Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for α-proteobacterial evolution

Critical Reviews in Microbiology

Volumn 31, Issue 2, 2005, Pages 101-135

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Alpha Proteobacteria Trees; Bacterial Phylogeny; Branching Order; Mitochondrial Origin; Protein Signatures; Rhizobiales; Rhodobacterales; Rickettsia prowazekii; Rickettsiales

Indexed keywords

ALANINE TRANSFER RNA LIGASE; AMIDOTRANSFERASE; BACTERIAL ENZYME; BACTERIAL PROTEIN; CYTOCHROME B; CYTOCHROME C OXIDASE; CYTOSOL AMINOPEPTIDASE; DNA GLYCOSYLASE MUTY; DNA TOPOISOMERASE (ATP HYDROLYSING) A; EXODEOXYRIBONUCLEASE VII; EXONUCLEASE; FTSZ PROTEIN; HOMOSERINE DEHYDROGENASE; INTEGRASE; OXOGLUTARATE DEHYDROGENASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; PROLIPOPROTEIN PHOSPHATIDYLGLYCEROL TRANSFERASE; PROTEIN CTAG; PROTEIN DNAB; PROTEIN FTSK; PROTEIN L19; PROTEIN LEPA; PROTEIN LYTB; PROTEIN MFD; PROTEIN MUTS; PROTEIN PURC; PROTEIN RP057; PROTEIN RP314; PROTEIN RP400; PROTEIN SIGMA 70; PROTEIN TGT; PROTEIN XERD; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; PYRUVATE PHOSPHATE DIKINASE; REPLICATION INITIATOR PROTEIN DNAA; RIBOSOME PROTEIN; RNA 16S; SERINE TRANSFER RNA LIGASE; SUCCINYL COENZYME A SYNTHETASE; TRANSFERASE; TRYPTOPHAN TRANSFER RNA LIGASE; UNCLASSIFIED DRUG;

ALPHAPROTEOBACTERIA; AMINO ACID SEQUENCE; ANAPLASMATACEAE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BRADYRHIZOBIACEAE; BRUCELLACEAE; CAULOBACTER; CAULOBACTERALES; GENE DELETION; GENE INSERTION; METHYLOBACTERIACEAE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NONHUMAN; PHYLLOBACTERIACEAE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; RHIZOBIACEAE; RHIZOBIALES; RHODOBACTERALES; RHODOSPIRILLALES; RICKETTSIA PROWAZEKII; RICKETTSIACEAE; RICKETTSIALES; SPHINGOMONADALES;

ALPHAPROTEOBACTERIA; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; EVOLUTION; GENES, RRNA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

ANAPLASMATACEAE; BACTERIA (MICROORGANISMS); BRADYRHIZOBIACEAE; BRUCELLACEAE; CAULOBACTER; CAULOBACTERALES; EPSILONPROTEOBACTERIA; EUKARYOTA; GAMMAPROTEOBACTERIA; METHYLOBACTERIACEAE; PHYLLOBACTERIACEAE; PROTEOBACTERIA; RHIZOBIACEAE; RHIZOBIALES; RHODOBACTERALES; RHODOSPIRILLALES; RICKETTSIA; RICKETTSIA PROWAZEKII; RICKETTSIACEAE; RICKETTSIALES; SPHINGOMONADALES;

EID: 19844378240     PISSN: 1040841X     EISSN: None     Source Type: Journal    
DOI: 10.1080/10408410590922393     Document Type: Review

References (113)

