is linked by a charged "coupling funnel" to the ionic gate about 20Å away. By comparing the active sites, fluoride inhibition data and the various models for ion transport, we conclude that membrane-integral PPases probably use binding of pyrophosphate to drive pumping. PMID:23684653

Kajander, Tommi; Kellosalo, Juho; Goldman, Adrian

2013-05-16

270

Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter.  

PubMed

The FeoB family proteins are widely distributed prokaryotic membrane proteins involved in Fe(2+) uptake. FeoB consists of N-terminal cytosolic and C-terminal transmembrane domains. The N-terminal region of the cytosolic domain is homologous to small GTPase (G) proteins and is considered to regulate Fe(2+) uptake. The spacer region connecting the G and TM domains reportedly functions as a GDP dissociation inhibitor (GDI)-like domain that stabilizes the GDP-binding state. However, the function of the G and GDI-like domains in iron uptake remains unclear. Here, we report the structural and functional analyses of the FeoB cytosolic domain from Thermotoga maritima. The structure-based mutational analysis indicated that the interaction between the G and GDI-like domains is important for both the GDI and Fe(2+) uptake activities. On the basis of these results, we propose a regulatory mechanism of Fe(2+) uptake. PMID:19733088

Hattori, Motoyuki; Jin, Yaohua; Nishimasu, Hiroshi; Tanaka, Yoshiki; Mochizuki, Masahiro; Uchiumi, Toshio; Ishitani, Ryuichiro; Ito, Koichi; Nureki, Osamu

2009-09-03

271

Crystallization and preliminary X-ray diffraction analysis of the truncated cytosolic domain of the iron transporter FeoB.  

PubMed

FeoB-family proteins are widely distributed in bacteria and archaea and are involved in high-affinity Fe(2+) uptake through the plasma membrane. FeoB consists of an N-terminal cytosolic region followed by a C-terminal transmembrane region. The cytosolic region contains small GTPase and GDP dissociation inhibitor-like domains, which serve a regulatory function. The truncated cytosolic region of the iron transporter FeoB from Thermotoga maritima was overexpressed, purified and crystallized. Four native or SeMet crystal forms in a nucleotide-free state or in complex with either GDP or GMPPNP diffracted to resolutions of between 1.5 and 2.1 A. PMID:19652339

Jin, Yaohua; Hattori, Motoyuki; Nisimasu, Hiroshi; Ishitani, Ryuichiro; Nureki, Osamu

2009-07-25

272

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

2008-09-19

273

Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii  

PubMed Central

In bacteria and plants, dihydrodipicolinate synthase (DHDPS) plays a key role in the (S)-lysine biosynthesis pathway. DHDPS catalyzes the first step of the condensation of (S)-aspartate-?-semialdehyde and pyruvate to form an unstable compound, (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. The activity of DHDPS is allosterically regulated by (S)-lysine, a feedback inhibitor. The crystal structure of DHDPS from Methanocaldococcus jannaschii (MjDHDPS) was solved by the molecular-replacement method and was refined to 2.2?Å resolution. The structure revealed that MjDHDPS forms a functional homo­tetramer, as also observed in Escherichia coli DHDPS, Thermotoga maritima DHDPS and Bacillus anthracis DHDPS. The binding-site region of MjDHDPS is essentially similar to those found in other known DHDPS structures.

Padmanabhan, Balasundaram; Strange, Richard W.; Antonyuk, Svetlana V.; Ellis, Mark J.; Hasnain, S. Samar; Iino, Hitoshi; Agari, Yoshihiro; Bessho, Yoshitaka; Yokoyama, Shigeyuki

2009-01-01

274

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

PubMed

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. PMID:11542160

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

1989-01-01

275

Plant-derived wildlife repellents  

US Patent & Trademark Office Database

Products from the plant species Nerium oleander and, Urginea maritima, are prepared and tested as wildlife repellents comparing them with digitalis products. Chemical compounds derived from these plants including oleandrin, oleandrigenin, scillirosidin, digitoxigenin and digoxigenin are shown to cause nausea and emesis at low doses in pigeons and to repel, mice, rats, gophers, meadow voles and mountain beavers. After ingestion these animals quickly learn to avoid targets treated with the plant-derived repellents. When the remembrance of a treated food or other target lasts for an extended period of time it can be termed an aversion conditioning agent. Such products can be used for the protection of other plants, seeds, buildings, structures, communication cables and animals exposed to wildlife.

Verbiscar; Anthony J. (Sierra Madre, CA)

1994-10-18

276

POLYPEPTIDE AND POLYSACCHARIDE PROCESSING IN HYPERTHERMOPHILIC MICROORGANISMS  

SciTech Connect

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

KELLY, ROBERT M.

2008-12-22

277

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

278

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

2014-02-17

279

Correlation between thermostability and stability of glycosidases in ionic liquid.  

PubMed

The activity and stability of a ?-glycosidase (Thermus thermophilus) and two ?-galactosidases (Thermotoga maritima and Bacillus stearothermophilus) were studied in different hydrophilic ionic liquid (IL)/water ratios. For the ILs used, the glycosidases showed the best stability and activity in 1,3-dimethylimidazolium methyl sulfate [MMIM][MeSO(4)] and 1,2,3-trimethylimidazolium methyl sulfate [TMIM][MeSO(4)]. A close correlation was observed between the thermostability of the enzymes and their stability in IL media. At high IL concentration (80%), a time-dependent irreversible denaturing effect was observed on glycosidases while, at lower concentration (<30%), a reversible inactivation affecting mainly the k (cat) was obtained. The results demonstrate that highly thermostable glycosidases are more suitable for biocatalytic reactions in water-miscible ILs. PMID:21331585

Ferdjani, Salim; Ionita, Marina; Roy, Bimalendu; Dion, Michel; Djeghaba, Zeineddine; Rabiller, Claude; Tellier, Charles

2011-02-18

280

Ligand-induced conformational changes in a thermophilic ribose-binding protein  

SciTech Connect

Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (appTm value is 108 C) than the mesophilic Escherichia coli homolog (ecRBP) (appTm value is 56 C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.

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

2009-05-21

281

Non-Complexed Four Cascade Enzyme Mixture: Simple Purification and Synergetic Co-stabilization  

PubMed Central

Cell-free biosystems comprised of synthetic enzymatic pathways would be a promising biomanufacturing platform due to several advantages, such as high product yield, fast reaction rate, easy control and access, and so on. However, it was essential to produce (purified) enzymes at low costs and stabilize them for a long time so to decrease biocatalyst costs. We studied the stability of the four recombinant enzyme mixtures, all of which originated from thermophilic microorganisms: triosephosphate isomerase (TIM) from Thermus thermophiles, fructose bisphosphate aldolase (ALD) from Thermotoga maritima, fructose bisphosphatase (FBP) from T. maritima, and phosphoglucose isomerase (PGI) from Clostridium thermocellum. It was found that TIM and ALD were very stable at evaluated temperature so that they were purified by heat precipitation followed by gradient ammonia sulfate precipitation. In contrast, PGI was not stable enough for heat treatment. In addition, the stability of a low concentration PGI was enhanced by more than 25 times in the presence of 20 mg/L bovine serum albumin or the other three enzymes. At a practical enzyme loading of 1000 U/L for each enzyme, the half-life time of free PGI was prolong to 433 h in the presence of the other three enzymes, resulting in a great increase in the total turn-over number of PGI to 6.2×109 mole of product per mole of enzyme. This study clearly suggested that the presence of other proteins had a strong synergetic effect on the stabilization of the thermolabile enzyme PGI due to in vitro macromolecular crowding effect. Also, this result could be used to explain why not all enzymes isolated from thermophilic microorganisms are stable in vitro because of a lack of the macromolecular crowding environment.

Myung, Suwan; Zhang, Y-H Percival

2013-01-01

282

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

283

The multiple target use of spirodiclofen (Envidor 240 SC) in IPM pomefruit in Belgium.  

PubMed

Envidor 240 SC, active ingredient spirodiclofen is a broad spectrum acaricide acting via lipid biosynthesis inhibition (LBI) with no cross resistance to currently available acaricides and with additional insecticidal properties. Envidor is positive IPM listed but in frame of resistance management limited to one application per season. In pear growing Envidor constitutes an important tool in pear sucker control in a tandem strategy with abamectine. Being totally selective on predatory bugs Anthocoris nemoralis, Envidor installs a favourable low prey/predator ratio avoiding any damage of further 3rd or 4th Psylla generations. The application of Envidor on the second Psylla generation coincides with the migration of Lepidosaphes ulmi scales and with the spread of rustmites Epitremerus pyri on which season long control is achieved. On apples, Envidor settled as an important tool for scales control especially on the wood but recently its acaricidal use revivals. This is induced by the withdrawal of totylfluanid with its regulating mite control and with the further efficacy decline of registered METI-acaricides. Even with full introduction of Typhlodromus pyri, mites and rustmites may unexpectedly flear up. On Typhlodromus pyri, Envidor is IOBC 2 classified (slightly harmful) but the favourable low prey/predator ratio and within season recovery make it full IPM compatible. On Aculus schlechtendali, apple rustmite with a short generation cyclus, the larval and fecundity effects of Envidor lead to an explicit knock down efficacy. On mixed populations of Panonychus ulmi with longer generation cyclus, Envidor shows a slow initial effect with culminating efficacy after 2-3 weeks and a long lasting efficacy of more than 100 days, avoiding any leaf or consequent fruit damage. High rain fastness and the right positioning at 30-50 % hatching of winter eggs make of Envidor a very consistent correction acaride. The addition of a surfactant is not recommended for mite control. Up to now, no shifting in susceptibility of Envidor on Panonychus ulmi or Tetranychus urticae is found in Belgian orchards. Since Envidor combines both in apples and pears an efficacy on multiple pests occurring simultaneously after flowering, with a good selectivity profile on predators, parasitoïds, syrphids, lacewings and earwigs, it remains a most important tool in modern IPM pomefruit. PMID:20218531

De Maeyer, Luk; Geerinck, Rik

2009-01-01

284

Effect of tidal flooding on metal distribution in pore waters of marsh sediments and its transport to water column (Tagus estuary, Portugal).  

PubMed

Sediment cores and flooding water were collected at 0, 5, 10 and 50 min of tidal inundation in two sites of the Rosário salt marsh located in the proximity of a heavy industrialised zone of Tagus estuary colonised by pure stands of Spartina maritima (low marsh) and Sarcocornia fruticosa (high marsh). The cores were sliced in 5 cm layers and sediment solids, pore water, and belowground biomass were separated in order to measure Fe, Mn, Zn, Cu, Pb and Cd. The pore waters and sediments colonised by S. fruticosa, as well as belowground biomass presented high concentrations of Zn, Cu, Pb and Cd. Belowground biomass exceeded in one order of magnitude the metal levels in sediments. Abundant belowground biomass and small dimension of S. fruticosa roots facilitates the root-sediment interactions and presumably the metal retention in the higher marsh. The novelty of this work is the result of tidal inundation on pore water concentrations of metals in salt marsh sediments and their exportation to the water column. Concentrations in pore waters varied at minute scales, but 50 min after inundation levels were comparable to the initial values. The metal levels in flooding water increased abruptly during the first 10-20 min of inundation. The concentration peaks (Fe = 60 ?M, Mn = 7.5 ?M, Zn = 1.7 ?M, Cu = 550 nM, Pb = 100 nM, Cd = 1.7 nM) reached one to two orders of magnitude above the values found in subsequent periods of inundation. The advective transports during the 50 min inundation during two daily pulses of inundation were: Fe (9520 and 1640), Mn (24), Zn (220 and 82), Cu (74 and 16), Pb (13 and 15) and Cd (0.3 and 0.08) for S. maritima and S. fruticosa, respectively. These quantities exceeded three to four orders of magnitude of the corresponding predicted diffusive fluxes (Fick 1st law) on a daily basis. This work emphasizes the importance of tidal flooding over salt marsh sediments to the metal exportation to the water column. PMID:20727578

Santos-Echeandía, Juan; Vale, Carlos; Caetano, Miguel; Pereira, Patrícia; Prego, Ricardo

2010-07-22

285

Spatial and temporal habitat partitioning by zooplankton in the Bornholm Basin (central Baltic Sea)  

NASA Astrophysics Data System (ADS)

The deep basins in the Baltic Sea such as the Bornholm Basin (BB) are subject to seasonal changes in the strength of physico-chemical stratification. These depth-related changes in key abiotic factors are strong drivers of habitat partitioning by the autochthonous zooplankton community. Species-specific ecophysiological preferences often result in both seasonal and inter-annual changes in vertical abundance that, when combined with depth-specific water currents, also lead to horizontal differences in spatial distribution. The present study documented the seasonal and depth-specific changes in the abundance and species composition of zooplankton in the BB based upon broad-scale survey data: 832 vertically-resolved (10 m) multinet samples collected at nine stations between March 2002 and May 2003. Changes in the zooplankton community were significantly correlated with changes in ambient hydrography. Each of five taxa (Bosmina coregoni maritima, Acartia spp., Pseudocalanus spp., Temora longicornis, Synchaeta spp.) contributed >10% to the zooplankton community composition. The appearance of cladocerans was mainly correlated with the phenology of thermocline development in the spring. The cladoceran B. coregoni maritima was a dominant member of this community during the warmest periods, preferring the surface waters above the thermocline. Copepods exhibited distinct, ontogenetic and seasonal changes in their distribution. The rotifers (Synchaeta sp.) were the most abundant zooplankton in May. Based on a multivariate approach and the evaluation of vertical distribution patterns, five major habitat utilisation modes were identified that were based, to a large extent, on the dynamics of thermal and haline stratification of the Baltic Sea. Our statistical analysis of one of the most thorough datasets collected on Baltic zooplankton in recent decades reveals some of the factors that make this stratified system highly dynamic with respect to the spatial overlap between predators and prey. As fish and gelatinous plankton often feed in distinct layers and/or exhibit feeding migrations, the inhomogeneous distribution of potential prey can result in a spatial mismatch. Based on the five modes identified at the community level for zooplankton, we discuss how climate-driven hydrographic variability may influence the strength of trophic coupling within the Bornholm Basin.

Schulz, Jan; Peck, Myron A.; Barz, Kristina; Schmidt, Jörn Oliver; Hansen, Frank C.; Peters, Janna; Renz, Jasmin; Dickmann, Miriam; Mohrholz, Volker; Dutz, Jörg; Hirche, Hans-Jürgen

2012-12-01

286

Tidal events and salt-marsh structure influence black mangrove (Avicennia germinans) recruitment across an ecotone.  

