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Scott A. Lesley - One of the best experts on this subject based on the ideXlab platform.

  • Three-dimensional structural view of the central metabolic network of Thermotoga Maritima.
    Science (New York N.Y.), 2009
    Co-Authors: Ying Zhang, Ashley M. Deacon, Scott A. Lesley, Lukasz Jaroszewski, Ines Thiele, Dana Weekes, Krzysztof Ginalski, John Wooley, Ian A. Wilson
    Abstract:

    Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga Maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.

  • A scaleable and integrated crystallization pipeline applied to mining the Thermotoga Maritima proteome.
    Journal of Structural and Functional Genomics, 2004
    Co-Authors: Michael Didonato, Ashley M. Deacon, Heath E. Klock, Daniel Mcmullan, Scott A. Lesley
    Abstract:

    The wealth of genomic data available for many organisms has set the stage for the next phase of structure—function analysis. High-throughput structural genomics is currently the method of choice for rapid analysis of protein structure—function relationships on a proteome-wide basis. The Joint Center for Structural Genomics (JCSG), established in 2000 under the NIH/NIGMS Protein Structure Initiative, has developed and implemented an integrated high-throughput structure pipeline and applied it in a 2-tiered approach to mining the proteome of the thermophilic bacterium Thermotoga Maritima. In the first tier, the successful application of this integrated pipeline has resulted in the cloning and expression of 73% of the T. Maritima proteome (1376 out of 1877 predicted genes), and has identified 465 proteins which produced crystal hits. These 465 proteins were compared with existing structural information and a subset of 269 targets were selected to process towards structure determination in a second tier effort. To date, the JCSG pipeline applied to the Thermotoga Maritima proteome has resulted in 55 new structures and has identified 6 novel folds and continues to identify structures with novel features.

  • Structural genomics of the Thermotoga Maritima proteome implemented in a high-throughput structure determination pipeline
    Proceedings of the National Academy of Sciences of the United States of America, 2002
    Co-Authors: Scott A. Lesley, Ashley M. Deacon, Heath E. Klock, Daniel Mcmullan, Peter Kuhn, Adam Godzik, I.i. Mathews, Andreas Kreusch, Glen Spraggon, Tanya Shin
    Abstract:

    Structural genomics is emerging as a principal approach to define protein structure–function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga Maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. Maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

Karl O. Stetter - One of the best experts on this subject based on the ideXlab platform.

  • gene transfer and genome plasticity in Thermotoga Maritima a model hyperthermophilic species
    Journal of Bacteriology, 2005
    Co-Authors: Emmanuel F Mongodin, Karl O. Stetter, Robert Huber, Claire M. Fraser, Ioana R Hance, Robert T Deboy, Steven R Gill, Sean C Daugherty, Karen E. Nelson
    Abstract:

    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.

  • Glycolipids from Thermotoga Maritima, a hyperthermophilic microorganism belonging to Bacteria domain.
    Biochimica et biophysica acta, 1992
    Co-Authors: M.cristina Manca, Agata Gambacorta, Robert Huber, Virginia Lanzotti, Barbara Nicolaus, Antonio Trincone, Jasna Peter-katalinic, Heinz Egge, Karl O. Stetter
    Abstract:

    Abstract Two novel glycolipids with a very rareα(1 → 4) diglucosyl structure have been isolated from the thermophilic bacterium Thermotoga Maritima. The structures of these compounds, on the basis of chemical procedures and spectroscopic studies (FAB-MS and NMR), were shown to be: 1(3),2- dipalmitoyl -3(1)-[ glucopyranosyl -(6- decanoyl )-α- d -(1→ 4)- glucopyranosyl -α- d ]- glycerol (Glycolipid 1) and 1(3), 2-dipalmitoyl-3(1)-[glucopyranosyl-α- d -(1 → 4)-glucopyranosyl-α- d ]-glycerol (Glycolipid 2).