1. Andersson, S.G., Zomorodipour, A., Andersson, J.O., Sicheritz-Ponten, T., Alsmark, U.C., Podowski, R.M., Naslund, A.K., Eriksson, A.S., Winkler, H.H., and Kurland, C.G. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396, 133-140.
2. Baldauf, S.L., and Palmer, J.D. 1993. Animals and fungi are each other's closest relatives: Congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90, 11558-11562.
3. Battistuzzi, F.U., Feijao, A., and Hedges, S.B. 2004. A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC. Evol. Biol. 4, 44.
4. Bengtsson, J., von Wachenfeldt, C., Winstedt, L., Nygaard, P., and Hederstedt, L. 2004. CtaG is required for formation of active cytochrome c oxidase in Bacillus subtilis. Microbiology 150, 415-425.
5. Boone, D.R., Castenholz, R.W., and Garrity, G.M. 2001. Bergey's Manual of Systematic Bacteriology. Springer, New York.
6. Boussau, B., Karlberg, E.O., Frank, A.C., Legault, B.A., and Andersson, S.G. 2004. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc. Natl. Acad. Sci. USA 101, 9722-9727.
7. Bridger, W.A., Wolodko, W.T., Henning, W., Upton, C., Majumdar, R., and Williams, S.P. 1987. The subunits of succinyl-coenzyme A synthetase-function and assembly. Biochem. Soc. Symp. 103-111.
8. Broughton, W. J. 2003. Roses by other names: Taxonomy of the Rhizobiaceae. J. Bacteriol. 185, 2975-2979.
9. Capiaux, H., Lesterlin, C., Perals, K., Louarn, J.M., and Cornet, F. 2002. A dual role for the FtsK protein in Escherichia coli chromosome segregation. EMBO Rep. 3, 532-536.
10. Chase, J.W., Rabin, B.A., Murphy, J.B., Stone, K.L., and Williams, K.R. 1986. Escherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA). J. Biol. Chem. 261, 14929-14935.
11. Daldal, F., Davidson, E., and Cheng, S. 1987. Isolation of the structural genes for the Rieske Fe-S protein, cytochrome b and cytochrome c1 all components of the ubiquinol: Cytochrome c2 oxidoreductase complex of Rhodopseudomonas capsulata. J. Mol. Biol. 195, 1-12.
12. Davidson, E., and Daldal, F. 1987. Primary structure of the bc1 complex of Rhodopseudomonas capsulata. Nucleodde sequence of the pet operon encoding the Rieske cytochrome b, and cytochrome c1 apoproteins. J. Mol. Biol. 195, 13-24.
13. De Ley, J. 1992. The Proteobacteria: Ribosomal RNA cistron similarities and bacterial taxonomy. In The Prokaryotes, eds. A. Balows, H.G. Trüper, M. Dworkin, W. Harder, and K.H. Schleifer, 2111-2140. Springer-Verlag, New York.
14. DelVecchio, V.G., Kapatral, V. Redkar, R.J., Patra, G., Mujer, C., Los, T., Ivanova, N., Anderson, I., Bhattacharyya, A., Lykidis, A., Reznik, G., Jablonski, L., Larsen, N., D'Souza, M., Bernal, A., Mazur, M., Goltsman, E., Selkov, E., Elzer, P. H., Hagius, S., O'Callaghan, D., Letesson, J. J., Haselkorn, R., and Kyrpides, N. 2002. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. USA 99, 443-448.
15. Dumler, J.S., Barbet, A.F., Bekker, C.P., Dasch, G.A., Palmer, G.H., Ray, S.C., Rikihisa, Y., and Rurangirwa, FR. 2001. Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: Unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and 'HGE agent' as subjective synonyms of Ehrlichia phagocytophila. Int. J. Syst. Evol. Microbiol. 51, 2145-2165.
16. Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41, 1105-1123.
17. Emelyanov, V.V. 2001a. Evolutionary relationship of Rickettsiae and mitochondria. FEBS Letters 501, 11-18.
18. Emelyanov, V.V. 2001b. Rickettsiaceae, rickettsia-like endosymbionts, and the origin of mitochondria. Biosci. Rep. 21, 1-17.
19. Emelyanov, V.V. 2003a. Common evolutionary origin of mitochondrial and rickettsial respiratory chains. Arch. Biochem. Biophys. 420, 130-141.
20. Emelyanov, V.V. 2003b. Mitochondrial connection to the origin of eukaryotic cell. Eur. J. Biochem. 270, 1599-1618.
