Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)

International Journal of Systematic and Evolutionary Microbiology

Volumn 59, Issue 2, 2009, Pages 285-294

  Gupta, Radhey S ^a   Gao, Beile ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING) A; PHOSPHOGLYCERATE DEHYDROGENASE; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RIBOSOME PROTEIN; BACTERIAL PROTEIN; DNA TOPOISOMERASE (ATP HYDROLYSING); RIBOSOMAL PROTEIN S2;

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; CALDICELLULOSIRUPTOR SACCHAROLYTICUS; CLADISTICS; CLOSTRIDIUM; CLOSTRIDIUM PERFRINGENS; CLOSTRIDIUM TETANI; CLOSTRIDIUM THERMOCELLUM; CONTROLLED STUDY; GENE DELETION; GENE INSERTION; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SPECIES DIFFERENTIATION; THERMOANAEROBACTER PSEUDETHANOLICUS; THERMOANAEROBACTER TENGCOGENSIS; UNINDEXED SEQUENCE; AMINO ACID SEQUENCE; CHEMISTRY; CLASSIFICATION; GENETICS; INDEL MUTATION; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

CALDICELLULOSIRUPTOR SACCHAROLYTICUS; CLOSTRIDIA; CLOSTRIDIUM; CLOSTRIDIUM PERFRINGENS; CLOSTRIDIUM TETANI; CLOSTRIDIUM THERMOCELLUM; THERMOANAEROBACTER;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CLOSTRIDIUM; DNA GYRASE; INDEL MUTATION; MITOCHONDRIAL PROTON-TRANSLOCATING ATPASES; MOLECULAR SEQUENCE DATA; PHOSPHOGLYCERATE DEHYDROGENASE; PHYLOGENY; RIBOSOMAL PROTEINS; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY;

EID: 63449115868     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.001792-0     Document Type: Article