  • Topographical and enzymatic characterization of amylases from the extremely thermophilic eubacterium Thermotoga Maritima.
    FEBS letters, 1991
    Co-Authors: Judith Schumann, Alexander Wrba, Rainer Jaenicke, Karl O. Stetter
    Abstract:

    The hyperthermophilic cubacterium Thermotoga Maritima uses starch as a substrate, without releasing amylase activity into the culture medium. The enzyme is associated with the ‘toga’. Its expression level is too low to allow the isolation of the pure enzyme. Using cycloheptaamylose and acarbose affinity chromatography and common chromatographic procedures, two enzyme fractions are obtained. They differ in specificity, pH-optimum, temperature dependence and stability. Substrate specificity and Ca2* dependence indicate α-, β- and gluco-amylase activity. Compared with α-amylase from Bacillus licheniformis (Tmax = 75°C), the amylasex from Thermotoga Maritima show exceedingly high thermal stability with an upper temperature limit at 95°C. Significant turnover occurs only 70 and 100°C, i.e. in the range of viability of the microorganism.

Rainer Jaenicke - One of the best experts on this subject based on the ideXlab platform.

  • [33] Thermostability of proteins from Thermotoga Maritima
    Methods in enzymology, 2001
    Co-Authors: Rainer Jaenicke, Gerald Böhm
    Abstract:

    Publisher Summary Proteins, independent of their mesophilic or thermophilic origin, consist exclusively of the 20 canonical natural amino acids. In the multicomponent system of the cytosol, these are known to undergo covalent modifications at the upper limit of temperature observed in the biosphere. Extremophiles must compensate for these degradation processes either by using compatible protectants or by enhanced synthesis and repair. Many studies on the thermal stability of proteins have focused on enzymes from hyperthermophiles. In this context, Thermotoga Maritima , with its temperature range of growth between 55° and 90°, has become one of the favorite organisms, because it is widespread in marine geothermal vents as well as in low-salinity solfataric springs, it can be cultivated in large-scale fermentations, and it has been characterized in detail with respect to its metabolic requirements. The bacterium is a strictly anaerobic fermentative organotroph that grows on various sugars, cellulose, starch, and glycogen as the carbon source: peptides are required for growth on carbohydrates because the organism does not utilize ammonia or free amino acids as the N source.

  • Dihydrofolate reductase from Thermotoga Maritima.
    Methods in enzymology, 2001
    Co-Authors: Thomas Dams, Rainer Jaenicke
    Abstract:

    Publisher Summary Dihydrofolate reductase (DHFR) plays a central role in the metabolism of both prokaryotes and eukaryotes. It catalyzes the NADPHdependent reduction of dihydrofolic acid (DHF) to tetrahydrofolic acid (THF), thereby restoring an important cofactor in one-carbon transfer reactions. The enzyme has been widely studied both structurally and mechanistically. Among the more than 40 DHFRs characterized so far, the enzyme from the hyperthermophilic bacterium Thermotoga Maritima (Tm DHFR) exhibits the highest intrinsic stability with the exceptional additional characteristic of forming a tightly associated homodimer. Tm DHFR may serve as a model system for structural and mechanistical comparisons with its mesophilic counterparts. As a dimer, it promises insight into mechanisms of thermophilic adaptation at all levels of the structural hierarchy of globular proteins. In this context, the extreme stability offers experimental advantages. However, there are difficulties in handling the enzyme, which are discussed in this chapter.

  • Topographical and enzymatic characterization of amylases from the extremely thermophilic eubacterium Thermotoga Maritima.
    FEBS letters, 1991
    Co-Authors: Judith Schumann, Alexander Wrba, Rainer Jaenicke, Karl O. Stetter
    Abstract:

    The hyperthermophilic cubacterium Thermotoga Maritima uses starch as a substrate, without releasing amylase activity into the culture medium. The enzyme is associated with the ‘toga’. Its expression level is too low to allow the isolation of the pure enzyme. Using cycloheptaamylose and acarbose affinity chromatography and common chromatographic procedures, two enzyme fractions are obtained. They differ in specificity, pH-optimum, temperature dependence and stability. Substrate specificity and Ca2* dependence indicate α-, β- and gluco-amylase activity. Compared with α-amylase from Bacillus licheniformis (Tmax = 75°C), the amylasex from Thermotoga Maritima show exceedingly high thermal stability with an upper temperature limit at 95°C. Significant turnover occurs only 70 and 100°C, i.e. in the range of viability of the microorganism.