21. Espeli, O., Lee, C., and Marians, K.J. 2003. A physical and functional interaction between Escherichia coli FtsK and topoisomerase IV. J. Biol. Chem. 278, 44639-44644.
22. Esser, C., Ahmadinejad, N., Wiegand, C., Rotte, C., Sebastiani, F., Gelius-Dietrich, G., Henze, K., Kretschmann, E., Richly, E., Leister, D., Bryant, D., Steel, M.A., Lockhart, P.J., Penny, D., and Martin, W. 2004. A Genome Phylogeny for Mitochondria Among {alpha}-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes. Mol. Biol. Evol. 21, 1643-1660.
23. Falah, M., and Gupta, R.S. 1994. Cloning of the hsp70 (dnaK) genes from Rhizobium meliloti and Pseudomonas cepacia: Phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence. J. Bacteriol. 176, 7748-7753.
24. Galibert, F., Finan, T.M., Long, S.R., Puhler, A., Abola, P., Ampe, F., Barloy-Hubler, F., Barnett, M. J., Becker, a., Boistard, P., Bothe, G., Boutry, M., Bowser, L., Buhrmester, J., Cadieu, E., Capela, D., Chain, P., Cowie, A., Davis, R. W., Dreano, s., Federspiel, N. A., Fisher, R. F., Gloux, S., godrie, T., Goffeau, A., Golding, B., Gouzy, J., Gurjal, M., Hernandez-Lucas, I., Hong, A., Huizar, L., Hyman, R. W., Jons, T., Kahn, D., Kahn, M. L., Kalman, S., Keating, D. H., Kiss, E., Komp. c., Lelaure, v., Masuy, d., Palm, C., Peck, M. C., Pohl, T. M., Portetelle, d., Purnelle, B., Ramsperger, U., Surzycki, r., Thebault, P., Vandenbol, M., Vorholter, F. J., Weidner, S., Wells, D. H., Wong, K., Yeh, K. C., and Batut, J. 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668-672.
25. Garrity, G.M., and Holt, J.G. 2001. The road map to the manual. In Bergey's Manual of Systematic Bacteriology, eds. D. R. Boone and R. W. Castenholz, 119-166. Springer-Verlag, Berlin.
26. Gaunt, M.W., Turner, S.L., Rigottier-Gois, L., Lloyd-Macgilp, S.A., and Young, J.P. 2001. Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int. J. Syst. Evol. Microbiol. 51, 2037-2048.
27. Gonzales, T., and Robert-Baudouy, J. 1996. Bacterial aminopeptidases: Properties and functions. FEMS Microbiol. Rev. 18, 319-344.
28. Gray, M.W. 1989. The evolutionary origins of organelles. Trends in Genet. 5, 294-299.
29. Gray, M.W., Burger, G., and Lang, B.F. 1999. Mitochondrial evolution. Science 283, 1476-1481.
30. Gray, M.W., and Doolittle, W.F. 1982. Has the endosymbiont hypothesis been proven?. Microbiol. Rev. 46, 1-42.
31. Griffiths, E., and 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.
32. Griffiths, E., and 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.
33. Griffiths, E., and Gupta, R.S. 2004b. Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. International Microbiol. 7, 41-52.
34. Gupta, R.S. 1995. Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol. Microbiol. 15, 1-11.
35. 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.
36. Gupta, R.S. 2000. The phylogeny of Proteobacteria: Relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol. Rev. 24, 367-402.
37. Gupta, R.S. 2001. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Inter. Microbiol. 4, 187-202.
38. Gupta, R.S. 2002. Phylogeny of Bacteria: Are we now close to understanding it?. ASM News. 68, 284-291.
39. Gupta, R.S. 2003. Evolutionary relationships among photosynthetic bacteria. Photosynth. Res. 76, 173-183.
40. Gupta, R.S. 2004. The phylogeny and signature sequences characteristics of Fibrobacters, Chlorobi and Bacteroidetes. Crit. Rev. Microbiol. 30, 123-143.
41. Gupta, R.S., Aitken, K., Falah, M., and Singh, B. 1994. Cloning of Giardia lamblia heat shock protein HSP70 homologs: Implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 91, 2895-2899.
42. Gupta, R.S., Bustard, K., Falah, M., and Singh, D. 1997. Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes. J. Bacteriol. 179, 345-357.
43. Gupta, R.S., and Golding, G.B. 1996. The origin of the eukaryotic cell. Trends Biochem. Sci.21, 166-171.
44. Gupta, R.S., and Griffiths, E. 2002. Critical issues in bacterial phylogenies. Theor. Popul. Biol. 61, 423-434.
45. Gupta, R.S., Pereira, M., Chandrasekera, C., and Johari, V. 2003. Molecular signatures in protein sequences that are characteristic of Cyanobacteria and plastid homologues. Int. J. Syst. Evol. Microbiol. 53, 1833-1842.
46. Gupta, R.S., and Singh, B. 1994. Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr. Biol. 4, 1104-1114.
47. Hiser, L., Di Valentin, M., Hamer, A.G., and Hosler, J.P. 2000. Cox11p is required for stable formation of the Cu(B) and magnesium centers of cytochrome c oxidase. J. Biol. Chem. 275, 619-623.
48. Hui, KM., and Morrison, D.A. 1993. Identification of a purC gene from Streptococcus pneumoniae. J. Bacteriol. 175, 6364-6367.
49. Ip, S.C., Bregu, M., Barre, F.X., and Sherratt, D.J. 2003. Decatenation of DNA circles by FtsK-dependent Xer site-specific recombination. EMBO J. 22, 6399-6407.
50. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., and Gibson, T.J. 1998. Multiple sequence alignment with Clustal x. Trends Biochem. Sci. 23, 403-405.
51. Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S., Watanabe, a., Idesawa, K., Ishikawa, a., Kawashima, K., Kimura, t., Kimura, T., Kishida, Y., Kiyokawa, c., Kohara, M., Matsumoto, M., Matsuno, a., Mochizuki, Y, Nakayama, S., Nakazaki, N., Shimpo, S., Sugimoto, M., Takeuchi, C., Yamada, M., and tabata, S., Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7, 331-338.
52. Kaneko, T., Nakamura, Y, Sato, S., Minamisawa, K., UCHIUMI, T., Sasamoto, s., Watanabe, A., Idesawa, K., Iriguchi, M., Kawashima, K., Kohara, M., Matsumoto, M., Shimpo, S., Tsuruoka, H., Wada, T., Yamada, M., and Tabata, S., 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189-197.
53. Karlin, S., and Brocchieri, L. 2000. Heat shock protein 60 sequence comparisons: Duplications, lateral transfer, and mitochondrial evolution. Proc. Natl. Acad. Sci. USA 97, 11348-11353.
54. Karlin, S., Brocchieri, L., Mrazek, J., Campbell, A.M., and Spormann, A.M. 1999. A chimeric prokaryotic ancestory of mitochondria and primitive eukaryotes. Proc. Natl. Acad. Sci. USA 96, 9190-9195.
55. Kersters, K., Devos, P., Gillis, M., Vandamme, P., and Stackebrandt, E. 2003. Introduction to the Proteobacteria. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, ed. M. e. al. Dworkin, Springer-Verlag, New York.
56. Kolber, Z.S., Plumley, F.G., Lang, A.S., Beatty, J.T., Blankenship, R.E., VanDover, C.L., Vetriani, C., Koblizek, M., Rathgeber, C., and Falkowski, P.G. 2001. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292, 2492-2495.
57. Ku, M.S., Kano-Murakami, Y., and Matsuoka, M. 1996. Evolution and expression of C4 photosynthesis genes. Plant Physiol. 111, 949-957.
58. Kurland, C.G., and Andersson, S.G. 2000. Origin and evolution of the mitochondrial proteome. Microbiol. Mol. Biol. Rev. 64, 786-820.
59. Lake, J.A., and Rivera, M.C. 1994. Was the nucleus the first endosymbiont? Proc. Natl. Acad. Sci. USA 91, 2880-2881.
60. Lang, B.F., Gray, M.W., and Burger, G. 1999. Mitochondrial genome evolution and the origin of eukaryotes. Annual Review of Genetics 33, 351-397.
61. Larimer, F.W., Chain, P., Hauser, L., Lamerdin, J. Malfatti, S., Do, L., Land, M. L., Pelletier, D. A., Beatty, J. t., Lang, A. S., Tabita, F. R., Gibson, J. L., Hanson, T. E., Bobst, C., Torres, J. L., Peres, C., Harrison, F. H., Gibson, J., and Harwood, C. S., 2004. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat. Biotechnol 22, 55-56.
62. Leyva, J.A., Bianchet, M.A., and Amzel, L.M. 2003. Understanding ATP synthesis: Structure and mechanism of the F1-ATPase (Review). Mol. Membr. Biol. 20, 27-33.
63. Lopez-Garcia, P., and Moreira, D. 1999. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem. Sci. 24, 88-93.
64. Ludwig, W., and Klenk, H.-P. 2001. Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systamatics. In Bergey's Manual of Systematic Bacteriology, eds. D. R. Boone and R. W. Castenholz, 49-65. Springer-Verlag, Berlin.
65. Ludwig, W., and Schleifer, K.H. 1999. Phylogeny of Bacteria beyond the 16S rRNA Standard. ASM News 65, 752-757.
66. 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., and Tiedje, J.M. 2001. The RDP-II (Ribosomal Database Project). Nucleic Adds Res. 29, 173-174.
67. Margulis, L. 1970. Origin of Eukaryotic cells. Yale University Press, New Haven, CT.
68. Margulis, L. 1993. Symbiosis in Cell Evolution. W.H. Freeman and Company, New York.
69. Margulis, L. 1996. Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life. Proc. Natl. Acad. Sci. USA 93, 1071-1076.
70. Martin, W., and Muller, M. 1998. The hydrogenosome hypothesis for the first eukaryote. Nature 392, 37-41.
71. Martins-Pinheiro, M., Galhardo, R.S., Lage, C., Lima-Bessa, K.M., Aires, K.A., and Menck, CF. 2004. Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group. BMC. Evol. Biol. 4, 29.
72. McLeod, M.P., Qin, X., Karpathy, S.E., Gioia, J., Highlander, S. K., Fox, G. E., McNeill, T. Z., Jiang, H., Muzny, d., Jacob, L. S., Hawes, A. C., Sodergren, E., Gill, R., Hume, J., Morgan, M., Fan, G., Amin, A. G., Gibbs, R. A., Hong, C., Yu, X. J., Walker, D. H., and Weinstock, G. M., 2004. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J. Bacteriol. 186, 5842-5855.
73. Messer, W. 2002. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 26, 355-374.
74. Morden, C.W., Delwiche, C.F., Kuhsel, M., and Palmer, J.D. 1992. Gene phylogenies and the endosymbiotic origin of plastids. Biosystems 28, 75-90.
75. Moreno, E., and Moriyon, I. 2001. The Genus Brucella. The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community. In ed. M. e. al. Dworkin. Springer-Verlag. New York.
76. Moulin, L., Bena, G., Boivin-Masson, C., and Stepkowski,T. 2004. Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene cotransfer within the Bradyrhizobium genus. Mol. Phylogenet. Evol. 30, 720-732.
77. Murray, R.G.E., Brenner, D.J., Colwell, R.R., De Vos, P., Goodfellow, M., Grimont, P.A.D., Pfennig, N., Stackebrandt, E., and Zavarzin, G.A. 1990. Report of the Ad Hoc Committee on approaches to taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol. 40, 213-215.
78. Nierman, W.C., Feldblyum, T.V. Laub, M.T., Paulsen, I.T., Nelson, K.E., Eisen, J., Heidelberg, J.F., Alley, M.R., Ohta, N., Maddock, J.R., Potocka, I., Nelson, W.C., Newton, A., Stephens, C., Phadke, N.D., Ely, B., DeBoy, R.T., Dodson, R.J., Durkin, A.S., Gwinn, M.L., Haft, D.H., Kolonay, J.F., Smit, J., Craven, M.B., Khouri, H., Shetty, J., Berry, K., Utterback, T., Tran, K., Wolf, A., Vamathevan, J., Ermolaeva, M., White, O., Salzberg, S.L., Venter, J.C., Shapiro, L., and Fraser, C.M. 2001. Complete genome sequence of Caulobacter crescentus. Proc. Natl. Acad. Sci. USA 98, 4136-4141.
79. Ogata, H., Audic, S., Renesto-Audiffren, P., Fournier, P.E., Barbe, V., Samson, D., Roux, V., Cossart, P., Weissenbach, J., Claverie, J.M., and Raoult, D. 2001. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 293, 2093-2098.
80. Olsen, G. J., Woese, C. R., and Overbeek, R. 1991. The winds of (evolutionary) change: Breathing new life into microbiology. J. Bacteriol. 176, 1-6.
81. Opperman, T., and Richardson, J.P. 1994. Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene. J. Bacteriol. 176, 5033-5043.
82. Parker, A.R., and Eshleman, J.R. 2003. Human MutY: Gene structure, protein functions and interactions, and role in carcinogenesis. Cell Mol. Life Sci. 60, 2064-2083.