PubMed

Field experiments were conducted at a black mangrove-salt-marsh ecotone in southwest Florida (U.S.A.) to investigate retention of propagules of the black mangrove, Avicennia germinans, by salt-marsh plants as a mechanism of facilitation operating on recruitment success at landward boundaries. Buoyant A. germinans propagules are dispersed by tides, and stranding is required for establishment; therefore, processes that enable stranding should facilitate mangrove recruitment. We expected the physical structure of salt-marsh vegetation to define propagule retention capacity, and we predicted that salt-marsh plants with distinct growth forms would differentially retain propagules. Experimental monoculture plots (1 m2) of salt-marsh plants with different growth forms (Sporobolus virginicus [grass], Sesuvium portulacastrum [succulent forb], and Batis maritima [succulent scrub]) were created, and A. germinans propagules were emplaced into these plots and monitored over time. For comparison, propagules were also placed into natural polyculture plots (1 m2). Polyculture plots contained at least two of the salt-marsh plant taxa selected for monoculture treatments, and S. virginicus was always present within these polyculture plots. Natural polyculture plots retained 59.3% +/- 11.0% (mean +/- SE) of emplaced propagules. Monocultures varied in their propagule retention capacities with plots of S. virginicus retaining on average 65.7% +/- 11.5% of transplanted propagules compared to 7.2% +/- 1.8% by B. maritima and 5.0% +/- 1.9% by S. portulacastrum. Plots containing S. virginicus retained a significantly greater percentage of emplaced propagules relative to the two succulent salt-marsh taxa. Furthermore, propagule entrapment, across all treatments, was strongly correlated with salt-marsh structure (r2 = 0.6253, P = 0.00001), which was estimated using an indirect quantitative metric (lateral obstruction) calculated from digital images of plots. Overall, our findings imply that entrapment of propagules by salt-marsh plants may be facilitative if propagules are dispersed beyond the established tree line by spring or storm tides, and that facilitation may be sustained over time. We conclude that salt-marsh ecotone permeability may modulate landward encroachment by A. germinans, and that interactions among the early life history stages of black mangroves and neighboring plants may direct community responses to climate change. PMID:22919911

Peterson, Jennifer M; Bell, Susan S

2012-07-01

287

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

PubMed

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. PMID:24121353

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

2013-10-02

288

Mesohaline submerged aquatic vegetation survey along the U.S. gulf of Mexico coast, 2001 and 2002: A salinity gradient approach  

USGS Publications Warehouse

Distribution of marine submerged aquatic vegetation (SAV; i.e., seagrass) in the northern Gulf of Mexico coast has been documented, but there are nonmarine submersed or SAV species occurring in estuarine salinities that have not been extensively reported. We sampled 276 SAV beds along the gulf coast in Florida, Alabama, Mississippi, Louisiana, and Texas in 2001 and 2002 in oligohaline to polyhaline (0 to 36 parts per thousand) waters to determine estuarine SAV species distribution and identify mesohaline SAV communities. A total of 20 SAV and algal species was identified and habitat characteristics such as salinity, water depth, pH, conductivity, turbidity, dissolved oxygen, and sediment composition were collected. Fourteen SAV species occurred two or more times in our samples. The most frequently occurring species was Ruppia maritima L. (n = 148), occurring in over half of SAV beds sampled. Eleocharis sp. (n = 47), characterized with an emergent rather than submerged growth form, was a common genus in the SAV beds sampled. A common marine species was Halodule wrightii Asch. (n = 36). Nonindigenous species Myriophyllum spicatum L. (n = 31) and Hydrilla verticillata (L. f.) Royle (n = 6) were present only in oligohaline water. Analyzing species occurrence and environmental characteristics using canonical correspondence and two-way indicator species analysis, we identify five species assemblages distinguished primarily by salinity and depth. Our survey increases awareness of nonmarine SAV as a natural resource in the gulf, and provides baseline data for future research. ?? 2009 by the Marine Environmental Sciences Consortium of Alabama.

Merino, J. H.; Carter, J.; Merino, S. L.

2009-01-01

289

Mesohaline submerged aquatic vegetation survey along the U.S. gulf of Mexico coast, 2000: A stratified random approach  

USGS Publications Warehouse

Estimates of submerged aquatic vegetative (SAV) along the U.S. Gulf of Mexico (Gulf) generally focus on seagrasses. In 2000, we attempted a synoptic survey of SAV in the mesohaline (5-20 ppt) zone of estuarine and nearshore areas of the northeastern Gulf. Areas with SAV were identified from existing aerial 1992 photography, and a literature review was used to select those areas that were likely to experience mesohaline conditions during the growing season. In 2000, a drought year, we visited 217 randomly selected SAV beds and collected data on species composition and environmental conditions. In general, sites were either clearly polyhaline (2: 20 ppt) or oligohaline (S 5 ppt), with only five sites measuring between 5 and 20 ppt. Ruppia maritima L. (13-35 ppt, n = 28) was the only species that occurred in mesohaline salinities. Halodule wrightii Asch. occurred in 73% of the beds. The nonindigenous Myriophyllum spicatum L. was present in four locations with salinities below 3 ppt. No nonindigenous macroalgae were identified, and no nonindigenous angiosperms occurred in salinities above 3 ppt. Selecting sample locations based on historical salinity data was not a successful strategy for surveying SAV in mesohaline systems, particularly during a drought year. Our ability to locate SAV beds within 50 m of their aerially located position 8 yr later demonstrates some SAV stability in the highly variable conditions of the study area. ?? 2009 by the Marine Environmental Silences Consortium of Alabama.

Carter, J.; Merino, J. H.; Merino, S. L.

2009-01-01

290

Assembly in vitro of Rhodococcus jostii RHA1 encapsulin and peroxidase DypB to form a nanocompartment.  

PubMed

Rhodococcus jostii RHA1 peroxidase DypB has been recently identified as a bacterial lignin peroxidase. The dypB gene is cotranscribed with a gene encoding an encapsulin protein, which has been shown in Thermotoga maritima to assemble to form a 60-subunit nanocompartment, and DypB contains a C-terminal sequence motif that is thought to target the protein to the encapsulin nanocompartment. R. jostii RHA1 encapsulin protein was overexpressed in R. jostii RHA1, and purified as a high-Mr assembly (Mr > 10(6)). The purified nanocompartment could be disassembled to form a low-Mr species by treatment at pH 3.0, and reassembled to form an assembly of similar size and shape, as assessed by dynamic light scattering. Recombinant DypB could be assembled in vitro with monomeric encapsulin to form an assembly of similar size to the encapsulin-only nanocompartment, as assessed by gel filtration. The assembled complex showed enhanced lignin degradation activity per milligram of DypB present as compared with native DypB, as determined with a nitrated lignin UV-visible assay method. The measured stoichiometry of 8.6 ?mol encapsulin/?mol DypB in the complex was similar to the value of 10 predicted from the crystal structure. PMID:23560779

Rahmanpour, Rahman; Bugg, Timothy D H

2013-04-08

291

Abiotic methyl bromide formation from vegetation, and its strong dependence on temperature.  

PubMed

Methyl bromide (CH3Br) is the most abundant brominated organic compound in the atmosphere. It is known to originate from natural and anthropogenic sources, although many uncertainties remain regarding strengths of both sources and sinks and the processes leading to its formation. In this study a potential new CH3Br source from vegetation has been examined, analogous to the recently discovered abiotic formation of methyl chloride from plant pectin. Several plant samples with known bromine content, including ash (Fraxinus excelsior), saltwort (Batis maritima), tomato reference material (NIST-1573a), hay reference material (IAEA V-10), and also bromine enriched pectin, were incubated in the temperature range of 25-50 degrees C and analyzed for CH3Br emission using gas chromatography/mass spectrometry. All plant samples inspected showed an exponential increase in CH3Br emission as a function of temperature increase, i.e., emissions were observed to approximately double with every 5 degrees C rise in temperature. Next to temperature, it was found that emissions of CH3Br were also dependent on the bromine content of the plants. The highest CH3Br release rates were found for the saltwort which contained the highest bromine concentration. Arrhenius plots confirmed that the observed emissions were from an abiotic origin. The contribution of abiotic CH3Br formation from vegetation to the global budget will vary geographically as a result of regional differences in both temperature and bromide content of terrestrial plants. PMID:18853797

Wishkerman, Asher; Gebhardt, Sarah; McRoberts, Colin W; Hamilton, John T G; Williams, Jonathan; Keppler, Frank

2008-09-15

292

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

293

Structure and electrostatic property of cytoplasmic domain of ZntB transporter.  

SciTech Connect

ZntB is the distant homolog of CorA Mg{sup 2+} transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn{sup 2+} and Cd{sup 2+}, but not Mg{sup 2+}. Here, we report the 1.90 {angstrom} crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn{sup 2+} or Cd{sup 2+} binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl{sup -} ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl{sup -} ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport.

Tan, K.; Sather, A.; Robertson, J. L.; Moy, S.; Roux, B.; Joachimiak, A.; Biosciences Division; Cornell Univ.; Univ. of Chicago

2009-10-01

294

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

295

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

296

Rational design of a fusion partner for membrane protein expression in E. coli  

PubMed Central

We have designed a novel protein fusion partner (P8CBD) to utilize the co-translational SRP pathway in order to target heterologous proteins to the E. coli inner membrane. SRP-dependence was demonstrated by analyzing the membrane translocation of P8CBD-PhoA fusion proteins in wt and SRP-ffh77 mutant cells. We also demonstrate that the P8CBD N-terminal fusion partner promotes over-expression of a Thermotoga maritima polytopic membrane protein by replacement of the native signal anchor sequence. Furthermore, the yeast mitochondrial inner membrane protein Oxa1p was expressed as a P8CBD fusion and shown to function within the E. coli inner membrane. In this example, the mitochondrial targeting peptide was replaced by P8CBD. Several practical features were incorporated into the P8CBD expression system to aid in protein detection, purification, and optional in vitro processing by enterokinase. The basis of membrane protein over-expression toxicity is discussed and solutions to this problem are presented. We anticipate that this optimized expression system will aid in the isolation and study of various recombinant forms of membrane-associated protein.

Luo, Jianying; Choulet, Julie; Samuelson, James C

2009-01-01

297

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

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

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

300

Comparative study of antioxidant properties and total phenolic content of 30 plant extracts of industrial interest using DPPH, ABTS, FRAP, SOD, and ORAC assays.  

PubMed

Aqueous extracts of 30 plants were investigated for their antioxidant properties using DPPH and ABTS radical scavenging capacity assay, oxygen radical absorbance capacity (ORAC) assay, superoxide dismutase (SOD) assay, and ferric reducing antioxidant potential (FRAP) assay. Total phenolic content was also determined by the Folin-Ciocalteu method. Antioxidant properties and total phenolic content differed significantly among selected plants. It was found that oak (Quercus robur), pine (Pinus maritima), and cinnamon (Cinnamomum zeylanicum) aqueous extracts possessed the highest antioxidant capacities in most of the methods used, and thus could be potential rich sources of natural antioxidants. These extracts presented the highest phenolic content (300-400 mg GAE/g). Mate (Ilex paraguariensis) and clove (Eugenia caryophyllus clovis) aqueous extracts also showed strong antioxidant properties and a high phenolic content (about 200 mg GAE/g). A significant relationship between antioxidant capacity and total phenolic content was found, indicating that phenolic compounds are the major contributors to the antioxidant properties of these plants. PMID:19199445

Dudonné, Stéphanie; Vitrac, Xavier; Coutière, Philippe; Woillez, Marion; Mérillon, Jean-Michel

2009-03-11

301

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

2013-07-23

302

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

303

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

304

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 (2.04M) 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 5days 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

2013-08-28

305

Ritual plants of Muslim graveyards in northern Israel  

PubMed Central

This article surveys the botanical composition of 40 Muslim graveyards in northern Israel, accompanied by an ethnobotanical study of the folkloristic traditions of the use of these plants in cemeteries. Three groups of plants were found to be repeated systematically and were also recognized for their ritual importance: aromatics herbs (especially Salvia fruticosa and Rosmarinus officinalis), white flowered plants (mainly Narcissus tazetta, Urginea maritima, Iris spp. and Pancratium spp.) and Cupressus sempervirens as the leading cemetery tree. As endemic use we can indicate the essential role of S. fruticosa as the main plant used in all human rites of passage symbolizing the human life cycle. The rosemary is of European origin while the use of basil is of Indian influence. The use of white flowers as cemeteries plants reflects an old European influence and almost the same species are used or their congeners. Most of the trees and shrubs that are planted in Muslim cemeteries in Israel have the same use in ancient as well in modern European cultures. In conclusion, our findings on the occurrence of plants in graveyards reflect the geographic situation of Israel as a crossroads in the cultural arena between Asia and Europe. Most of the traditions are common to the whole Middle East showing high relatedness to the classical world as well as to the present-day Europe.

Dafni, Amots; Lev, Efraim; Beckmann, Sabine; Eichberger, Christian

2006-01-01

306

Mercury in sediments and vegetation in a moderately contaminated salt marsh (Tagus Estuary, Portugal).  

PubMed

Depth variations of total mercury (Hg) and methylmercury (MeHg) concentrations were studied in cores from non-colonized sediments, sediments colonized by Halimione portulacoides, Sarcocorniafruticosa and Spartina maritima and belowground biomass, in a moderately contaminated salt marsh (Tagus Estuary, Portugal). Concentrations in belowground biomass exceeded up to 3 (Hg) and 15 (MeHg) times the levels in sediments, and up to 198 (Hg) and 308 (MeHg) times those found in aboveground parts. Methylmercury in colonized sediments reached 3% of the total Hg, 50 times above the maximum values found in non-colonized sediments. The absence of correlations between total Hg concentrations in sediments and the corresponding MeHg levels suggested that methylation was only dependent on the environmental and microbiological factors. The analysis of belowground biomass at high-depth resolution (2 cm) provided evidence that Hg and MeHg were actively absorbed from sediments, with higher enrichment factors at layers where higher microbial activity was probably occurring. The results obtained in this study indicated that the biotransformation of Hg to the toxic MeHg could increase the toxicity of plant-colonized sediments. PMID:21179951

Canário, João; Vale, Carlos; Poissant, Laurier; Nogueira, Marta; Pilote, Martin; Branco, Vasco

2010-01-01

307

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

308

Structure-guided discovery of new deaminase enzymes.  