David W. Rice - One of the best experts on this subject based on the ideXlab platform.

  • Crystallization and preliminary X‐ray crystallographic studies on 4‐α‐glucanotransferase from Thermotoga Maritima
    Acta Crystallographica Section D Biological Crystallography, 2001
    Co-Authors: Anna Roujeinikova, Carsten Raasch, Svetlana E. Sedelnikova, Wolfgang Liebl, David W. Rice
    Abstract:

    Thermotoga Maritima 4-α-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 I212121, with unit-cell parameters a = 92.6, b = 180.3, c = 199.2 A.

  • Crystallization and preliminary X-ray crystallographic studies on 4-alpha-glucanotransferase from Thermotoga Maritima.
    Acta crystallographica. Section D Biological crystallography, 2001
    Co-Authors: Anna Roujeinikova, Carsten Raasch, Svetlana E. Sedelnikova, Wolfgang Liebl, David W. Rice
    Abstract:

    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.

  • Crystallization and preliminary X-ray crystallographic studies on maltosyltransferase from Thermotoga Maritima.
    Acta crystallographica. Section D Biological crystallography, 2000
    Co-Authors: J Burke, Anna Roujeinikova, Carsten Raasch, Svetlana E. Sedelnikova, Wolfgang Liebl, P J Baker, David W. Rice
    Abstract:

    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.

Karen E. Nelson - One of the best experts on this subject based on the ideXlab platform.

  • gene transfer and genome plasticity in Thermotoga Maritima a model hyperthermophilic species
    Journal of Bacteriology, 2005
    Co-Authors: Emmanuel F Mongodin, Karl O. Stetter, Robert Huber, Claire M. Fraser, Ioana R Hance, Robert T Deboy, Steven R Gill, Sean C Daugherty, Karen E. Nelson
    Abstract:

    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.

  • Genome of Thermotoga Maritima MSB8.
    Methods in enzymology, 2001
    Co-Authors: Karen E. Nelson, Jonathan A. Eisen, Claire M. Fraser
    Abstract:

    Publisher Summary Thermotoga Maritima has a temperature optimum for growth of 80° and can metabolize many simple and complex carbohydrates, including glucose, sucrose, starch, xylan, and cellulose. Both xylan and cellulose are complex plant polymers; xylan represents the most abundant noncellulosic polysaccharide in angiosperms, where it accounts for 20-30% of the dry weight of wood tissues. Cellulose is the most abundant biopolymer occurring in nature, estimated to account for 75 × 10 9 tons of dry plant biomass annually. Both cellulose and xylan, through conversion to fuels (e.g., H 2 ), have major potential as renewable carbon and energy sources. Most other Thermotoga strains have been isolated in continental oil reservoirs and oil-producing wells. All, however, demonstrate the characteristic toga-like sheath structure that surrounds the cells and an ability to ferment a range of carbohydrate substrates. From an evolutionary standpoint, the Thermotogales are significant, as small subunit ribosomal RNA (SSU rRNA) phylogenetic analysis of T. Maritima placed the bacterium as the deepest and most slowly evolving lineage in the Eubacteria.

  • structural analysis of dna sequence evidence for lateral gene transfer in Thermotoga Maritima
    Nucleic Acids Research, 2000
    Co-Authors: Peder Worning, Karen E. Nelson, Lars Juhl Jensen, Soren Brunak, David W Ussery
    Abstract:

    The recently published complete DNA sequence of the bacterium Thermotoga Maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, which brings independent evidence for the lateral gene transfer in the genome of T.Maritima. The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms of different origin. The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea. Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure.