Microbial Phylogeny and Evolution Based on Protein Sequences (The Change from Targeted Genes to Proteins)

Mass Spectrometry for Microbial Proteomics

Volumn , Issue , 2010, Pages 35-53

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Bacterial phylogeny overview and key unresolved issues; Branching order and interrelationships among bacterial phyla; Comparative analyses of genomic sequences protein based markers for understanding microbial phylogeny; Evolutionary relationships Fibrobacter Chlorobi and Bacteroidetes species and species distribution patterns; Genome sequence data enabling identification of protein based markers, as CSIs and CSPs; Mass spectrometry for microbial proteomics; Microbial phylogeny and evolution based on protein sequences from targeted genes to proteins; Molecular markers elucidating evolutionary relationships among proteobacteria; Molecular markers for Bacteroidetes Chlorobi phyla; Protein markers, for discovering properties of different groups of bacteria

Indexed keywords

EID: 84860505886     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470665497.ch2     Document Type: Chapter

References (77)

1. Blankenship , R.E. ( 1992 ) Origin and early evolution of photosynthesis . Photosyn. Res. , 33 , 91 - 111 .
2. 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 .
3. Danchin, A . ( 1999 ) From protein sequence to function . Curr. Opin. Struct. Biol., 9, 363 - 367 .
4. Daubin, V., Ochman, H. ( 2004 ) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli . Genome Res., 14, 1036 - 1042 .
5. Delsuc, F., Brinkmann, H., Philippe, H. ( 2005 ) Phylogenomics and the reconstruction of the tree of life . Nat. Rev. Genet., 6, 361 - 375 .
6. Doerks, T., von Mering, C., Bork, P. ( 2004 ) Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes . Nucleic Acids Res., 32, 6321 - 6326 .
7. Duncan, M.J. ( 2003 ) Genomics of oral bacteria . Crit. Rev. Oral Biol. Med ., 14, 175 - 187 .
8. Dutilh, B.E., Snel, B., Ettema, T.J., Huynen, M.A. ( 2008 ) Signature genes as a phylogenomic tool . Mol. Biol. Evol ., 25, 1659 - 1667 .
9. Felsenstein, J. ( 2004 ) Inferring Phylogenies . Sinauer Associates, Inc., Sunderland, MA .
10. Frigaard, N.U., Chew, A.G., Li, H., Maresca, J.A., Bryant, D.A. ( 2003 ) Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence . Photosynth. Res., 78, 93 - 117 .
11. Galperin, M.Y., Koonin, E.V. ( 2004 ) ' Conserved hypothetical ' proteins: prioritization of targets for experimental study . Nucleic Acids Res., 32, 5452 - 5463 .
12. 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 .
13. Gao, B., Gupta, R.S. ( 2007 ) Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis . BMC Genomics, 8, 86 .
14. Gao, B., Mohan, R., Gupta, R.S. ( 2009 ) Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria . Int. J. Syst. Evol. Microbiol., 59, 234 - 247 .
15. 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 .
16. Garrity, G.M., Bell, J.A., Lilburn, T.G. ( 2005 ) The revised road map to the manual . In: Brenner, D.J., Krieg, N.R., Staley, J.T. (eds) Bergey ' s Manual of Systematic Bacteriology, Volume 2, Part A, Introductory Essays. Springer, New York, pp. 159 - 220 .
17. Griffiths, E., Gupta, R.S. ( 2001 ) The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga - Flavobacterium - Bacteroides division . Microbiology, 147, 2611 - 2622 .
18. Griffiths, E., Gupta, R.S. ( 2002 ) Protein signatures distinctive of chlamydial species: Horizontal transfer of cell wall biosynthesis genes glmU from Archaebacteria to Chlamydiae, and murA between Chlamydiae and Streptomyces . Microbiology, 148, 2541 - 2549 .
19. Griffiths, E., Gupta, R.S. ( 2004a ) Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the Deinococcus - Thermus phylum . J. Bacteriol., 186, 3097 - 3107 .
20. Griffi ths, E., Gupta, R.S. ( 2004b ) Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquifi cales . Int. Microbiol., 7, 41 - 52 .
21. Griffiths, E., Gupta, R.S. ( 2006 ) Molecular signatures in protein sequences that are characteristics of the Phylum Aquifi cales . Int. J. Syst. Evol. Microbiol., 56, 99 - 107 .
22. Griffiths, E., Gupta, R.S. ( 2007a ) Identifi cation of signature proteins that are distinctive of the Deinococcus - Thermus phylum . Int. Microbiol., 10, 201 - 208 .
23. Griffiths, E., Gupta, R.S. ( 2007b ) Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free - living relatives of chlamydiae, Microbiology, 153, 2648 - 2654 .
24. 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 identifi cation . Microbiology, 151, 2647 - 2657 .
25. 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 .
26. 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 .
27. Gupta, R.S. ( 2000 ) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes . FEMS Microbiol. Rev., 24, 367 - 402 .
28. Gupta, R.S. ( 2001 ) The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins . Int. Microbiol., 4, 187 - 202 .
29. Gupta, R.S. ( 2002 ) Phylogeny of Bacteria: Are we now close to understanding it?. ASM News, 68, 284 - 291 .
30. Gupta, R.S. ( 2003 ) Evolutionary relationships among photosynthetic bacteria . Photosynth. Res., 76, 173 - 183 .
31. Gupta, R.S. ( 2004 ) The phylogeny and signature sequences characteristics of Fibrobacters, Chlorobi and Bacteroidetes . Crit. Rev. Microbiol., 30, 123 - 143 .
32. Gupta, R.S. ( 2005a ) Molecular sequences and the early history of life . In: Sapp, J. (ed.) Microbial Phylogeny and Evolution: Concepts and Controversies . Oxford University Press, New York, pp. 160 - 183 .
33. Gupta, R.S. ( 2005b ) Protein signatures distinctive of Alpha proteobacteria and its subgroups and a model for Alpha proteobacterial evolution . Crit Rev. Microbiol., 31, 135 .
34. Gupta, R.S. ( 2006 ) Molecular signatures (unique proteins and conserved Indels) that are specifi c for the epsilon proteobacteria (Campylobacterales) . BMC Genomics, 7, 167 .
35. Gupta, R.S. ( 2009 ) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades . Int. J. Syst. Evol. Microbiol., 59, 2510 - 2526 .
36. Gupta, R.S., Griffiths, E. ( 2002 ) Critical issues in bacterial phylogenies . Theor. Popul. Biol., 61, 423 - 434 .
37. Gupta, R.S., Griffi ths, E. ( 2006 ) Chlamydiae - specifi c proteins and indels: novel tools for studies . Trends Microbiol., 14, 527 - 535 .
38. Gupta, R.S., Lorenzini, E. ( 2007 ) Phylogeny and molecular signatures (conserved proteins and indels) that are specifi c for the Bacteroidetes and Chlorobi species . BMC Evol. Biol., 7, 71 .
39. Gupta, R.S., Mok, A. ( 2007 ) Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups . BMC Microbiol., 7, 106 .
40. Gupta, R.S., Sneath, P.H.A. ( 2007 ) Application of the character compatibility approach to generalized molecular sequence data: Branching order of the proteobacterial subdivisions . J. Mol. Evol., 64, 90 - 100 .
41. Gupta, R.S., Pereira, M., Chandrasekera, C., Johari, V. ( 2003 ) Molecular signatures in protein sequences that are characteristic of Cyanobacteria and plastid homologues . Int. J. Syst. Evol. Microbiol., 53, 1833 - 1842 .
42. Kainth, P., Gupta, R.S. ( 2005 ) Signature proteins that are distinctive of alpha proteobacteria . BMC Genomics, 6, 94 .
43. Kersters, K., Devos, P., Gillis, M., Swings, J., Vandamme, P., Stackebrandt, E. ( 2006 ) Introduction to the proteobacteria . In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H., Stackebrandt, E. (eds) The Prokaryotes: A Handbook on the Biology of Bacteria . Springer, New York, pp. 3 - 37 .
44. Korbel, J.O., Doerks, T., Jensen, L.J., Perez - Iratxeta, C., Kaczanowski, S., Hooper, S.D., Andrade, M.A., Bork, P. ( 2005 ) Systematic association of genes to phenotypes by genome and literature mining . PLoS Biol., 3, e134 .
45. Lake, J.A., Herbold, C.W., Rivera, M.C., Servin, J.A., Skophammer, R.G. ( 2007 ) Rooting the tree of life using nonubiquitous genes . Mol. Biol. Evol., 24, 130-136 .
46. Lerat, E., Daubin, V., Ochman, H., Moran, N.A. ( 2005 ) Evolutionary origins of genomic repertoires in bacteria . PLoS. Biol., 3, e130 .
47. Ludwig, W., Klenk, H.-P. ( 2005 ) Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systamatics . In: Brenner, D.J., Krieg, N.R., Staley, J.T., Garrity, G.M. (eds) Bergey ' s Manual of Systematic Bacteriology . Springer-Verlag, Berlin, pp. 49-65 .
48. Ludwig, W., Schleifer, K.H. ( 1999 ) Phylogeny of Bacteria beyond the 16S rRNA standard . ASM News, 65, 752-757 .
49. Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker, C.T., Jr, Saxman, P.R., Farris, R.J., Garrity, G.M., Olsen, G.J., Schmidt, T.M., Tiedje, J.M. ( 2001 ) The RDP-II (Ribosomal Database Project) . Nucleic Acids Res., 29, 173-174 .
50. Mulkidjanian, A.Y., Koonin, E.V., Makarova, K.S., Mekhedov, S.L., Sorokin, A., Wolf, Y.I., Dufresne, A., Partensky, F., Burd, H., Kaznadzey, D., Haselkorn, R., Galperin, M.Y. ( 2006 ) The cyanobacterial genome core and the origin of photosynthesis . Proc. Natl Acad. Sci. USA, 103, 13 126-13 131 .
51. Murray, R.G.E., Brenner, D.J., Colwell, R.R., De Vos, P., Goodfellow, M., Grimont, P.A.D., Pfennig, N., Stackebrandt, E., Zavarzin, G.A. ( 1990 ) Report of the Ad Hoc Committee on Approaches to Taxonomy within the Proteobacteria . Int. J. Syst. Bacteriol., 40, 213-215 .
52. Nelson, K.E., Paulsen, I.T., Fraser, C.M. ( 2001 ) Microbial genome sequencing: A window into evolution and physiology . ASM News, 67, 310-317 .
53. Ohkuma, M., Noda, S., Hongoh, Y., Kudo, T. ( 2002 ) Diverse bacteria related to the bacteroides subgroup of the CFB phylum within the gut symbiotic communities of various termites . Biosci. Biotechnol. Biochem., 66, 78-84 .
54. Olsen, G.J., Woese, C.R., Overbeek R. ( 1994 ) The winds of (evolutionary) change: breathing new life into microbiology . J. Bacteriol., 176, 1-6 .
55. Oren, A., Stackebrandt, E. ( 2002 ) Prokaryote taxonomy online: challenges ahead . Nature, 419, 15 .
56. Overmann, J. ( 2006 ) The family Chlorobiaceae . In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H., Stackebrandt, E. (eds) The Prokaryotes, Vol. 7, Proteobacteria: Delta and Epsilon Subclass . Springer, New York, pp. 359-378 .
57. Paster, B.J., Boches, S.K., Galvin, J.L., Ericson, R.E., Lau, C.N., Levanos, V.A., Sahasrabudhe, A., Dewhirst, F.E. ( 2001 ) Bacterial diversity in human subgingival plaque . J. Bacteriol., 183, 3770-3783 .
58. Paster, B.J., Dewhirst, F.E., Olsen, I., Fraser, G.J. ( 1994 ) Phylogeny of bacteroides, prevotella, and porphyromonas spp. and related bacteria . J. Bacteriol., 176, 725-732 .
59. Reichenbach, H. ( 1992 ) The Order Cytophagales . In: Balows, A., Truper, H.G., Dworkin, M., Harder, W., Schleifer, K.H. (eds) The Prokaryotes . Springer-Verlag, New York, pp. 3631-3675 .
60. Roberts, R.J. ( 2004 ) Identifying protein function-a call for community action . PLoS. Biol., 2, E42 .
61. Rokas, A., Holland, P.W. ( 2000 ) Rare genomic changes as a tool for phylogenetics . Trends Ecol. Evol., 15, 454-459 .
62. Salyers, A.A. ( 1984 ) Bacteroides of the human lower intestinal tract . Annu. Rev. Microbiol., 38, 293-313 .
63. Shah, H.N. ( 1992 ) The genus Bacteroides and related taxa . In: Balows, A., Truper, H.G., Dworkin, M., Harder, W., Schleifer, K.H. (eds) The Prokaryotes . Springer-Verlag, New York, pp. 3593-3607 .
64. Shah, H.N., Gharbia, S.E., Duerden, B.I. ( 1998 ) Bacteroides, Prevotella and Porphyromonas . In: Balows, A., Duerden, B.I. (eds) Topley &Wilson ' s Microbiology and Microbial Infections, vol. 2. Systematic Bacteriology . Arnold, London, pp. 1305-1330 .
65. Shah, H.N., Gharbia, S.E., Olsen, I. ( 2005 ) Bacteroides, Prevotella, and Porphyromonas . In: Borrelio, S.P., Murray, P.R., Funke, G. (eds) Topley &Wilson ' s Microbiology and Microbial Infections . Hodder Arnold, London, pp. 1913-1944 .
66. Shah, H.N., Olsen, I., Bernard, K., Finegold, S.M., Gharbia, S.E., Gupta, R.S. ( 2009 ) Approaches to the study of the systematics of anaerobic, Gram-negative, non-spore-forming rods: current status and perspectives . Anaerobe, 15, 179-194 .
67. Siew, N., Fischer, D. ( 2003 ) Analysis of singleton ORFans in fully sequenced microbial genomes . Proteins, 53, 241-251 .
68. Singh, B., Gupta, R.S. ( 2009 ) Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth . Mol. Genet. Genom., 281, 361-373 .
69. Stackebrandt, E. ( 2006 ) Defi ning taxonomic ranks . In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E. (eds) The Prokaryotes . Springer, New York, pp. 29-57 .
70. Staley, J.T. ( 2006 ) The bacterial species dilemma and the genomic-phylogenetic species concept; Philos . Trans. R. Soc. London, Ser. B, 361, 1899-1909 .
71. Truper, H.G., Pfennig, N. ( 1992) The family Chlorobiaceae . In: Balows, A., Truper, H.G., Dworkin, M., Harder, W., Schleifer, K.H. (eds) The Prokaryotes . Springer-Verlag, New York, pp. 3583-3592 .
72. Ward, N., Fraser, C.M. ( 2005 ) How genomics has affected the concept of microbiology . Curr. Opin. Microbiol., 8, 564-571 .
73. Williams, K.P., Sobral, B.W., Dickerman, A.W. ( 2007 ) A robust species tree for the Alphaproteobacteria. J. Bacteriol., 189, 4578-4586 .
74. Woese, C.R. ( 1987 ) Bacterial evolution . Microbiol. Rev., 51, 221-271 .
75. Woese, C.R., Kandler, O., Wheelis, M.L. ( 1990 ) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya . Proc. Natl Acad. Sci. USA, 87, 4576-4579 .
76. Woese, C.R., Stackebrandt, E., Macke, R.J., Fox, G.E. ( 1985 ) A phylogenetic defi nition of the major eubacterial taxa . System. Appl. Microbiol., 6, 143-151 .
77. Woese, C.R., Stackebrandt, E., Weisburg, W.G., Paster, B.J., Madigan, M.T., Fowler, C.M.R., Hahn, C.M., Blanz, P., Gupta, R., Nealson, K.H., Fox G.E. ( 1984 ) The phylogeny of purple bacteria: the alpha subdivision . System. Appl. Microbiol., 5, 315-326 .