PubMed

A substantial challenge for genomic enzymology is the reliable annotation for proteins of unknown function. Described here is an interrogation of uncharacterized enzymes from the amidohydrolase superfamily using a structure-guided approach that integrates bioinformatics, computational biology, and molecular enzymology. Previously, Tm0936 from Thermotoga maritima was shown to catalyze the deamination of S-adenosylhomocysteine (SAH) to S-inosylhomocysteine (SIH). Homologues of Tm0936 homologues were identified, and substrate profiles were proposed by docking metabolites to modeled enzyme structures. These enzymes were predicted to deaminate analogues of adenosine including SAH, 5'-methylthioadenosine (MTA), adenosine (Ado), and 5'-deoxyadenosine (5'-dAdo). Fifteen of these proteins were purified to homogeneity, and the three-dimensional structures of three proteins were determined by X-ray diffraction methods. Enzyme assays supported the structure-based predictions and identified subgroups of enzymes with the capacity to deaminate various combinations of the adenosine analogues, including the first enzyme (Dvu1825) capable of deaminating 5'-dAdo. One subgroup of proteins, exemplified by Moth1224 from Moorella thermoacetica, deaminates guanine to xanthine, and another subgroup, exemplified by Avi5431 from Agrobacterium vitis S4, deaminates two oxidatively damaged forms of adenine: 2-oxoadenine and 8-oxoadenine. The sequence and structural basis of the observed substrate specificities were proposed, and the substrate profiles for 834 protein sequences were provisionally annotated. The results highlight the power of a multidisciplinary approach for annotating enzymes of unknown function. PMID:23968233

Hitchcock, Daniel S; Fan, Hao; Kim, Jungwook; Vetting, Matthew; Hillerich, Brandan; Seidel, Ronald D; Almo, Steven C; Shoichet, Brian K; Sali, Andrej; Raushel, Frank M

2013-09-04

309

A possible degree of motional freedom in bacterial chemoreceptor cytoplasmic domains and its potential role in signal transduction  

PubMed Central

We describe an array of gaps in an antiparallel four-helix bundle structure, the cytoplasmic domains of bacterial chemoreceptors. For a given helix, the side chain interactions that define a helix’s position are analyzed in terms of residue interfaces, the most important of which are a-a, g-g, d-d, g-d, and a-d. It was found that the interdigitation of the side groups does not entirely fill the space along the long axis of the structure, which results in a rather regular array of gaps. A simulated piston motion of helix CD1 along the helical axis direction by 1.2Å shows that 85% of the side chain interactions still satisfy Van der Waals criteria, while the remaining clashes could be avoided by small rotations of side chains. Therefore, two states could exist in the structure, related by a piston motion. Analysis of the crystal structure of a small four-helix bundle, the P1short domain of CheA in Thermotoga Maritima, reveals that the two coexisting states related by a 1.3-1.7Å piston motion are defined by the same mechanism. This two-state model is a plausible candidate mechanism for the long distance signal transduction in bacterial chemoreceptors and is qualitatively consistent with literature chemoreceptor mutagenesis results. Such a mechanism could exist in many other structures with interdigitating ?-helices.

Hu, Weiguo

2011-01-01

310

Analysis of 13 asteroid lightcurves obtained at the Palmer Divide Observatory  

NASA Astrophysics Data System (ADS)

The lightcurves for the following asteroids were obtained and then analyzed to find the synodic period and amplitude. 321 Florentina: 2.8711±0.0003h, 0.37±0.02m; 787 Moskva: 6.056±0.001h, 0.61±0.02m; 839 Valborg: 10.366±0.005h, 0.14±0.02m; 912 Maritima: 48.43±0.05h, >0.12±0.02m; 1176 Lucidor: 4.0791±0.0006h, 0.06±0.02m; 1862 Apollo: 3.0680±0.0002h, 0.30-1.20±0.02m; 2266 Tchaikovsky: 4.883±0.003h, 0.04±0.01m; 2951 Perepadin: 4.7808±0.0001h, 0.60±0.02m; 5108 Lubeck: 8.769±0.003, 0.43±0.02m; (17864) 1998 KK38: 6.56±0.01h, 0.17±0.02m; (18582) 1997 XK9: 114±10h, 0.94±0.02m; (20231) 1997 YK: 48.2±0.1h, >0.22±0.02m. Asteroid 868 Lova was also observed but its long period is only constrained as >24h.

Warner, Brian D.

2006-06-01

311

The effect of nitrogen loading on a brackish estuarine faunal community: A stable isotope approach  

USGS Publications Warehouse

Coastal ecosystems worldwide face increased nutrient enrichment from shoreline and watershed development and atmospheric pollution. We investigated the response of the faunal community of a small microtidal estuary dominated by Ruppia maritima (widgeon grass) in Maine, United States, to increased nitrogen loading using an in situ mesocosm enrichment experiment. Community response was characterized by assessing quantitative shifts in macroin-vertebrate community composition and identifying changes in food web structure using stable carbon and nitrogen isotope ratios of producers and consumers. The community was dominated by brackish water invertebrates including midge larvae, oligochaetes, damselfly larvae, amphipods, and ostracods. Experimental nutrient additions resulted in significantly lower densities of herbivorous chironomids and predatory damselflies and greater densities of deposit feeding oligochaetes. Grazing midge larvae (Chironomidae: Dicrotendipes, Cricotopus) consumed epiphytic algae under both natural and enriched conditions. Deposit feeding Chironomus was dependent on allochthonous sources of detritus under natural conditions and exhibited a shift to autochthonous sources of detritus under enriched conditions. Predatory Enallagma primarily consumed grazing chironomids under all but the highest loading conditions. Experimental nutrient loading resulted in an increase in generalist deposit feeders dependent on autochthonous sources of detritus.

Keats, R.A.; Osher, L.J.; Neckles, H. A.

2004-01-01

312

Ecology of mysid shrimps in the Bornholm Basin (central Baltic Sea)  

NASA Astrophysics Data System (ADS)

Mysid shrimps are an important trophic link in the food web of the Baltic Sea. In 2002 and 2003 we investigated species composition, distribution, life cycle and prey in the Bornholm Basin (central Baltic). Three species and one genus were identified: Mysis mixta, Neomysis integer, Mesopodopsis slabberi and Praunus sp . The dominant M. mixta and N. integer occurred in the whole study area but were more abundant in the peripheral, more shallow regions. Size frequency distribution indicated one generation for M. mixta and probably two for N. integer. Main prey of all size classes in both species was the cladoceran Bosmina coregoni maritima during summer and autumn. In spring and winter also copepods of the species Temora longicornis and Pseudocalanus acuspes were important prey items. Detritus and phytoplankton cells were of minor importance and many individuals had empty guts. Mysid shrimps in the deep basin might be advected from more shallow areas, as the abundance of all species was much lower than in coastal regions. The deep Bornholm Basin does not seem to be a favourable habitat, probably due to the inaccessibility of the oxygen deficient bottom layer. Under current hydrographic conditions mysids are probably not important predators of zooplankton and thus not competitors of planktivorous fish in the Bornholm Basin.

Barz, Kristina; Hirche, Hans-Jürgen

2009-12-01

313

A robust protein host for anchoring chelating ligands and organocatalysts.  

PubMed

In order to put the previously proposed concept of directed evolution of hybrid catalysts (proteins that harbor synthetic transition-metal catalysts or organocatalysts) into practice, several prerequisites must be met. The availability of a robust host protein that can be expressed in sufficiently large amounts, and that can be purified in a simple manner is crucial. The thermostable enzyme tHisF from Thermotoga maritima, which constitutes the synthase subunit of a bi-enzyme complex that is instrumental in the biosynthesis of histidine, fulfills these requirements. In the present study, fermentation has been miniaturized and parallelized, as has purification of the protein by simple heat treatment. Several mutants with strategically placed cysteines for subsequent bioconjugation have been produced. One of the tHisF mutants, Cys9Ala/Asp11Cys, was subjected to bioconjugation by the introduction of a variety of ligands for potential metal ligation, of a ligand/metal moiety, and of several organocatalytic entities that comprise a flavin or thiazolium salts. Characterization by mass spectrometry and tryptic digestion was achieved. As a result of this study, a platform for performing future directed evolution of these hybrid catalysts is now available. PMID:18273849

Reetz, Manfred T; Rentzsch, Martin; Pletsch, Andreas; Taglieber, Andreas; Hollmann, Frank; Mondière, Régis J G; Dickmann, Norbert; Höcker, Birte; Cerrone, Simona; Haeger, Michaela C; Sterner, Reinhard

2008-03-01

314

Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer.  

PubMed

The transmembrane conformation of Thermotoga maritima CorA, a magnesium transport system, has been studied in its Mg(2+)-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 toward the five-fold symmetry axis in position to electrostatically influence divalent ion translocation. Electrostatic analysis of our model suggest that, in agreement with the crystal structure, Mg(2+) -bound CorA is in a closed conformation. The present results suggest that long-range structural rearrangements are necessary to allow Mg(2+) translocation. PMID:20637423

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

2010-07-14

315

Reconstruction of the Chemotaxis Receptor-Kinase Assembly  

SciTech Connect

In bacterial chemotaxis, an assembly of transmembrane receptors, the CheA histidine kinase and the adaptor protein CheW processes environmental stimuli to regulate motility. The structure of a Thermotoga maritima receptor cytoplasmic domain defines CheA interaction regions and metal ion-coordinating charge centers that undergo chemical modification to tune receptor response. Dimeric CheA-CheW, defined by crystallography and pulsed ESR, positions two CheWs to form a cleft that is lined with residues important for receptor interactions and sized to clamp one receptor dimer. CheW residues involved in kinase activation map to interfaces that orient the CheW clamps. CheA regulatory domains associate in crystals through conserved hydrophobic surfaces. Such CheA self-contacts align the CheW receptor clamps for binding receptor tips. Linking layers of ternary complexes with close-packed receptors generates a lattice with reasonable component ratios, cooperative interactions among receptors and accessible sites for modification enzymes.

Park,S.; Borbat, P.; Gonzalez-Bonet, G.; Bhatnagar, J.; Pollard, A.; Freed, J.; Bilwes, A.; Crane, B.

2006-01-01

316

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

317

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

318

A ConA-like lectin from Dioclea guianensis Benth. has antifungal activity against Colletotrichum gloeosporioides, unlike its homologues, ConM and ConA.  

PubMed

This study reports on the antifungal activity of Dgui, a ConA-like lectin from Dioclea guianensis seeds. Dgui inhibited conidial germination but not mycelial growth of Colletotrichum gloeosporioides. The lectins ConA and ConM from Canavalia ensiformis and Canavalia maritima, respectively, share high levels of amino acid sequence similarity (>84%) with Dgui and have the same specificity toward glucose/mannose but had no effect on the fungus. Fluorescence microscopy showed that both Dgui and ConM bind to C. gloeosporioides ungerminated conidia. However, Dgui did not bind to C. gloeosporioides germinated conidia and germ tubes and was not inhibitory to mycelial growth. Because only Dgui inhibited germination of the fungus, C. gloeosporioides conidia might have surface-specific germination targets recognized by Dgui but not by its homologues, ConM and ConA. Therefore, Dgui is a candidate for biotechnological approaches for improving the resistance of various nutritionally and commercially important crops that are affected by C. gloeosporioides. PMID:20201549

Araújo-Filho, José H; Vasconcelos, Ilka M; Martins-Miranda, Aparecida S; Gondim, Darcy M F; Oliveira, José T A

2010-04-14

319

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

320

Long-term effects of mercury in a salt marsh: hysteresis in the distribution of vegetation following recovery from contamination.  

PubMed

During four decades, the Ria de Aveiro was subjected to the loading of mercury from a chlor-alkali industry, resulting in the deposition of several tons of mercury in the sediments. The present study evaluates the impact of this disturbance and the recovery processes, temporally and spatially, by means of examining the richness of the species of salt marsh plants and mercury concentrations in sediments over the last fifty years. The temporal assessment showed that the mercury loading induced a shift in the species composition of the salt marsh from a non-disturbed salt marsh with higher species richness to an alternative state dominated by Phragmites australis. The horizontal assessment, through a mercury gradient, presents the same trend, indicating that P. australis is the species most tolerant to higher mercury concentrations, comparative to Halimione portulacoides, Arthrocnemum fruticosum, Triglochin maritima, Juncus maritimus and Scirpus maritimus. After the reduction of mercury discharges in 1994, the salt marsh shows a slowly return path recovery response. The hysteresis in the response results in the temporal gap between the reduction in mercury concentrations in the sediment and the salt marsh species richness response, comparatively to the existing diversity in the local reference marsh. PMID:18061237

Válega, M; Lillebø, A I; Pereira, M E; Duarte, A C; Pardal, M A

2007-12-03

321

Floral developmental evidence for the systematic position of Batis (Bataceae).  

PubMed

Molecular phylogenies have associated Bataceae with Salvadoraceae and Koeberliniaceae in an expanded Brassicales. Despite a long taxonomic history, the knowledge of the flower of Batis is still fragmentary. The floral development of pistillate and staminate inflorescences of Batis maritima was investigated to understand homologies of floral structures and to discuss the phylogenetic position of Bataceae within the Brassicales. There has been considerable controversy in the past about the male flower, especially on the nature of the petals and the tubular structure enclosing the flower. Developmental evidence confirms that the male flower is built on a basic tetramerous bauplan and that the tubular structure is derived from four congenitally fused sepal lobes with the three anterior lobes highly reduced. The development of petals and stamens is unidirectional, and the androecium initiates the median stamens before the lateral stamens, suggesting the existence of two whorls. The pistillate flowers are reduced to the bare minimum with two transversal carpels enclosed by a bract. Partial inflorescences function as a swollen dispersal unit. The vestigial stipules probably represent colleters and are not homologous with true stipules. Several characters of Batis are reminiscent of the Brassicaceae, although a link with Salvadoraceae and Koeberliniaceae cannot be excluded. PMID:21652455

Ronse De Craene, Louis P

2005-04-01

322

Identification of unknown protein function using metabolite cocktail screening  

PubMed Central

Summary Proteins of unknown function comprise a significant fraction of sequenced genomes. Defining the roles of these proteins is vital to understanding cellular processes. Here, we describe a method to determine a protein function based on the identification of its natural ligand(s) by the crystallographic screening of the binding of a metabolite library, followed by a focused search in the metabolic space. The method was applied to two protein families with unknown function, PF01256 and YjeF_N. The PF01256 proteins, represented by YxkO from Bacillus subtilis and the C-terminal domain of Tm0922 from Thermotoga maritima, were shown to catalyze ADP/ATP-dependent NAD(P)H-hydrate dehydratation, a previously described orphan activity. The YjeF_N proteins, represented by mouse apolipoprotein A-I binding protein and the N-terminal domain of Tm0922, were found to interact with an adenosine diphosphoribose-related substrate and likely serve as ADP-ribosyltransferases. Crystallographic screening of metabolites serves as an efficient tool in functional analyses of uncharacterized proteins.

Shumilin, Igor A.; Cymborowski, Marcin; Chertihin, Olga; Jha, Kula N.; Herr, John C.; Lesley, Scott A.; Joachimiak, Andrzej; Minor, Wladek

2012-01-01

323

A survey of zinc, copper and cadmium concentrations in salt marsh plants along the Dutch coast.  

PubMed

In autumn 1986, plants and soil were collected from the lower and the higher salt marsh zones of salt marshes along the Dutch coast. The main purpose was to get an overview of Zn, Cu and Cd concentrations in six dominant species of salt marsh plants. The roots and shoots of the plants were analysed for Zn, Cu and Cd. The highest heavy metal concentrations were found in plants collected from salt marshes near harbour areas and/or that are known to receive contaminated fluvial sediment. Dicotyledonous plant species tended to have similar heavy metal concentrations in roots and shoots, whereas in monocotyledonous species the concentrations in the roots were two to three times higher than in the shoots. Differences in accumulation in the roots between elements and between plant species were found. Cd was accumulated more than Zn or Cu. Triglochin maritima shows a low Cd uptake by roots, whereas Spartina anglica and Scirpus maritimus tend to accumulate it. The fraction of soil particles smaller than 63 microm, loss on ignition and Zn, Cu and Cd concentrations were determined in soil samples. The highest Zn, Cu and Cd concentrations in the soil were found at salt marshes in the Western Scheldt area and were nine, five and 20 times higher than background levels, respectively. PMID:15092100

Otte, M L; Bestebroer, S J; van der Linden, J M; Rozema, J; Broekman, R A

1991-01-01

324

Structure-based design and screening of inhibitors for an essential bacterial GTPase, Der.  

PubMed

Der is an essential and widely conserved GTPase that assists assembly of a large ribosomal subunit in bacteria. Der associates specifically with the 50S subunit in a GTP-dependent manner and the cells depleted of Der accumulate the structurally unstable 50S subunit, which dissociates into an aberrant subunit at a lower Mg(2+) concentration. As Der is an essential and ubiquitous protein in bacteria, it may prove to be an ideal cellular target against which new antibiotics can be developed. In the present study, we describe our attempts to identify novel antibiotics specifically targeting Der GTPase. We performed the structure-based design of Der inhibitors using the X-ray crystal structure of Thermotoga maritima Der (TmDer). Virtual screening of commercially available chemical library retrieved 257 small molecules that potentially inhibit Der GTPase activity. These 257 chemicals were tested for their in vitro effects on TmDer GTPase and in vivo antibacterial activities. We identified three structurally diverse compounds, SBI-34462, -34566 and -34612, that are both biologically active against bacterial cells and putative enzymatic inhibitors of Der GTPase homologs. We also presented the possible interactions of each compound with the Der GTP-binding site to understand the mechanism of inhibition. Therefore, our lead compounds inhibiting Der GTPase provide scaffolds for the development of novel antibiotics against antibiotic-resistant pathogenic bacteria. PMID:22377538

Hwang, Jihwan; Tseitin, Vladimir; Ramnarayan, Kal; Shenderovich, Mark D; Inouye, Masayori

2012-02-29

325

Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8.  

PubMed

The crystal structure of PurL from Thermus thermophilus HB8 (TtPurL; TTHA1519) was determined in complex with an adenine nucleotide, PO(4)(3-) and Mg(2+) at 2.35 Å resolution. TtPurL consists of 29 ?-helices and 28 ?-strands, and one loop is disordered. TtPurL consists of four domains, A1, A2, B1 and B2, and the structures of the A1-B1 and A2-B2 domains were almost identical to each other. Although the sequence identity between TtPurL and PurL from Thermotoga maritima (TmPurL) is higher than that between TtPurL and the PurL domain of the large PurL from Salmonella typhimurium (StPurL), the secondary structure of TtPurL is much more similar to that of StPurL than to that of TmPurL. PMID:22232163

Suzuki, Sakiko; Yanai, Hisaaki; Kanagawa, Mayumi; Tamura, Satoko; Watanabe, Yuzo; Fuse, Kyotaro; Baba, Seiki; Sampei, Gen-ichi; Kawai, Gota

2011-12-24

326

The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.  

SciTech Connect

Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 Angstroms resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an aminopropyltransferase, reveals deep cavities for binding substrate and cofactor, and a loop that envelops the active site. The AdoDATO binding site is lined with residues conserved in PAPT enzymes from bacteria to humans, suggesting a universal catalytic mechanism. Other conserved residues act sterically to provide a structural basis for polyamine specificity. The enzyme is tetrameric; each monomer consists of a C-terminal domain with a Rossmann-like fold and an N-terminal {beta}-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.

Korolev, S.; Ikeguchi, Y.; Skarina, T.; Beasley, S.; Arrowsmith, C.; Edwards, A.; Joachimiak, A.; Pegg, A. E.; Savchenko, A.; Pennsylvania State Univ. Coll. of Medicine; Milton S. Hershey Medical Center; Banting and Best Department of Medical Research; Univ. of Health Network

2002-01-01

327

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

328

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes  

PubMed Central

Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I ?70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the ? subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the ?70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance.

Dekhtyar, Michael; Morin, Amelie; Sakanyan, Vehary

2008-01-01

329

Ritual plants of Muslim graveyards in northern Israel.  

PubMed

This article surveys the botanical composition of 40 Muslim graveyards in northern Israel, accompanied by an ethnobotanical study of the folkloristic traditions of the use of these plants in cemeteries. Three groups of plants were found to be repeated systematically and were also recognized for their ritual importance: aromatics herbs (especially Salvia fruticosa and Rosmarinus officinalis), white flowered plants (mainly Narcissus tazetta, Urginea maritima, Iris spp. and Pancratium spp.) and Cupressus sempervirens as the leading cemetery tree. As endemic use we can indicate the essential role of S. fruticosa as the main plant used in all human rites of passage symbolizing the human life cycle. The rosemary is of European origin while the use of basil is of Indian influence. The use of white flowers as cemeteries plants reflects an old European influence and almost the same species are used or their congeners. Most of the trees and shrubs that are planted in Muslim cemeteries in Israel have the same use in ancient as well in modern European cultures. In conclusion, our findings on the occurrence of plants in graveyards reflect the geographic situation of Israel as a crossroads in the cultural arena between Asia and Europe. Most of the traditions are common to the whole Middle East showing high relatedness to the classical world as well as to the present-day Europe. PMID:16961931

Dafni, Amots; Lev, Efraim; Beckmann, Sabine; Eichberger, Christian

2006-09-10

330

A ??-barrel built by the combination of fragments from different folds  

PubMed Central

Combinatorial assembly of protein domains plays an important role in the evolution of proteins. There is also evidence that protein domains have come together from stable subdomains. This concept of modular assembly could be used to construct new well folded proteins from stable protein fragments. Here, we report the construction of a chimeric protein from parts of a (??)8-barrel enzyme from histidine biosynthesis pathway (HisF) and a protein of the (??)5-flavodoxin-like fold (CheY) from Thermotoga maritima that share a high structural similarity. We expected this construct to fold into a full (??)8-barrel. Our results show that the chimeric protein is a stable monomer that unfolds with high cooperativity. Its three-dimensional structure, which was solved to 3.1 ? resolution by x-ray crystallography, confirms a barrel-like fold in which the overall structures of the parent proteins are highly conserved. The structure further reveals a ninth strand in the barrel, which is formed by residues from the HisF C terminus and an attached tag. This strand invades between ?-strand 1 and 2 of the CheY part closing a gap in the structure that might be due to a suboptimal fit between the fragments. Thus, by a combination of parts from two different folds and a small arbitrary fragment, we created a well folded and stable protein.

Bharat, Tanmay A. M.; Eisenbeis, Simone; Zeth, Kornelius; Hocker, Birte

2008-01-01

331

Bio-dependent bed parameters as a proxy tool for sediment stability in mixed habitat intertidal areas  

NASA Astrophysics Data System (ADS)

The stability of cohesive and non-cohesive sediments in a mixed intertidal habitat within the Ria Formosa tidal lagoon, Portugal, was examined during two field campaigns as part of the EU F-ECTS project. The cohesive strength meter Mk III was used to determine critical erosion shear stress ( ?c) within a variety of different intertidal habitats and substrata, including Spartina maritima fields and Zostera noltii beds. The best predictor(s) for ?c were derived from a range of properties measured for the surface sediments (chlorophyll a, colloidal carbohydrate, water, organic content, % fraction <63 ?m, and seabed elevation). Pigment biomarkers were used to identify the dominant algal groups within the surface phytobenthic assemblage. Strong, seasonally dependent relationships were found between ?c and habitat type, chl a, colloidal carbohydrate and bed elevation. Typically, critical erosion thresholds decreased seawards, reflecting a change from biostabilisation by cyanobacteria in the upper intertidal areas, to biostabilisation by diatoms on the bare substrata of the channel edges. In the late summer/early autumn, cyanobacteria were the main sediment stabilisers, and colloidal carbohydrate was the best bio-dependent predictor of ?c across the entire field area. In the late winter/early spring, cyanobacterial activity was lower, and sediment stabilisation by Enteromorpha clathrata was important; the best predictor of ?c was bed elevation. The implications and use of proxies for sediment stability are discussed in terms of feedback and sedimentation processes operating across the intertidal area.

Friend, P. L.; Ciavola, P.; Cappucci, S.; Santos, R.

2003-11-01

332

'Hot' Macromolecular Crystals  

SciTech Connect

Transcriptional regulator protein TM1030 from the hyperthermophile Thermotoga maritima, as well as its complex with DNA, was crystallized at a wide range of temperatures. Crystallization plates were incubated at 4, 20, 37, and 50 C over 3 weeks. The best crystals of TM1030 in complex with DNA were obtained at 4, 20, and 37 C, while TM1030 alone crystallized almost equally well in all temperatures. The crystals grown at different temperatures were used for X-ray diffraction experiments and their structures were compared. Surprisingly, the models of TM1030 obtained from crystals grown at different temperatures are similar in quality. While there are some examples of structures of proteins grown at elevated temperatures in the PDB, these temperatures appear to be underrepresented. Our studies show that crystals of some proteins may be grown and are stable at broad range of temperatures. We suggest that crystallization experiments at elevated temperatures could be used as a standard part of the crystallization protocol.

Koclega, Katarzyna D.; Chruszcz, Maksymilian; Zimmerman, Matthew D.; Bujacz, Grzegorz; Minor, Wladek (UV); (ITB-Poland)

2010-09-07

333

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

2013-06-14

334

Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study  

PubMed Central

Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg2+ ions with binding free energy ?7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

Zhang, Tong; Mu, Yuguang

2012-01-01

335

Structure of a complex of the ATPase SecA and the protein-translocation channel  

SciTech Connect

Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum resolution of 4.5 {angstrom}, obtained for components from Thermotoga maritima. One copy of SecA in an intermediate state of ATP hydrolysis is bound to one molecule of the SecY complex. Both partners undergo important conformational changes on interaction. The polypeptide-cross-linking domain of SecA makes a large conformational change that could capture the translocation substrate in a 'clamp'. Polypeptide movement through the SecY channel could be achieved by the motion of a 'two-helix finger' of SecA inside the cytoplasmic funnel of SecY, and by the coordinated tightening and widening of SecA's clamp above the SecY pore. SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening.

Zimmer, Jochen; Nam, Yunsun; Rapoport, Tom A. (Harvard-MED)

2009-01-23

336

Structure of Sir2Tm bound to a propionylated peptide.  

PubMed

Lysine propionylation is a recently identified post-translational modification that has been observed in proteins such as p53 and histones and is thought to play a role similar to acetylation in modulating protein activity. Members of the sirtuin family of deacetylases have been shown to have depropionylation activity, although the way in which the sirtuin catalytic site accommodates the bulkier propionyl group is not clear. We have determined the 1.8 Å structure of a Thermotoga maritima sirtuin, Sir2Tm, bound to a propionylated peptide derived from p53. A comparison with the structure of Sir2Tm bound to an acetylated peptide shows that hydrophobic residues in the active site shift to accommodate the bulkier propionyl group. Isothermal titration calorimetry data show that Sir2Tm binds propionylated substrates more tightly than acetylated substrates, but kinetic assays reveal that the catalytic rate of Sir2Tm deacylation of propionyl-lysine is slightly reduced to acetyl-lysine. These results serve to broaden our understanding of the newly identified propionyl-lysine modification and the ability of sirtuins to depropionylate, as well as deacetylate, substrates. PMID:21080423

Bheda, Poonam; Wang, Jennifer T; Escalante-Semerena, Jorge C; Wolberger, Cynthia

2011-01-01

337

Use of digital multispectral videography to assess seagrass distribution in San Quinti??n Bay, Baja California, Mexico [Uso de videografi??a multiespectral digital para evaluar la distributio??n del pasto marino en Bahi??a San Quinti??n, Baja California, Me??xico  

USGS Publications Warehouse

Apparent threats to the spatial distribution of seagrass in San Quinti??n Bay prompted us to make a detailed assessment of habitats in the bay. Six coastal habitats and three seagrass subclasses were delineated using airborne digital multispectral videography (DMSV), Eelgrass, Zostera marina, was the predominant seagrass and covered 40% (1949 ha) of the areal extent of the bay in 1999. Eelgrass grew over a wide range of tidal depths from about -3.0 in mean lower low water (MLLW) to about 1.0 m MLLW, but greatest spatial extent occurred in intertidal areas -0.6 m to 1.0 m MLLW. Exposed-continuous (i.e., high density) eelgrass was the most abundant habitat in the bay. Widgeongrass, Ruppia maritima, was the only other seagrass present and covered 3% (136 ha) of the areal extent of the entire bay. Widgeongrass grew in single species stands in the upper intertidal (??? 0.4 MLLW) and intermixed with eelgrass at lower tidal depths. Overall accuracy of the six habitat classes and three subclasses in the DMSV map was relatively high at 84%. Our detailed map of San Quintin Bay can be used in future change detection analyses to monitor the health of seagrasses in the bay.

Ward, D. H.; Tibbitts, T. L.; Morton, A.; Carrera-Gonzalez, E.; Kempka, R.

2004-01-01

338

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

339

The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation  

PubMed Central

The hexameric membrane-spanning ATP-dependent metalloprotease FtsH is universally conserved in eubacteria, mitochondria, and chloroplasts, where it fulfills key functions in quality control and signaling. As a member of the self-compartmentalizing ATPases associated with various cellular activities (AAA+ proteases), FtsH converts the chemical energy stored in ATP via conformational rearrangements into a mechanical force that is used for substrate unfolding and translocation into the proteolytic chamber. The crystal structure of the ADP state of Thermotoga maritima FtsH showed a hexameric assembly consisting of a 6-fold symmetric protease disk and a 2-fold symmetric AAA ring. The 2.6 ? resolution structure of the cytosolic region of apo-FtsH presented here reveals a new arrangement where the ATPase ring shows perfect 6-fold symmetry with the crucial pore residues lining an open circular entrance. Triggered by this conformational change, a substrate-binding edge beta strand appears within the proteolytic domain. Comparison of the apo- and ADP-bound structure visualizes an inward movement of the aromatic pore residues and generates a model of substrate translocation by AAA+ proteases. Furthermore, we demonstrate that mutation of a conserved glycine in the linker region inactivates FtsH.

Bieniossek, Christoph; Niederhauser, Barbara; Baumann, Ulrich M.

2009-01-01

340

The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation.  

PubMed

The hexameric membrane-spanning ATP-dependent metalloprotease FtsH is universally conserved in eubacteria, mitochondria, and chloroplasts, where it fulfills key functions in quality control and signaling. As a member of the self-compartmentalizing ATPases associated with various cellular activities (AAA+ proteases), FtsH converts the chemical energy stored in ATP via conformational rearrangements into a mechanical force that is used for substrate unfolding and translocation into the proteolytic chamber. The crystal structure of the ADP state of Thermotoga maritima FtsH showed a hexameric assembly consisting of a 6-fold symmetric protease disk and a 2-fold symmetric AAA ring. The 2.6 A resolution structure of the cytosolic region of apo-FtsH presented here reveals a new arrangement where the ATPase ring shows perfect 6-fold symmetry with the crucial pore residues lining an open circular entrance. Triggered by this conformational change, a substrate-binding edge beta strand appears within the proteolytic domain. Comparison of the apo- and ADP-bound structure visualizes an inward movement of the aromatic pore residues and generates a model of substrate translocation by AAA+ proteases. Furthermore, we demonstrate that mutation of a conserved glycine in the linker region inactivates FtsH. PMID:19955424

Bieniossek, Christoph; Niederhauser, Barbara; Baumann, Ulrich M

2009-12-02

341

Interactions of Endoglucanases with Amorphous Cellulose Films Resolved by Neutron Reflectometry and Quartz Crystal Microbalance with Dissipation Monitoring  

SciTech Connect

A study of the interaction of four endoglucanases with amorphous cellulose films by neutron reflectometry (NR) and quartz crystal microbalance with dissipation monitoring (QCM-D) is reported. The endoglucanases include a mesophilic fungal endoglucanase (Cel45A from H. insolens), a processive endoglucanase from a marine bacterium (Cel5H from S. degradans), and two from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima). The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. The endoglucanases displayed highly diverse behavior. Cel45A and Cel5H, which possess carbohydrate-binding modules (CBMs), penetrated and digested within the bulk of the films to a far greater extent than Cel9A and Cel5A, which lack CBMs. While both Cel45A and Cel5H were active within the bulk of the films, striking differences were observed. With Cel45A, substantial film expansion and interfacial broadening were observed, whereas for Cel5H the film thickness decreased with little interfacial broadening. These results are consistent with Cel45A digesting within the interior of cellulose chains as a classic endoglucanase, and Cel5H digesting predominantly at chain ends consistent with its designation as a processive endoglucanase.

Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Kent, Michael S [Sandia National Laboratories (SNL); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Michael, Jablin [Los Alamos National Laboratory (LANL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Halbert, Candice E [ORNL; Datta, Supratim [Joint Bioenergy Institute; Chao, Wang [Virginia Polytechnic Institute and State University (Virginia Tech); Brown, Page [Sandia National Laboratories (SNL)

2012-01-01

342

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

343

Functional characterization of two M42 aminopeptidases erroneously annotated as cellulases.  

PubMed

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. PMID:23226342

Dutoit, Raphaël; Brandt, Nathalie; Legrain, Christianne; Bauvois, Cédric

2012-11-30

344

X-ray Crystallography and Isothermal Titration Calorimetry Studies of the Salmonella Zinc Transporter ZntB  

PubMed Central

SUMMARY The ZntB Zn2+ efflux system is important for maintenance of Zn2+ homeostasis in Enterobacteria. We report crystal structures of ZntB cytoplasmic domains from Salmonella enterica serovar Typhimurium (StZntB) in dimeric and physiologically relevant homopentameric forms at 2.3 Å and 3.1 Å resolutions, respectively. The funnel-like structure is similar to that of the homologous Thermotoga maritima CorA Mg2+ channel and a Vibrio parahaemolyticus ZntB (VpZntB) soluble domain structure. However, the central ?7 helix forming the inner wall of the StZntB funnel is oriented perpendicular to the membrane instead of the marked angle seen in CorA or VpZntB. Consequently, the StZntB funnel pore is cylindrical, not tapered, which may represent an “open” form of the ZntB soluble domain. Our crystal structures and isothermal titration calorimetry data indicate that there are three Zn2+ binding sites in the full-length ZntB, two of which could be involved in Zn2+ transport.

Wan, Qun; Ahmad, Md Faiz; Fairman, James; Gorzelle, Bonnie; de la Fuente, Maria; Dealwis, Chris; Maguire, Michael E.

2011-01-01

345

Comparison of three thermostable ?-glucosidases for application in the hydrolysis of soybean isoflavone glycosides.  

PubMed

A novel thermostable ?-glucosidase (Te-BglA) from Thermoanaerobacter ethanolicus JW200 was cloned, characterized and compared for its activity against isoflavone glycosides with two ?-glucosidases (Tm-BglA, Tm-BglB) from Thermotoga maritima. Te-BglA exhibited maximum hydrolytic activity toward pNP-?-d-glucopyranoside (pNPG) at 80 °C and pH 7.0, was stable for a pH range of 4.6-7.8 and at 65 °C for 3 h, and had the lowest K(m) for the natural glycoside salicin and the highest relative substrate specificity (k(cat)/K(m))((salicin))/(k(cat)/K(m))((pNPG)) among the three enzymes. It converted isoflavone glycosides, including malonyl glycosides, in soybean flour to their aglycons more efficiently than Tm-BglA and Tm-BglB. After 3 h of incubation at 65 °C, Te-BglA produced complete hydrolysis of four isoflavone glycosides (namely, daidzin, genistin and their malonylated forms), exhibiting higher productivity of genistein and daidzein than the other two ?-glucosidases. Our results suggest that Te-BglA is preferable to Tm-BglA and Tm-BglB, but all three enzymes have great potential applications in converting isoflavone glycosides into their aglycons. PMID:21294581

Song, Xiangfei; Xue, Yemin; Wang, Qilei; Wu, Xixi

2011-02-02

346

The impact of sika deer grazing on the vegetation and infauna of Arne saltmarsh.  

PubMed

Arne saltmarsh, an RSPB reserve, is situated in Poole Harbour on the English south coast. In recent years, there has been concern about possible changes in the suitability of the site for Redshank (Trigna totanus) due to sika deer (Cervus nippon) grazing. In order to assess these changes, 50 plots were established in three different locations: 20 in grazed areas, 20 in ungrazed areas and 10 fenced enclosures. Deer grazing was found to significantly affect structural and species diversity of the saltmarsh vegetation. Spartina anglica dominated in ungrazed areas whilst Salicornia ramosissima and, to a lesser extent, Puccinellia maritima dominated in grazed sites. In grazed areas the vegetation cover was significantly lower, as was vegetation height and volume. In addition, significant changes were observed in the root biomass, which was lower in grazed areas. Infaunal diversity was generally low throughout the survey area. However, significant variations were observed. Invertebrates abundance was more abundant in grazed plots than in ungrazed plots, and least abundant in fenced plots. The study indicated that in its current condition, localised areas of Arne saltmarsh do not provide adequate habitat requirements for Tringa totanus. PMID:16246379

Hannaford, Justine; Pinn, Eunice H; Diaz, Anita

2005-10-24

347

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum  

PubMed Central

Large and functionally heterogeneous families of transcription factors have complex evolutionary histories. What shapes specificities toward effectors and DNA sites in paralogous regulators is a fundamental question in biology. Bacteria from the deep-branching lineage Thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (ROK) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. We applied an integrated genomic approach to study functions and specificities of regulators from this family. A comparative analysis of 11 Thermotogae genomes revealed novel mechanisms of transcriptional regulation of the sugar utilization networks, DNA-binding motifs and specific functions. Reconstructed regulons for seven groups of ROK regulators were validated by DNA-binding assays using purified recombinant proteins from the model bacterium Thermotoga maritima. All tested regulators demonstrated specific binding to their predicted cognate DNA sites, and this binding was inhibited by specific effectors, mono- or disaccharides from their respective sugar catabolic pathways. By comparing ligand-binding domains of regulators with structurally characterized kinases from the ROK family, we elucidated signature amino acid residues determining sugar-ligand regulator specificity. Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family.

Kazanov, Marat D.; Li, Xiaoqing; Gelfand, Mikhail S.; Osterman, Andrei L.; Rodionov, Dmitry A.

2013-01-01

348

Structure of the Cytoplasmic Segment of Histidine Kinase Receptor QseC, a Key Player in Bacterial Virulence†  

PubMed Central

QseC is a histidine kinase (HK) receptor involved in quorum sensing, a mechanism by which bacteria respond to fluctuations in cell population. We conducted a structural study of the cytoplasmic domain of QseC (QseC-CD) using X-ray crystallography. The 2.5 Å structure of the apo-enzyme revealed that the kinase domain of QseC retains the overall fold of the typical HK kinase domain. The construct that we used is inactive in the autokinase reaction and its inactivity is most likely caused by its atypical dimerization interface, as compared to that observed in the T.maritima HK cytoplasmic domain structure. Restoration of the activity may require that the entire dimerization domain be present in the protein construct. QseC, which plays an important role in bacterial pathogenesis, is a promising drug target and the structure of QseCCD provides a platform for developing more potent inhibitors of pathogen virulence.

Xie, Wei; Dickson, Chris; Kwiatkowski, Witek; Choe, Senyon

2012-01-01

349

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

SciTech Connect

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two ({beta}{alpha}){sub 8} barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys){sub 3}Zn site in the related enzymes, MetH and betaine-homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E {center_dot} Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

Pejcha, Robert; Ludwig, Martha L. (Michigan)

2010-03-08

350

Aquatic Insects of New York Salt Marsh Associated with Mosquito Larval Habitat and their Potential Utility as Bioindicators  

PubMed Central

The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insectbased index of biological integrity for salt marsh health assessment.

Rochlin, Ilia; Dempsey, Mary E.; Iwanejko, Tom; Ninivaggi, Dominick V.

2011-01-01

351

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

352

Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.  

PubMed

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. PMID:17567048

Hall, Richard S; Brown, Shoshana; Fedorov, Alexander A; Fedorov, Elena V; Xu, Chengfu; Babbitt, Patricia C; Almo, Steven C; Raushel, Frank M

2007-06-13

353

Ocean acidification and the loss of phenolic substances in marine plants.  

PubMed

Rising atmospheric CO(2) often triggers the production of plant phenolics, including many that serve as herbivore deterrents, digestion reducers, antimicrobials, or ultraviolet sunscreens. Such responses are predicted by popular models of plant defense, especially resource availability models which link carbon availability to phenolic biosynthesis. CO(2) availability is also increasing in the oceans, where anthropogenic emissions cause ocean acidification, decreasing seawater pH and shifting the carbonate system towards further CO(2) enrichment. Such conditions tend to increase seagrass productivity but may also increase rates of grazing on these marine plants. Here we show that high CO(2) / low pH conditions of OA decrease, rather than increase, concentrations of phenolic protective substances in seagrasses and eurysaline marine plants. We observed a loss of simple and polymeric phenolics in the seagrass Cymodocea nodosa near a volcanic CO(2) vent on the Island of Vulcano, Italy, where pH values decreased from 8.1 to 7.3 and pCO(2) concentrations increased ten-fold. We observed similar responses in two estuarine species, Ruppia maritima and Potamogeton perfoliatus, in in situ Free-Ocean-Carbon-Enrichment experiments conducted in tributaries of the Chesapeake Bay, USA. These responses are strikingly different than those exhibited by terrestrial plants. The loss of phenolic substances may explain the higher-than-usual rates of grazing observed near undersea CO(2) vents and suggests that ocean acidification may alter coastal carbon fluxes by affecting rates of decomposition, grazing, and disease. Our observations temper recent predictions that seagrasses would necessarily be "winners" in a high CO(2) world. PMID:22558120

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

2012-04-25

354

Two Alternative Pathways for the Synthesis of the Rare Compatible Solute Mannosylglucosylglycerate in Petrotoga mobilis?  

PubMed Central

The compatible solute mannosylglucosylglycerate (MGG), recently identified in Petrotoga miotherma, also accumulates in Petrotoga mobilis in response to hyperosmotic conditions and supraoptimal growth temperatures. Two functionally connected genes encoding a glucosyl-3-phosphoglycerate synthase (GpgS) and an unknown glycosyltransferase (gene Pmob_1143), which we functionally characterized as a mannosylglucosyl-3-phosphoglycerate synthase and designated MggA, were identified in the genome of Ptg. mobilis. This enzyme used the product of GpgS, glucosyl-3-phosphoglycerate (GPG), as well as GDP-mannose to produce mannosylglucosyl-3-phosphoglycerate (MGPG), the phosphorylated precursor of MGG. The MGPG dephosphorylation was determined in cell extracts, and the native enzyme was partially purified and characterized. Surprisingly, a gene encoding a putative glucosylglycerate synthase (Ggs) was also identified in the genome of Ptg. mobilis, and an active Ggs capable of producing glucosylglycerate (GG) from ADP-glucose and d-glycerate was detected in cell extracts and the recombinant enzyme was characterized, as well. Since GG has never been identified in this organism nor was it a substrate for the MggA, we anticipated the existence of a nonphosphorylating pathway for MGG synthesis. We putatively identified the corresponding gene, whose product had some sequence homology with MggA, but it was not possible to recombinantly express a functional enzyme from Ptg. mobilis, which we named mannosylglucosylglycerate synthase (MggS). In turn, a homologous gene from Thermotoga maritima was successfully expressed, and the synthesis of MGG was confirmed from GDP-mannose and GG. Based on the measurements of the relevant enzyme activities in cell extracts and on the functional characterization of the key enzymes, we propose two alternative pathways for the synthesis of the rare compatible solute MGG in Ptg. mobilis.

Fernandes, Chantal; Mendes, Vitor; Costa, Joana; Empadinhas, Nuno; Jorge, Carla; Lamosa, Pedro; Santos, Helena; da Costa, Milton S.

2010-01-01

355

Two alternative pathways for the synthesis of the rare compatible solute mannosylglucosylglycerate in Petrotoga mobilis.  