References (48)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein databases search programs. Nucleic Acids Res 25, 3389-3402.
2. Belda, E., Moya, A. & Silva, F. J. (2005). Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Mol Biol Evol 22, 1456-1467.
3. Bettegowda, C., Huang, X., Lin, J., Cheong, I., Kohli, M., Szabo, S. A., Zhang, X., Diaz, L. A., Jr, Velculescu, V. E. & other authors (2006). The genome and transcriptomes of the anti-tumor agent Clostridium novyi NT. Nat Biotechnol 24, 1573-1580.
4. Binnewies, T. T., Motro, Y., Hallin, P. F., Lund, O., Dunn, D., La, T., Hampson, D. J., Bellgard, M., Wassenaar, T. M. & Ussery, D. W. (2006). Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics 6, 165-185.
5. Brown, J. R. & Volker, C. (2004). Phylogeny of γ-proteobacteria: resolution of one branch of the universal tree? Bioessays 26, 463-468.
6. Brüggemann, H., Bäumer, S., Fricke, W. F., Wiezer, A., Liesegang, H., Decker, I., Herzberg, C., Martinez-Arias, R., Merkl, R. & other authors (2003). The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci U S A 100, 1316-1321.
7. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552.
8. Cato, E. P. & Stackebrandt, E. (1989). Taxonomy and phylogeny. In Clostridia, pp. 1-26. Edited by N. P. Minton & D. J. Clarke. New York: Plenum Press.
9. AL. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1141-1200. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
10. Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287.
11. Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H., Farrow, J. A. E. & other authors (1994). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44, 812-826.
12. Corbett, K. D. & Berger, J. M. (2004). Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu Rev Biophys Biomol Struct 33, 95-118.
13. Fang, G., Rocha, E. & Danchin, A. (2005). How essential are nonessential genes? Mol Biol Evol 22, 2147-2156.
14. Finegold, S. M., Song, Y. & Liu, C. (2002). Taxonomy - general comments and update on taxonomy of clostridia and anaerobic cocci. Anaerobe 8, 283-285.
15. Galperin, M. Y. & Koonin, E. V. (2004). 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32, 5452-5463.
16. Gao, B. & Gupta, R. S. (2005). Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 55, 2401-2412.
17. Gao, B., Parmanathan, R. & Gupta, R. S. (2006). Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups. Antonie van Leeuwenhoek 90, 69-91.
18. Griffiths, E. & Gupta, R. S. (2004). Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the Deinococcus-Thermus phylum. J Bacteriol 186, 3097-3107.
19. Griffiths, E., Petrich, A. & Gupta, R. S. (2005). Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification. Microbiology 151, 2647-2657.
20. Griffiths, E., Ventresca, M. S. & Gupta, R. S. (2006). BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species. BMC Genomics 7, 14.
21. Gupta, R. S. (1998). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62, 1435-1491.
22. Gupta, R. S. (2006). Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales). BMC Genomics 7, 167.
23. Gupta, R. S. & Griffiths, E. (2006). Chlamydiae-specific proteins and indels: novel tools for studies. Trends Microbiol 14, 527-535.
24. Gupta, R. S. & Lorenzini, E. (2007). Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. BMC Evol Biol 7, 71.
25. Gupta, R. S. & Mok, A. (2007). Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups. BMC Microbiol 7, 106.
26. Harris, J. K., Kelley, S. T., Spiegelman, G. B. & Pace, N. R. (2003). The genetic core of the universal ancestor. Genome Res 13, 407-412.
27. Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G. & Gibson, T. J. (1998). Multiple sequence alignment with CLUSTAL_X. Trends Biochem Sci 23, 403-405.
28. Johnson, J. L. & Francis, B. S. (1975). Taxonomy of the clostridia: ribosomal ribonucleic acid homologies among the species. J Gen Microbiol 88, 229-244.
29. Koonin, E. V. & Galperin, M. Y. (1997). Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev 7, 757-763.
30. Lawson, P. A., Llop-Perez, P., Hutson, R. A., Hippe, H. & Collins, M. D. (1993). Towards a phylogeny of the clostridia based on 16S rRNA sequences. FEMS Microbiol Lett 113, 87-92.
31. Levine, C., Hiasa, H. & Marians, K. J. (1998). DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim Biophys Acta 1400, 29-43.
32. McKitrick, J. C. & Pizer, L. I. (1980). Regulation of phosphoglycerate dehydrogenase levels and effect on serine synthesis in Escherichia coli K-12. J Bacteriol 141, 235-245.
33. Myers, G. S., Rasko, D. A., Cheung, J. K., Ravel, J., Seshadri, R., DeBoy, R. T., Ren, Q., Varga, J., Awad, M. M. & other authors (2006). Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res 16, 1031-1040.
34. Nolling, J., Breton, G., Omelchenko, M. V., Makarova, K. S., Zeng, Q., Gibson, R., Lee, H. M., Dubois, J., Qiu, D. & other authors (2001). Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183, 4823-4838.
35. Rivera, M. C. & Lake, J. A. (1992). Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257, 74-76.
36. Rokas, A. & Holland, P. W. (2000). Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15, 454-459.
37. Rokas, A., Williams, B. L., King, N. & Carroll, S. B. (2003). Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798-804.
38. Rood, J. I. (2006). Clostridium perfringens and histologic disease. In The Prokaryotes: a Handbook on the Biology of Bacteria, 3rd edn, vol. 4, pp. 753-770. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer.
39. Schaffer, A. A., Aravind, L., Madden, T. L., Shavirin, S., Spouge, J. L., Wolf, Y. I., Koonin, E. V. & Altschul, S. F. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29, 2994-3005.
40. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. (2002). TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504.
41. Sebaihia, M., Wren, B. W., Mullany, P., Fairweather, N. F., Minton, N., Stabler, R., Thomson, N. R., Roberts, A. P., Cerdeño-Tárraga, A. M. & other authors (2006). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38, 779-786.
42. Sebaihia, M., Peck, M. W., Minton, N. P., Thomson, N. R., Holden, M. T., Mitchell, W. J., Carter, A T., Bentley, S. D., Mason, D. R. & other authors (2007). Genome sequence of a proteolytic (group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res 17, 1082-1092.
43. Seedorf, H., Fricke, W. F., Veith, B., Brüggemann, H., Liesegang, H., Strittmatter, A., Miethke, M., Buckel, W., Hinderberger, J. & other authors (2008). The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci U S A 105, 2128-2133.
44. Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., Shiba, T., Ogasawara, N., Hattori, M., Kuhara, S. & Hayashi, H. (2002). Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci U S A 99, 996-1001.
45. Stackebrandt, E., Kramer, I., Swiderski, J. & Hippe, H. (1999). Phylogenetic basis for a taxonomic dissection of the genus Clostridium. FEMS Immunol Med Microbiol 24, 253-258.
46. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
47. Van de Peer, Y. & De Wachter, R. (1994). TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10, 569-570.
48. Wiegel, J., Tanner, R. & Rainey, F. A. (2006). An introduction to the family Clostridiaceae. In The Prokaryotes: a Handbook on the Biology of Bacteria, 3rd edn, vol. 4, pp. 654-678. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. Springer: New York.