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PSI Plasmid of the Month

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Each month we will highlight a different PSI plasmid or plasmid collection which may interest you.

Thermotoga maritima genome collection(1800 of 1877 ORFs)

Thermotoga maritima is hyperthemophilic, rod-shaped gram-negative bacterium originally isolated from geothermal-heated marine sediment in Vulcano, Italy. Thermotoga maritima is phylogenetically very important, because it appears to represent one of the deepest lineages in Eubacteria. Since the Thermotoga maritima genome has the highest percentage (24%) of genes similar to Archeal genes, it would appear to be an ideal system to study domain organization and identify new or highly diverged protein folds in both Eubacteria and Archea. The genome of T. maritima is a single circular chromosome of approximately 1.8 Megabases in size, encoding for an estimated 1877 proteins. Its optimal growth temperature is approximately 80°C (176°F).

T. maritima has unique metabolic properties related to its capacity to process a diverse set of carbohydrates, utilizing sulfur as an electron receptor and producing hydrogen during fermentative growth. Its genome was sequenced in 1999 and surprisingly revealed many genes of archeal origin  (1) suggesting possible similarities to GC-rich gram-positive bacteria, such as Clostridia or Mycoplasma. At the time of its discovery, it appeared to be a unique organism, but now the phylum Thermatogales has more than 20 known members including mesophilic and moderate temperature-adapted species. Its exact phylogenetic position in the Tree of Life is still hotly debated.

Because of its compact size, Thermotoga maritima is an ideal model for systems biology and metabolic reconstruction simulations. It has one of the smallest genomes among free-living bacteria, with a very rich set of carbohydrate metabolic genes, as well as an extensive set of diverse transmembrane transporters. Its unique features, both from phylogenetic and metabolic perspectives, are the focus of intensive research.

The Joint Center for Structural Genomics (JCSG) initiated the Thermotoga maritima structural genomics project at the outset of the NIGMS Protein Structure Initiative (PSI) (2) with the eventual goal to provide complete structural and functional coverage of this emerging model system. Structures of over 170 unique Thermotoga maritima proteins have been determined at the JCSG, with many interesting results described in a number of papers (see publications listed below). Highlights include the structure-based discovery of a novel thymidylate synthase (3-9), structure determination of the integral membrane transporter (CorA) (10), exploration of protein thermostability (11-12), and many other structures (13-22).

Expression, purification and structural determination of Thermotoga maritima proteins at the JCSG were critical for the development of the JCSG high-throughput pipeline and have been described in a number of publications (23-32). In the latest development in this project, a complete three-dimensional reconstruction of the central metabolic network of this organism was achieved by a combination of experimental structure determination and comparative modeling (33).

In total, 1800 of the 1877 Thermotoga maritima ORFs were cloned into expression vectors at the JCSG.  The PSI-Materials Repository now has 1134 fully sequence-verified clones from this collection available for requestors. The full list of clones can be found here.