PubMed

The compatible solute mannosylglucosylglycerate (MGG), recently identified in Petrotoga miotherma, also accumulates in Petrotoga mobilis in response to hyperosmotic conditions and supraoptimal growth temperatures. Two functionally connected genes encoding a glucosyl-3-phosphoglycerate synthase (GpgS) and an unknown glycosyltransferase (gene Pmob_1143), which we functionally characterized as a mannosylglucosyl-3-phosphoglycerate synthase and designated MggA, were identified in the genome of Ptg. mobilis. This enzyme used the product of GpgS, glucosyl-3-phosphoglycerate (GPG), as well as GDP-mannose to produce mannosylglucosyl-3-phosphoglycerate (MGPG), the phosphorylated precursor of MGG. The MGPG dephosphorylation was determined in cell extracts, and the native enzyme was partially purified and characterized. Surprisingly, a gene encoding a putative glucosylglycerate synthase (Ggs) was also identified in the genome of Ptg. mobilis, and an active Ggs capable of producing glucosylglycerate (GG) from ADP-glucose and d-glycerate was detected in cell extracts and the recombinant enzyme was characterized, as well. Since GG has never been identified in this organism nor was it a substrate for the MggA, we anticipated the existence of a nonphosphorylating pathway for MGG synthesis. We putatively identified the corresponding gene, whose product had some sequence homology with MggA, but it was not possible to recombinantly express a functional enzyme from Ptg. mobilis, which we named mannosylglucosylglycerate synthase (MggS). In turn, a homologous gene from Thermotoga maritima was successfully expressed, and the synthesis of MGG was confirmed from GDP-mannose and GG. Based on the measurements of the relevant enzyme activities in cell extracts and on the functional characterization of the key enzymes, we propose two alternative pathways for the synthesis of the rare compatible solute MGG in Ptg. mobilis. PMID:20061481

Fernandes, Chantal; Mendes, Vitor; Costa, Joana; Empadinhas, Nuno; Jorge, Carla; Lamosa, Pedro; Santos, Helena; da Costa, Milton S

2010-01-08

356

Creation of metal-independent hyperthermophilic L-arabinose isomerase by homologous recombination.  

PubMed

Hyperthermophilic L-arabinose isomerases (AIs) are useful in the commercial production of D-tagatose as a low-calorie bulk sweetener. Their catalysis and thermostability are highly dependent on metals, which is a major drawback in food applications. To study the role of metal ions in the thermostability and catalysis of hyperthermophilic AI, four enzyme chimeras were generated by PCR-based hybridization to replace the variable N- and C-terminal regions of hyperthermophilic Thermotoga maritima AI (TMAI) and thermophilic Geobacillus stearothermophilus AI (GSAI) with those of the homologous mesophilic Bacillus halodurans AI (BHAI). Unlike Mn(2+)-dependent TMAI, the GSAI- and TMAI-based hybrids with the 72 C-terminal residues of BHAI were not metal-dependent for catalytic activity. By contrast, the catalytic activities of the TMAI- and GSAI-based hybrids containing the N-terminus (residues 1-89) of BHAI were significantly enhanced by metals, but their thermostabilities were poor even in the presence of Mn(2+), indicating that the effects of metals on catalysis and thermostability involve different structural regions. Moreover, in contrast to the C-terminal truncate (?20 residues) of GSAI, the N-terminal truncate (?7 residues) exhibited no activity due to loss of its native structure. The data thus strongly suggest that the metal dependence of the catalysis and thermostability of hyperthermophilic AIs evolved separately to optimize their activity and thermostability at elevated temperatures. This may provide effective target regions for engineering, thereby meeting industrial demands for the production of d-tagatose. PMID:22103589

Hong, Young-Ho; Lee, Dong-Woo; Pyun, Yu-Ryang; Lee, Sung Haeng

2011-12-06

357

Defining amino acid residues involved in DNA-protein interactions and revelation of 3'-exonuclease activity in endonuclease V.  

PubMed

Endonuclease V is an enzyme that initiates a conserved DNA repair pathway by making an endonucleolytic incision at the 3' side one nucleotide from a deaminated base lesion. Site-directed mutagenesis analysis was conducted at seven conserved motifs of the thermostable Thermotoga maritima endonuclease V to probe for residues that affect DNA-protein interactions. Y80, G83, and L85 in motif III, H116 and G121 in motif IV, A138 in motif V, and S182 in motif VI affect binding of both the double-stranded inosine-containing DNA substrate and the nicked double-stranded inosine-containing DNA product, resulting in multiple enzymatic turnovers. The substantially reduced DNA cleavage activity observed in G113 in motif IV and G136 in motif V can be partly attributed to their defect in metal cofactor coordination. Alanine substitution at amino acid 118 primarily reduces the level of binding to the nicked product, suggesting that R118 plays a significant role in postcleavage DNA-protein interaction. Binding and cleavage analyses of multiple mutants at positions Y80 and H116 underscore the role these residues play in protein-DNA interaction and implicate their potential involvement as a hydrogen bond donor in recognition of deaminated DNA bases. DNA cleavage analysis using mutants defective in DNA binding reveals a novel 3'-exonuclease activity in endonuclease V. An alternative model is proposed that entails lesion specific cleavage and endonuclease to 3'-exonuclease mode switch by endonuclease V for removal of deaminated base lesions during endonuclease V-mediated repair. PMID:16114885

Feng, Hong; Dong, Liang; Klutz, Athena M; Aghaebrahim, Nima; Cao, Weiguo

2005-08-30

358

Structure of the invertebrate fauna in salt marshes of the Wadden Sea coast of Schleswig-Holstein influenced by sheep-grazing  

NASA Astrophysics Data System (ADS)

Results of investigations on the influence of five different sheep grazing intensities on the invertebrate fauna of two mainland salt marsh sites of the German Wadden Sea coast are presented for the years 1990 and 1991. The investigation of the invertebrate fauna has been carried out since 1989 in the Puccinellia maritima zone, and the Festuca-Puccinellia as well as the Festuca-Armeria zones, with trapping transects arranged along an inundation gradient. Apart from specific biotic effects, grazing causes changes in environmental characteristics. Effects on microclimate comprise higher ranges of variance in soil-surface temperature on grazed sites. Decreasing food resources caused by grazing bring disadvantages to herbivores, the major part of the invertebrate fauna, due to merotope destruction (e. g. inflorescences of Aster tripolium) and the decline of host plant stands (e. g. A. tripolium, Plantago ssp.). Flower visitors and pollen feeding species that depend on A. tripolium have become extinct. Increasing food resources, caused by grazing, lead to higher population densities of a few specialized grass-feeding and surface-grazing invertebrates (e. g. Mayetiola ssp., Psammotettix putoni, Bledius tricornis). Soil characteristics in the lower salt marsh have not been altered significantly by grazing; hence, the direct effect of grazing and trampling leads to a decrease in population density of many species such as Assiminea grayana, Orchestia gammarellus and collembolans. The biomass and abundance of detritivores and many herbivores increased from 1990 to 1991 on the totally grazed fields, whereas predators diminished in numbers at the same time. A descriptive model is presented, involving grazing, winter temperature, and precipitation as basic factors.

Meyer, H.; Fock, H.; Haase, A.; Reinke, H. D.; Tulowitzki, I.

1995-03-01

359

Functional implications of cold-stable microtubules in kinetochore fibers of insect spermatocytes during anaphase  

PubMed Central

In normal anaphase of crane fly spermatocytes, the autosomes traverse most of the distance to the poles at a constant, temperature-dependent velocity. Concurrently, the birefringent kinetochore fibers shorten while retaining a constant birefringent retardation (BR) and width over most of the fiber length as the autosomes approach the centrosome region. To test the dynamic equilibrium model of chromosome poleward movement, we abruptly cooled or heated primary spermatocytes of the crane fly Nephrotoma ferruginea (and the grasshopper Trimerotropis maritima) during early anaphase. According to this model, abrupt cooling should induce transient depolymerization of the kinetochore fiber microtubules, thus producing a transient acceleration in the poleward movement of the autosomal chromosomes, provided the poles remain separated. Abrupt changes in temperature from 22 degrees C to as low as 4 degrees C or as high as 31 degrees C in fact produced immediate changes in chromosome velocity to new constant velocities. No transient changes in velocity were observed. At 4 degrees C (10 degrees C for grasshopper cells), chromosome movement ceased. Although no nonkinetochore fiber BR remained at these low temperatures, kinetochore fiber BR had changed very little. The cold stability of the kinetochore fiber microtubules, the constant velocity character of chromosome movement, and the observed Arrhenius relationship between temperature and chromosome velocity indicate that a rate-limiting catalyzed process is involved in the normal anaphase depolymerization of the spindle fiber microtubules. On the basis of our birefringence observations, the kinetochore fiber microtubules appear to exist in a steady-state balance between comparatively irreversible, and probably different, physiological pathways of polymerization and depolymerization.

1980-01-01

360

Early embryonic determination of the sexual dimorphism in segment number in geophilomorph centipedes  

PubMed Central

Background Most geophilomorph centipedes show intraspecific variability in the number of leg-bearing segments. This intraspecific variability generally has a component that is related to sex, with females having on average more segments than males. Neither the developmental basis nor the adaptive role of this dimorphism is known. Results To determine when this sexual dimorphism in segment number is established, we have followed the development of Strigamia maritima embryos from the onset of segmentation to the first post-embryonic stage where we could determine the sex morphologically. We find that males and females differ in segment number by Stage 6.1, a point during embryogenesis when segment addition pauses while the embryo undergoes large-scale movements. We have confirmed this pattern by establishing a molecular method to determine the sex of single embryos, utilising duplex PCR amplification for Y chromosomal and autosomal sequences. This confirms that male embryos have a modal number of 43 segments visible at Stage 6, while females have 45. In our Strigamia population, adult males have a modal number of 47 leg-bearing segments, and females have 49. This implies that the sexual dimorphism in segment number is determined before the addition of the last leg-bearing segments and the terminal genital segments. Conclusions Sexual dimorphism in segment number is not associated with terminal segment differentiation, but must instead be related to some earlier process during segment patterning. The dimorphism may be associated with a difference in the rate and/or duration of segment addition during the main phase of rapid segment addition that precedes embryonic Stage 6. This suggests that the adaptive role, if any, of the dimorphism is likely to be related to segment number per se, and not to sexual differentiation of the terminal region.

2013-01-01

361

Evolution of the pair rule gene network: Insights from a centipede.  

PubMed

Comparative studies have examined the expression and function of homologues of the Drosophila melanogaster pair rule and segment polarity genes in a range of arthropods. The segment polarity gene homologues have a conserved role in the specification of the parasegment boundary, but the degree of conservation of the upstream patterning genes has proved more variable. Using genomic resources we identify a complete set of pair rule gene homologues from the centipede Strigamia maritima, and document a detailed time series of expression during trunk segmentation. We find supportive evidence for a conserved hierarchical organisation of the pair rule genes, with a division into early- and late-activated genes which parallels the functional division into primary and secondary pair rule genes described in insects. We confirm that the relative expression of sloppy-paired and paired with respect to wingless and engrailed at the parasegment boundary is conserved between myriapods and insects; suggesting that functional interactions between these genes might be an ancient feature of arthropod segment patterning. However, we find that the relative expression of a number of the primary pair rule genes is divergent between myriapods and insects. This corroborates suggestions that the evolution of upper tiers in the segmentation gene network is more flexible. Finally, we find that the expression of the Strigamia pair rule genes in periodic patterns is restricted to the ectoderm. This suggests that any direct role of these genes in segmentation is restricted to this germ layer, and that mesoderm segmentation is either dependent on the ectoderm, or occurs through an independent mechanism. PMID:23810931

Green, Jack; Akam, Michael

2013-06-26

362

Ancestral patterning of tergite formation in a centipede suggests derived mode of trunk segmentation in trilobites.  

PubMed

Trilobites have a rich and abundant fossil record, but little is known about the intrinsic mechanisms that orchestrate their body organization. To date, there is disagreement regarding the correspondence, or lack thereof, of the segmental units that constitute the trilobite trunk and their associated exoskeletal elements. The phylogenetic position of trilobites within total-group Euarthropoda, however, allows inferences about the underlying organization in these extinct taxa to be made, as some of the fundamental genetic processes for constructing the trunk segments are remarkably conserved among living arthropods. One example is the expression of the segment polarity gene engrailed, which at embryonic and early postembryonic stages is expressed in extant panarthropods (i.e. tardigrades, onychophorans, euarthropods) as transverse stripes that define the posteriormost region of each trunk segment. Due to its conservative morphology and allegedly primitive trunk tagmosis, we have utilized the centipede Strigamia maritima to study the correspondence between the expression of engrailed during late embryonic to postembryonic stages, and the development of the dorsal exoskeletal plates (i.e. tergites). The results corroborate the close correlation between the formation of the tergite borders and the dorsal expression of engrailed, and suggest that this association represents a symplesiomorphy within Euarthropoda. This correspondence between the genetic and phenetic levels enables making accurate inferences about the dorsoventral expression domains of engrailed in the trunk of exceptionally preserved trilobites and their close relatives, and is suggestive of the widespread occurrence of a distinct type of genetic segmental mismatch in these extinct arthropods. The metameric organization of the digestive tract in trilobites provides further support to this new interpretation. The wider evolutionary implications of these findings suggest the presence of a derived morphogenetic patterning mechanism responsible for the reiterated occurrence of different types of trunk dorsoventral segmental mismatch in several phylogenetically distant, extinct and extant, arthropod groups. PMID:23285116

Ortega-Hernández, Javier; Brena, Carlo

2012-12-28

363

Reining in polyoma virus associated nephropathy: design and characterization of a template mimicking BK viral coat protein cellular binding.  

PubMed

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 characteristics 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. PMID:23002929

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

2012-10-02

364

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

PubMed

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. PMID:23671075

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

2013-05-13

365

Identification of an Intermediate Methyl Carrier in the Radical S-Adenosylmethionine Methylthiotransferases RimO and MiaB.  

PubMed

RimO and MiaB are radical S-adenosylmethionine (SAM) enzymes that catalyze the attachment of methylthio (-SCH3) groups to macromolecular substrates. RimO attaches a methylthio group at C3 of aspartate 89 of protein S12, a component of the 30S subunit of the bacterial ribosome. MiaB attaches a methylthio group at C2 of N(6)-(isopentenyl)adenosine, found at nucleotide 37 in several prokaryotic tRNAs. These two enzymes are prototypical members of a subclass of radical SAM enzymes called methylthiotransferases (MTTases). It had been assumed that the sequence of steps in MTTase reactions involves initial sulfur insertion into the organic substrate followed by capping of the inserted sulfur atom with a SAM-derived methyl group. In this work, however, we show that both RimO and MiaB from Thermotoga maritima catalyze methyl transfer from SAM to an acid/base labile acceptor on the protein in the absence of their respective macromolecular substrates. Consistent with the assignment of the acceptor as an iron-sulfur cluster, denaturation of the SAM-treated protein with acid results in production of methanethiol. When RimO or MiaB is first incubated with SAM in the absence of substrate and reductant and then incubated with excess S-adenosyl-l-[methyl-d3]methionine in the presence of substrate and reductant, production of the unlabeled product precedes production of the deuterated product, showing that the methylated species is chemically and kinetically competent to be an intermediate. PMID:23991893

Landgraf, Bradley J; Arcinas, Arthur J; Lee, Kyung-Hoon; Booker, Squire J

2013-10-03

366

The enzymology of alanine aminotransferase (AlaAT) isoforms from Hordeum vulgare and other organisms, and the HvAlaAT crystal structure.  