Publications

  1. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM (1999). Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature, 399, 323-9. (Pub Med ID: 10360571)
  2. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC (2002). Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A, 99, 11664-9. PMCID: 129326. (Pub Med ID: 12193646)
  3. Koehn EM, Fleischmann T, Conrad JA, Palfey BA, Lesley SA, Mathews, II, Kohen A (2009). An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature, 458, 919-23. PMCID: 2759699. (Pub Med ID: 19370033)          
  4. Kuhn P, Lesley SA, Mathews, II, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Hodgson KO, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JM, Kreusch AT, McMullan D, McPhillips TM, Miller MA, Miller M, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, Taylor SS, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Wooley J, Wilson IA (2002). Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 Å resolution. Proteins, 49, 142-5. (Pub Med ID: 12211025)
  5. Wang Z, Chernyshev A, Koehn EM, Manuel TD, Lesley SA, Kohen A (2009). Oxidase activity of a flavin-dependent thymidylate synthase. FEBS J, 276, 2801-10. PMCID: 2749737. PMCID: PMC2749737. (Pub Med ID: 19459936)
  6. Chernyshev A, Fleischmann T, Koehn EM, Lesley SA, Kohen A (2007). The relationships between oxidase and synthase activities of flavin dependent thymidylate synthase (FDTS). Chem Commun (Camb), 53, 2861-3. (Pub Med ID: 17609801)
  7. Mason A, Agrawal N, Washington MT, Lesley SA, Kohen A (2006). A lag-phase in the reduction of flavin dependent thymidylate synthase (FDTS) revealed a mechanistic missing link. Chem Commun (Camb), 21, 1781-3. (Pub Med ID: 16609803)
  8. Agrawal N, Lesley SA, Kuhn P, Kohen A (2004). Mechanistic studies of a flavin-dependent thymidylate synthase. Biochemistry, 43, 10295-301. (Pub Med ID: 15301527)
  9. Mathews, II, Deacon AM, Canaves JM, McMullan D, Lesley SA, Agarwalla S, Kuhn P (2003). Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein. Structure, 11, 677-90. (Pub Med ID: 12791256)
  10. Eshaghi S, Niegowski D, Kohl A, Martinez Molina D, Lesley SA, Nordlund P (2006). Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution. Science, 313, 354-7. (Pub Med ID: 16857941)
  11. Robinson-Rechavi M, Alibes A, Godzik A (2006). Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol, 356, 547-57. (Pub Med ID: 16375925)
  12. Robinson-Rechavi M, Godzik A (2005). Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure, 13, 857-60. (Pub Med ID: 15939017)
  13. Zheng M, Cooper DR, Grossoehme NE, Yu M, Hung LW, Cieslik M, Derewenda U, Lesley SA, Wilson IA, Giedroc DP, Derewenda ZS (2009). Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Acta Crystallogr D Biol Crystallogr, 65, 356-65. PMCID: PMC2659884. (Pub Med ID: 19307717)
  14. Johnson HA, Hampton E, Lesley SA (2009). The Thermotoga maritima Trk potassium transporter--from frameshift to function. J Bacteriol, 191, 2276-84. PMCID: 2655489. (Pub Med ID: 19168617)
  15. McCleverty CJ, Columbus L, Kreusch A, Lesley SA (2008). Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634. Protein Sci, 17, 869-77. PMCID: 2327271. (Pub Med ID: 18369189)
  16. Huang S, Romanchuk G, Pattridge K, Lesley SA, Wilson IA, Matthews RG, Ludwig M (2007). Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269. Protein Sci, 16, 1588-95. PMCID: 2203375. (Pub Med ID: 17656578)
  17. Etezady-Esfarjani T, Placzek WJ, Herrmann T, Wuthrich K (2006). Solution structures of the putative anti-sigma-factor antagonist TM1442 from Thermotoga maritima in the free and phosphorylated states. Magn Reson Chem, 44 Spec No, S61-70. (Pub Med ID: 16826544)
  18. Almeida MS, Herrmann T, Peti W, Wilson IA, Wuthrich K (2005). NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins. Protein Sci, 14, 2880-6. PMCID: 2253223. (Pub Med ID: 16199668)
  19. Xu Q, Schwarzenbacher R, McMullan D, von Delft F, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA (2004). Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 Å resolution. Proteins, 56, 171-5. (Pub Med ID: 15162497)
  20. Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA (2004). Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-Å resolution. Proteins, 55, 474-8. (Pub Med ID: 15048837)
  21. Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA (2003). Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase. J Mol Biol, 330, 309-21. (Pub Med ID: 12823970)
  22. Etezady-Esfarjani T, Peti W, Wuthrich K (2003). NMR assignment of the conserved hypothetical protein TM1290 of Thermotoga maritima. J Biomol NMR, 25, 167-8. (Pub Med ID: 12652129)
  23. Canaves JM, Page R, Wilson IA, Stevens RC (2004). Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol, 344, 977-91. (Pub Med ID: 15544807)
  24. Page R, Deacon AM, Lesley SA, Stevens RC (2005). Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins. J Struct Funct Genomics, 6, 209-17. (Pub Med ID: 16211521)
  25. Pantazatos D, Kim JS, Klock HE, Stevens RC, Wilson IA, Lesley SA, Woods VL, Jr. (2004). Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc Natl Acad Sci U S A, 101, 751-6. PMCID: 321753. (Pub Med ID: 14715906)
  26. Slabinski L, Jaroszewski L, Rychlewski L, Wilson IA, Lesley SA, Godzik A (2007). XtalPred: a web server for prediction of protein crystallizability. Bioinformatics, 23, 3403-5. (Pub Med ID: 17921170)
  27. Slabinski L, Jaroszewski L, Rodrigues AP, Rychlewski L, Wilson IA, Lesley SA, Godzik A (2007). The challenge of protein structure determination--lessons from structural genomics. Protein Sci, 16, 2472-82. PMCID: 2211687. (Pub Med ID: 17962404)
  28. Etezady-Esfarjani T, Herrmann T, Peti W, Klock HE, Lesley SA, Wuthrich K (2004). NMR structure determination of the hypothetical protein TM1290 from Thermotoga maritima using automated NOESY analysis. J Biomol NMR, 29, 403-6. (Pub Med ID: 15213441)
  29. Columbus L, Lipfert J, Klock H, Millett I, Doniach S, Lesley SA (2006). Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination. Protein Sci, 15, 961-75. PMCID: 2242514. (Pub Med ID: 16597824)
  30. DiDonato M, Deacon AM, Klock HE, McMullan D, Lesley SA (2004). A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome. J Struct Funct Genomics, 5, 133-46. (Pub Med ID: 15263852)
  31. Peti W, Etezady-Esfarjani T, Herrmann T, Klock HE, Lesley SA, Wuthrich K (2004). NMR for structural proteomics of Thermotoga maritima: screening and structure determination. J Struct Funct Genomics, 5, 205-15. (Pub Med ID: 15263836)
  32. Page R, Grzechnik SK, Canaves JM, Spraggon G, Kreusch A, Kuhn P, Stevens RC, Lesley SA (2003). Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome. Acta Crystallogr D Biol Crystallogr, 59, 1028-37. (Pub Med ID: 12777766)
  33. Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A (2009). Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325, 1544-9. PMCID: PMC2833182. (Pub Med ID: 19762644)

 

Updated for April/May 2010