PubMed

In this paper we describe the expression, purification, kinetics and biophysical characterization of alanine aminotransferase (AlaAT) from the barley plant (Hordeum vulgare). This dimeric PLP-dependent enzyme is a pivotal element of several key metabolic pathways from nitrogen assimilation to carbon metabolism, and its introduction into transgenic plants results in increased yield. The enzyme exhibits a bi-bi ping-pong reaction mechanism with a K(m) for alanine, 2-oxoglutarate, glutamate and pyruvate of 3.8, 0.3, 0.8 and 0.2 mM, respectively. Barley AlaAT catalyzes the forward (alanine-forming) reaction with a k(cat) of 25.6 s(-1), the reverse (glutamate-forming) reaction with k(cat) of 12.1 s(-1) and an equilibrium constant of ~0.5. The enzyme is also able to utilize aspartate and oxaloacetate with ~10% efficiency as compared to the native substrates, which makes it much more specific than related bacterial/archaeal enzymes (that also have lower K(m) values). We have crystallized barley AlaAT in complex with PLP and l-cycloserine and solved the structure of this complex at 2.7 Å resolution. This is the first example of a plant AlaAT structure, and it reveals a canonical aminotransferase fold similar to structures of the Thermotoga maritima, Pyrococcus furiosus, and human enzymes. This structure bridges our structural understanding of AlaAT mechanism between three kingdoms of life and allows us to shed some light on the specifics of the catalysis performed by these proteins. PMID:22750542

Duff, Stephen M G; Rydel, Timothy J; McClerren, Amanda L; Zhang, Wenlan; Li, Jimmy Y; Sturman, Eric J; Halls, Coralie; Chen, Songyang; Zeng, Jiamin; Peng, Jiexin; Kretzler, Crystal N; Evdokimov, Artem

2012-06-29

367

Evolution of the pair rule gene network: Insights from a centipede?  

PubMed Central

Comparative studies have examined the expression and function of homologues of the Drosophila melanogaster pair rule and segment polarity genes in a range of arthropods. The segment polarity gene homologues have a conserved role in the specification of the parasegment boundary, but the degree of conservation of the upstream patterning genes has proved more variable. Using genomic resources we identify a complete set of pair rule gene homologues from the centipede Strigamia maritima, and document a detailed time series of expression during trunk segmentation. We find supportive evidence for a conserved hierarchical organisation of the pair rule genes, with a division into early- and late-activated genes which parallels the functional division into primary and secondary pair rule genes described in insects. We confirm that the relative expression of sloppy-paired and paired with respect to wingless and engrailed at the parasegment boundary is conserved between myriapods and insects; suggesting that functional interactions between these genes might be an ancient feature of arthropod segment patterning. However, we find that the relative expression of a number of the primary pair rule genes is divergent between myriapods and insects. This corroborates suggestions that the evolution of upper tiers in the segmentation gene network is more flexible. Finally, we find that the expression of the Strigamia pair rule genes in periodic patterns is restricted to the ectoderm. This suggests that any direct role of these genes in segmentation is restricted to this germ layer, and that mesoderm segmentation is either dependent on the ectoderm, or occurs through an independent mechanism.

Green, Jack; Akam, Michael

2013-01-01

368

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

369

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

370

Cloning and sequencing of the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences.  

PubMed Central

The gene glnA encoding glutamine synthetase I (GSI) from the archaeum Pyrococcus woesei was cloned and sequenced with the Sulfolobus solfataricus glnA gene as the probe. An operon reading frame of 448 amino acids was identified within a DNA segment of 1,528 bp. The encoded protein was 49% identical with the GSI of Methanococcus voltae and exhibited conserved regions characteristic of the GSI family. The P. woesei GSI was aligned with available homologs from other archaea (S. solfataricus, M. voltae) and with representative sequences from cyanobacteria, proteobacteria, and gram-positive bacteria. Phylogenetic trees were constructed from both the amino acid and the nucleotide sequence alignments. In accordance with the sequence similarities, archaeal and bacterial sequences did not segregate on a phylogeny. On the basis of sequence signatures, the GSI trees could be subdivided into two ensembles. One encompassed the GSI of cyanobacteria and proteobacteria, but also that of the high-G + C gram-positive bacterium Streptomyces coelicolor (all of which are regulated by the reversible adenylylation of the enzyme subunits); the other embraced the GSI of the three archaea as well as that of the low-G + C gram-positive bacteria (Clostridium acetobutilycum, Bacillus subtilis) and Thermotoga maritima (none of which are regulated by subunit adenylylation). The GSIs of the Thermotoga and the Bacillus-Clostridium lineages shared a direct common ancestor with that of P. woesei and the methanogens and were unrelated to their homologs from cyanobacteria, proteobacteria, and S. coelicolor. The possibility is presented that the GSI gene arose among the archaea and was then laterally transferred from some early methanogen to a Thermotoga-like organism. However, the relationship of the cyanobacterial-proteobacterial GSIs to the Thermotoga GSI and the GSI of low-G+C gram-positive bacteria remains unexplained.

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

1993-01-01

371

Carbon isotope ratios for chloromethane of biological origin: potential tool in determining biological emissions.  

PubMed

Chloromethane (CH3Cl) with a global atmospheric burden of 5.3 million t is the most abundant halocarbon in the atmosphere. However, the origin of ca. 50% of the estimated annual global input of 4 million t of the gas to the atmosphere has yet to be determined. As the oceanic contribution to the global CH3Cl flux is now tightly constrained, an important terrestrial source is either underestimated or unrecognized. It has recently been proposed that higher plants may represent a CH3Cl source of sufficient magnitude to resolve the global budget imbalance. A potentially useful tool in validating CH3Cl emission flux estimates is comparison of the carbon isotope ratio of atmospheric CH3Cl with those of CH3Cl originating from various sources. Here we report the first measurements of delta13C for CH3Cl produced biologically. The CH3Cl released by the higher plant species Batis maritima and Solanum tuberosum was dramatically depleted in 13C with respect to plant tissue (delta13C = -36.8/1000 and -34.5/1000, respectively); CH3Cl released by the fungus Phellinus pomaceus also showed significant 13C depletion with respect to the wood growth substrate (delta13C = -17.9/1000). When reliable delta13C values for the other major sources of atmospheric CH3Cl become available, the distinctive isotopic signature of plant-derived CH3Cl should help constrain the contribution to the atmospheric burden from this source. PMID:11783636

Harper, D B; Kalin, R M; Hamilton, J T; Lamb, C

2001-09-15

372

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

2010-11-19

373

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

374

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

2011-04-27

375

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

376

A selection that reports on protein-protein interactions within a thermophilic bacterium.  

PubMed

Many proteins can be split into fragments that exhibit enhanced function upon fusion to interacting proteins. While this strategy has been widely used to create protein-fragment complementation assays (PCAs) for discovering protein-protein interactions within mesophilic organisms, similar assays have not yet been developed for studying natural and engineered protein complexes at the temperatures where thermophilic microbes grow. We describe the development of a selection for protein-protein interactions within Thermus thermophilus that is based upon growth complementation by fragments of Thermotoga neapolitana adenylate kinase (AK(Tn)). Complementation studies with an engineered thermophile (PQN1) that is not viable above 75 degrees C because its adk gene has been replaced by a Geobacillus stearothermophilus ortholog revealed that growth could be restored at 78 degrees C by a vector that coexpresses polypeptides corresponding to residues 1-79 and 80-220 of AK(Tn). In contrast, PQN1 growth was not complemented by AK(Tn) fragments harboring a C156A mutation within the zinc-binding tetracysteine motif unless these fragments were fused to Thermotoga maritima chemotaxis proteins that heterodimerize (CheA and CheY) or homodimerize (CheX). This enhanced complementation is interpreted as arising from chemotaxis protein-protein interactions, since AK(Tn)-C156A fragments having only one polypeptide fused to a chemotaxis protein did not complement PQN1 to the same extent. This selection increases the maximum temperature where a PCA can be used to engineer thermostable protein complexes and to map protein-protein interactions. PMID:20418388

Nguyen, Peter Q; Silberg, Jonathan J

2010-04-23

377

Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA  

PubMed Central

EngA proteins form a unique family of bacterial GTPases with two GTP-binding domains in tandem, namely GD1 and GD2, followed by a KH (K-homology) domain. They have been shown to interact with the bacterial ribosome and to be involved in its biogenesis. Most prokaryotic EngA possess a high GTPase activity in contrast to eukaryotic GTPases that act mainly as molecular switches. Here, we have purified and characterized the GTPase activity of the Bacillus subtilis EngA and two shortened EngA variants that only contain GD1 or GD2-KH. Interestingly, the GTPase activity of GD1 alone is similar to that of the whole EngA, whereas GD2-KH has a 150-fold lower GTPase activity. At physiological concentration, potassium strongly stimulates the GTPase activity of each protein construct. Interestingly, it affects neither the affinities for nucleotides nor the monomeric status of EngA or the GD1 domain. Thus, potassium likely acts as a chemical GTPase-activating element as proposed for another bacterial GTPase like MnmE. However, unlike MnmE, potassium does not promote dimerization of EngA. In addition, we solved two crystal structures of full-length EngA. One of them contained for the first time a GTP-like analogue bound to GD2 while GD1 was free. Surprisingly, its overall fold was similar to a previously solved structure with GDP bound to both sites. Our data indicate that a significant structural change must occur upon K+ binding to GD2, and a comparison with T. maritima EngA and MnmE structures allowed us to propose a model explaining the chemical basis for the different GTPase activities of GD1 and GD2.

Foucher, Anne-Emmanuelle; Reiser, Jean-Baptiste; Ebel, Christine; Housset, Dominique; Jault, Jean-Michel

2012-01-01

378

Structural Analysis of a Periplasmic Binding Protein in the Tripartite ATP-independent Transporter Family Reveals a Tetrameric Assembly That May Have a Role in Ligand Transport*  

PubMed Central

Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 Å resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 Å root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 Å) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides ?-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.

Cuneo, Matthew J.; Changela, Anita; Miklos, Aleksandr E.; Beese, Lorena S.; Krueger, Joanna K.; Hellinga, Homme W.

2008-01-01

379

Thermophilic anaerobic oxidation of methane by marine microbial consortia.  

PubMed

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. PMID:21697963

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

2011-06-23

380

Impacts of summer ozone exposure on the growth and overwintering of UK upland vegetation  

NASA Astrophysics Data System (ADS)

The effects of ozone exposure on species of an upland grassland were assessed. Thirty-three species from Snowdonia, North Wales, UK, were exposed for 10 weeks to a weekly episodic ozone regime in solardomes representing predicted future concentrations. Two solardomes were used as controls, with ozone added to charcoal-filtered air to give a continuous ozone concentration of 30 ppb (O 3(30)). A weekly episodic ozone regime was applied to two other solardomes, with concentrations rising for 8 h per day to 80 ppb on day 1, 100 ppb on days 2 and 3, and 80 ppb on day 4; ozone concentrations remained at 30 ppb at all other times (O 3(30+peaks)). The control and background ozone concentrations of 30 ppb were maintained throughout the night as well as during the daytime. During exposure to the episodic ozone regime, some species were sensitive to ozone and showed ozone-specific leaf injury symptoms (e.g . Carex echinata) and/or premature senescence (e.g. Festuca rubra) and/or changes in above-ground biomass (e.g. Armeria maritima), whereas other species (e.g Holcus lanatus and Carex demissa) showed no effects. Some species, although showing no effects during the 10-week ozone exposure, showed carry-over effects on biomass the following spring, after a winter period of ambient ozone exposure (e.g. Galium saxatile, Nardus stricta and Saxifraga stellaris). The carry-over effects shown in this study indicate the potential ecological impact of ozone on semi-natural vegetation species and indicate the importance of longer-term studies on the effects of ozone on plants.

Hayes, Felicity; Mills, Gina; Williams, Philip; Harmens, Harry; Büker, Patrick

381

Rusty, Jammed, and Well-Oiled Hinges: Mutations Affecting the Interdomain Region of FliG, a Rotor Element of the Escherichia coli Flagellar Motor  

PubMed Central

The FliG protein is a central component of the bacterial flagellar motor. It is one of the first proteins added during assembly of the flagellar basal body, and there are 26 copies per motor. FliG interacts directly with the Mot protein complex of the stator to generate torque, and it is a crucial player in switching the direction of flagellar rotation from clockwise (CW) to counterclockwise and vice versa. A primarily helical linker joins the N-terminal assembly domain of FliG, which is firmly attached to the FliF protein of the MS ring of the basal body, to the motility domain that interacts with MotA/MotB. We report here the results of a mutagenic analysis focused on what has been called the hinge region of the linker. Residue substitutions in this region generate a diversity of phenotypes, including motors that are strongly CW biased, infrequent switchers, rapid switchers, and transiently or permanently paused. Isolation of these mutants was facilitated by a “sensitizing” mutation (E232G) outside of the hinge region that was accidentally introduced during cloning of the chromosomal fliG gene into our vector plasmid. This mutation partially interferes with flagellar assembly and accentuates the defects associated with mutations that by themselves have little phenotypic consequence. The effects of these mutations are analyzed in the context of a conformational-coupling model for motor switching and with respect to the structure of the C-terminal 70% of FliG from Thermotoga maritima.

Van Way, Susan M.; Millas, Stephanos G.; Lee, Aaron H.; Manson, Michael D.

2004-01-01

382

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

383

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

384

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

385

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

2013-06-15

386

Insertion of endocellulase catalytic domains into thermostable consensus ankyrin scaffolds: effects on stability and cellulolytic activity.  

PubMed

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. PMID:23974146

Cunha, Eva S; Hatem, Christine L; Barrick, Doug

2013-08-23

387

Hirschia litorea sp. nov., isolated from seashore sediment, and emended description of the genus Hirschia.  

PubMed

A Gram-negative, non-spore-forming, non-flagellated, coccoid-, oval- or rod-shaped strain, designated M-M23(T), was isolated from seashore sediment at Geoje island, South Korea. Strain M-M23(T) grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 2?% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain M-M23(T) clustered with the type strains of the two species of the genus Hirschia, with which it exhibited 97.6-98.1?% 16S rRNA gene sequence similarity. Sequence similarity with the type strains of other recognized species was <90.8?%. Strain M-M23(T) contained Q-10 as the predominant ubiquinone and C18?:?1?7c and C16?:?0 as the major fatty acids. The major polar lipids of strain M-M23(T) were phosphatidylglycerol and two unidentified lipids. The DNA G+C content of strain M-M23(T) was 45.4 mol%. DNA-DNA relatedness between the isolate and Hirschia baltica DSM 5838(T) and Hirschia maritima JCM 14974(T) was 22±7.2 and 14±5.6?%, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain M-M23(T) is separate from the other described members of the genus Hirschia. On the basis of the data presented, strain M-M23(T) is considered to represent a novel species of the genus Hirschia, for which the name Hirschia litorea sp. nov. is proposed. The type strain is M-M23(T) (?=?KCTC 32081(T) ?=?CCUG 62793(T)). An emended description of the genus Hirschia is also provided. PMID:22904229

Park, Sooyeon; Yoon, Jung-Hoon

2012-08-17

388

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

2011-12-06

389

On the distribution and evaluation of Na, Mg and Cl in leaves of selected halophytes  

NASA Astrophysics Data System (ADS)

Diverse physiological, biochemical and morphological adaptations enable plants to survive in extreme saline environments where osmotic and ionic stresses limit growth and development. Halophytes are salt-tolerant plants that can withstand extraordinarily high levels of Na and Cl in their leaves. The tissue and cellular distribution patterns of salt ions can be linked to the underlying mechanisms of salt tolerance. Application of fast, reliable, multi-elemental and quantitative techniques such as micro-proton-induced X-ray emission (micro-PIXE) will significantly contribute to and accelerate studies of plant salt tolerance, especially as micro-PIXE also provides spatially resolved quantitative data for light elements, such as Na and Mg. The spatial concentration distributions of Na, Mg, Cl, K, P and S in leaves of four halophytes (Bassia indica, Atriplex prostrata, Spartina maritima and Limonium angustifolium) were determined using micro-PIXE, to study the salt-tolerance strategies of the selected halophytes. Different distribution patterns of the studied elements were seen in the leaves; however, in all four of these plant species, Na was excluded from photosynthetically active chlorophyl tissues. With the exception of L. angustifolium, Cl, P and S contents (representing chloride, phosphate and sulphate ionic forms, respectively) did not ensure charge balance in the leaves, which suggests other anionic compounds, such as nitrate and organic anions, have crucial roles in maintaining electroneutrality in these halophytes. By increasing soil salinisation worldwide, the possibility to reliably complement spatial distributions of Na, Mg, Cl, K, P and S with plant structural morphology will contribute significantly to our understanding of plant tolerance mechanisms at the tissue and cell levels. In addition, these kinds of studies are of particular value for designing crop plants with high salt tolerance and for the development of phytoremediation technologies.

Pongrac, Paula; Vogel-Mikuš, Katarina; Regvar, Marjana; Kaligari?, Mitja; Vavpeti?, Primož; Kelemen, Mitja; Grlj, Nataša; Shelef, Oren; Golan-Goldhirsh, Avi; Rachmilevitch, Shimon; Pelicon, Primož

2013-07-01

390

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

391

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

2009-03-04

392

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites  

PubMed Central

The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-? factor antagonist, and A2LD1 (gi:13879369), a mouse ?-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298?K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100?K and 1.6?Å resolution and at 100?K and 1.9?Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the millisecond time scale that appears to be frozen in the crystals. These observations suggest that a search for molecular regions showing increased structural disorder and slow dynamic processes in solution while being well ordered in the corresponding crystal structure might be a valid initial step in the challenge of identifying putative active sites in functionally unannotated proteins with known three-dimensional structure.

Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-Andre; Wilson, Ian A.; Wuthrich, Kurt

2010-01-01

393

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

394

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

395

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

396

Pullulanase Type I from Fervidobacterium pennavorans Ven5: Cloning, Sequencing, and Expression of the Gene and Biochemical Characterization of the Recombinant Enzyme  

PubMed Central

The gene encoding the type I pullulanase from the extremely thermophilic anaerobic bacterium Fervidobacterium pennavorans Ven5 was cloned and sequenced in Escherichia coli. The pulA gene from F. pennavorans Ven5 had 50.1% pairwise amino acid identity with pulA from the anaerobic hyperthermophile Thermotoga maritima and contained the four regions conserved among all amylolytic enzymes. The pullulanase gene (pulA) encodes a protein of 849 amino acids with a 28-residue signal peptide. The pulA gene was subcloned without its signal sequence and overexpressed in E. coli under the control of the trc promoter. This clone, E. coli FD748, produced two proteins (93 and 83 kDa) with pullulanase activity. A second start site, identified 118 amino acids downstream from the ATG start site, with a Shine-Dalgarno-like sequence (GGAGG) and TTG translation initiation codon was mutated to produce only the 93-kDa protein. The recombinant purified pullulanases (rPulAs) were optimally active at pH 6 and 80°C and had a half-life of 2 h at 80°C. The rPulAs hydrolyzed ?-1,6 glycosidic linkages of pullulan, starch, amylopectin, glycogen, ?-?-limited dextrin. Interestingly, amylose, which contains only ?-1,4 glycosidic linkages, was not hydrolyzed by rPulAs. According to these results, the enzyme is classified as a debranching enzyme, pullulanase type I. The extraordinary high substrate specificity of rPulA together with its thermal stability makes this enzyme a good candidate for biotechnological applications in the starch-processing industry.

Bertoldo, Costanzo; Duffner, Fiona; Jorgensen, Per L.; Antranikian, Garabed

1999-01-01

397

Aquatic insects of New York salt marsh associated with mosquito larval habitat and their potential utility as bioindicators.  

PubMed

The aquatic insect fauna of salt marshes is poorly characterized, with the possible exception of biting Diptera. Aquatic insects play a vital role in salt marsh ecology, and have great potential importance as biological indicators for assessing marsh health. In addition, they may be impacted by measures to control mosquitoes such as changes to the marsh habitat, altered hydrology, or the application of pesticides. Given these concerns, the goals of this study were to conduct the first taxonomic survey of salt marsh aquatic insects on Long Island, New York, USA and to evaluate their utility for non-target pesticide impacts and environmental biomonitoring. A total of 18 species from 11 families and five orders were collected repeatedly during the five month study period. Diptera was the most diverse order with nine species from four families, followed by Coleoptera with four species from two families, Heteroptera with three species from three families, then Odonata and the hexapod Collembola with one species each. Water boatmen, Trichocorixa verticalis Fieber (Heteroptera: Corixidae) and a shore fly, Ephydra subopaca Loew (Diptera: Ephydridae), were the two most commonly encountered species. An additional six species; Anurida maritima Guérin-Méneville (Collembola: Neanuridae), Mesovelia mulsanti White (Heteroptera: Mesovelidae), Enochrus hamiltoni Horn (Coleoptera: Hydrophilidae), Tropisternus quadristriatus Horn (Coleoptera: Hydrophilidae), Dasyhelea pseudocincta Waugh and Wirth (Diptera: Ceratopogonidae), and Brachydeutera argentata Walker (Diptera: Ephydridae), were found regularly. Together with the less common Erythrodiplax berenice Drury (Odonata: Libellulidae), these nine species were identified as the most suitable candidates for pesticide and environmental impact monitoring due to abundance, position in the food chain, and extended seasonal occurrence. This study represents a first step towards developing an insect-based index of biological integrity for salt marsh health assessment. PMID:22957707

Rochlin, Ilia; Dempsey, Mary E; Iwanejko, Tom; Ninivaggi, Dominick V

2011-01-01

398

A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products.  

PubMed

Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with five molecules of isopentenyl pyrophosphate (IPP) to generate C(40) octaprenyl pyrophosphate (OPP) which constitutes the side chain of menaquinone. We have previously reported the X-ray structure of OPPs from Thermotoga maritima, which is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity [Guo, R. T., Kuo, C. J., Ko, T. P., Chou, C. C., Shr, R. L., Liang, P. H., and Wang, A. H.-J. (2004) J. Biol. Chem. 279, 4903-4912]. A76 and S77 are located on top of the active site close to where FPP is bound. A76Y and A76Y/S77F OPPs mutants produce C(20), indicating that the substituted larger residues interfere with the substrate chain elongation. Surprisingly, the A76Y/S77F mutant synthesizes a larger amount of C(20) than the A76Y mutant. In the crystal structure of the A76Y/S77F mutant, F77 is pushed away by Y76, thereby creating more space between those two large amino acids to accommodate the C(20) product. A large F132 residue at the bottom of the tunnel-shaped active site serves as the "floor" and determines the final product chain length. The substitution of F132 with a small Ala, thereby removing the blockade, led to the synthesis of a C(50) product larger than that produced by the wild-type enzyme. On the basis of the structure, we have sequentially mutated the large amino acids, including F132, L128, I123, and D62, to Ala underneath the tunnel. The products of the F132A/L128A/I123A/D62A mutant reach C(95), beyond the largest chain length generated by all known trans-prenyltransferases. Further modifications of the enzyme reaction conditions, including new IPP derivatives, may allow the preparation of high-molecular weight polyprenyl products resembling the rubber molecule. PMID:15196010

Guo, Rey-Ting; Kuo, Chih-Jung; Ko, Tzu-Ping; Chou, Chia-Cheng; Liang, Po-Huang; Wang, Andrew H-J

2004-06-22

399

Vibrational analysis of mononitrosyl complexes in hemerythrin and flavodiiron proteins: relevance to detoxifying NO reductase.  

PubMed

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 N(2)O [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 semibridging 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 N(2)O. 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). PMID:22449095

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

2012-04-09

400

A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2  

PubMed Central

Background tRNase Z removes the 3'-trailer sequences from precursor tRNAs, which is an essential step preceding the addition of the CCA sequence. tRNase Z exists in the short (tRNase ZS) and long (tRNase ZL) forms. Based on the sequence characteristics, they can be divided into two major types: bacterial-type tRNase ZS and eukaryotic-type tRNase ZL, and one minor type, Thermotoga maritima (TM)-type tRNase ZS. The number of tRNase Zs is highly variable, with the largest number being identified experimentally in the flowering plant Arabidopsis thaliana. It is unknown whether multiple tRNase Zs found in A. thaliana is common to the plant kingdom. Also unknown is the extent of sequence and structural conservation among tRNase Zs from the plant kingdom. Results We report the identification and analysis of candidate tRNase Zs in 27 fully sequenced genomes of green plants, the great majority of which are flowering plants. It appears that green plants contain multiple distinct tRNase Zs predicted to reside in different subcellular compartments. Furthermore, while the bacterial-type tRNase ZSs are present only in basal land plants and green algae, the TM-type tRNase ZSs are widespread in green plants. The protein sequences of the TM-type tRNase ZSs identified in green plants are similar to those of the bacterial-type tRNase ZSs but have distinct features, including the TM-type flexible arm, the variant catalytic HEAT and HST motifs, and a lack of the PxKxRN motif involved in CCA anti-determination (inhibition of tRNase Z activity by CCA), which prevents tRNase Z cleavage of mature tRNAs. Examination of flowering plant chloroplast tRNA genes reveals that many of these genes encode partial CCA sequences. Based on our results and previous studies, we predict that the plant TM-type tRNase ZSs may not recognize the CCA sequence as an anti-determinant. Conclusions Our findings substantially expand the current repertoire of the TM-type tRNase ZSs and hint at the possibility that these proteins may have been selected for their ability to process chloroplast pre-tRNAs with whole or partial CCA sequences. Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants.

2011-01-01

401

Interaction between submerged aquatic vegetation and turbulence generated by the wind: an experimental study  

NASA Astrophysics Data System (ADS)

In wetlands wind-induced turbulence significantly affects the bottom boundary, and the interaction between turbulence and plant canopies is therefore particularly important. The aim of this study is to advance understanding of the impact of this interaction in submerged aquatic vegetation (SAV) on vertical mixing in a fluid dominated by turbulence. Wind-generated turbulence was simulated in the laboratory using an oscillating grid. We quantify the vertical distribution of turbulent kinetic energy (TKE) above and within different types of vegetation, measured by an acoustic Doppler velocimeter. Experimental conditions are analysed in two canopy models (rigid and semi-rigid) with seven solid plant fractions (SPFs), three stem diameters (d), three oscillation grid frequencies (f) and four natural SAVs (Cladium mariscus, Potamogeton nodosus, Myriophyllum verticillatum and Ruppia maritima). Our observations suggest that the TKE above the constructed canopies was higher than that found without plants. The vertical profile varied according to the diameters of the individual stems and the SPF. Within the canopies, two zones could be distinguished. The 'transition zone', situated a few centimetres below the top of the canopy, was characterised by a reduction in the TKE. Below the transition zone, the TKE progressively decayed as the stems dissipated the turbulence, creating a zone where the TKE was lower than in the zone without stems. This is a well-known effect of SAV on turbulence, called sheltering or dampening. This phenomenon was enhanced by a decrease in the stem diameter and an increase in the SPF of the canopies, due to the reduction of the plant-to-plant distance. We have, therefore, not only observed a sheltering, but quantified it. The development of the sheltering slowed as the frequency increased, because the vegetation could not prevent the penetration of the turbulence. In the semi-rigid model, no transition zone was found inside the canopies, while sheltering was found from the very top of the plants and was intensified inside the canopies. Finally, sheltering for SAVs was similar to sheltering produced by semi-rigid plants with widespread sheltering inside the canopy.

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

2010-05-01

402

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

403

[Cardiac glycosides: From ancient history through Withering's foxglove to endogeneous cardiac glycosides].  

PubMed

For centuries, drugs that increase the power of contraction of the failing heart have been used for the treatment of congestive heart failure (dropsy). The cardiac effect is due to the content of cardiac glycosides. Squill or sea onion, Urginea (Scilla) maritima, a seashore plant, was known by the ancient Romans and Syrians and possibly also by the ancient Egyptians. Squills were used erratically, but some prescriptions indicate that they may have been used for the treatment of oedematous states. The toxic effect of strophanthus species was known from poisoned arrows used by the natives in Africa. Digitalis, derived form the foxglove plant, Digitalis purpurea, is mentioned in writings as early as 1250; a Welsh family, known as the Physicians of Myddvai, collected different herbs and digitalis was included in their prescriptions. However, the druge was used erratically until the 18th century, when William Withering, an English physician and botanist, published a monograph describing the clinical effects of an extract of the foxglove plant. Later, in 1785, the indication and the toxicity of digitalis were reported in his book, "An account of the Foxglove and some of its medical uses with practical remarks on dropsy, and other diseases". In Denmark, the leaves of Digitalis purpurea or Digitalis lanata were tested for cardiac glycoside activity. The standardized digitalis powder was used in tinctures, infusions, and tablets. The preparations were included in successive editions of the Danish pharmacopoeia, some of the tinctures already in 1828, i.e. before the standardization of the drug. Isolation of cardiac glycosides from digitalis, strophanthus and squill and determination of their chemical structures initiated biochemical and pharmacological studies. The scientific advances led to an understanding of cardiac muscle con