83. Paulsen, I.T., Seshadri, R., Nelson, K.E., Eisen, J.A. Heidelberg, J. F., Read, T. D., Dodson, R. J., Umayam, L., Brinkac, L. M., Beanan, M. J., Daugherty, s. C., DeBoy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, r., Nelson, W. C., Ayodeji, B., Kraul, M., Shetty, J., Malek, J., Van Aken, S. E., Reidmuller, S., Tettelin, H., Gill, S. R., White, O., Salzberg, S. L., Hoover, D. L., Lindler, L. E., Hailing, s. M., Boyle, S. M., and Fraser, C. M., 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. USA 99, 13148-13153.
84. Qi, H.Y., Sankaran, K., Can, K., and Wu, H.C. 1995. Structure-function relationship of bacterial prolipoprotein diacylglyceryl transferase: Functionally significant conserved regions. J. Bacteriol. 177, 6820-6824.
85. Reuter, K., and Ficner, R. 1995. Sequence analysis and overexpression of the Zymomonas mobilis tgt gene encoding tRNA-guanine transglycosylase: Purification and biochemical characterization of the enzyme. J. Bacteriol. 177, 5284-5288.
86. Ribeiro, S., and Golding, G.B. 1998. The mosaic nature of the eukaryotic nucleus. Mol. Biol. Evol. 15, 779-788.
87. Rivera, M.C., and Lake, J.A. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257, 74-76.
88. Rivera, M.C., and Lake, J.A. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431, 152-155.
89. Rokas, A., and Holland, P.W. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454-459.
90. Romanowski, M.J., Bonanno, J.B., and Burley, S.K. 2002. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins 47, 563-567.
91. Sadowsky, M.J. and P.H. Graham. 2000. Root and Stem Nodule Bacteria of Legumes. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, ed. M. e. al. Dworkin. Springer-Verlag, New York.
92. Sawada, H., Kuykendall, L.D., and Young, J.M. 2003. Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J. Gen. Appl. Microbiol. 49, 155-179.
93. Sicheritz-Ponten. T., Kurland, C.G., and Andersson, S.G. 1998. A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae. Biochim. Biophys. Acta. 1365, 545-551.
94. Sixma, T.K. 2001. DNA mismatch repair: MutS structures bound to mismatches. Curr. Opin. Struct. Biol. 11, 47-52.
95. Soni, R.K., Mehra, P., Choudhury, N.R., Mukhopadhyay, G., and Dhar, S.K. 2003. Functional characterization of Helicobacter pylori DnaB helicase. Nucleic Acids Res. 31, 6828-6840.
96. Stackebrandt, E. 2000. Defining Taxonomic Ranks. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, ed. M. e. al. Dworkin. Springer-Verlag, New York.
97. Stackebrandt, E., Murray, R.G.E., and Trüper, H.G. 1988. Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "Purple bacteria and their Relatives." Int. J. Syst. Bacteriol. 38, 321-325.
98. Stepkowski, T., Czaplinska, M., Miedzinska, K., and Moulin, L. 2003. The variable part of the dnaK gene as an alternative marker for phylogenetic studies of rhizobia and related alpha Proteobacteria. Syst. Appl. Microbiol. 26, 483-494.
99. Stryer, L. 1995. Biochemistry. W.H. Freeman and Co., New York.
100. Taillardat-Bisch, A.V., Raoult, D., and Drancourt, M. 2003. RNA polymerase beta-subunit-based phylogeny of Ehrlichia spp., Anaplasma spp., Neorickettsia spp. and Wolbachia pipientis. Int. J. Syst. Evol. Microbiol. 53, 455-458.
101. van Berkum, P., Terefework, Z., Paulin, L., Suomalainen, S., Lindstrom, K., and Eardly, B.D. 2003. Discordant phylogenies within the rrn loci of Rhizobia. J. Bacteriol. 185, 2988-2998.
102. Van Sluys, M.A., Momeiro-Vitorello, C.B., Camargo, L.E., Menck, C.F., da Silva, A.C., Ferro, J.A., Oliveira, M.C., Setubal, J.C., Kitajima, J.P., and Simpson, A.J. 2002. Comparative genomic analysis of plant-associated bacteria. Annu. Rev. Phytopathol. 40, 169-189.
103. Viale, A.M., and Arakaki, A.K. 1994. The chaperone connection to the origins of the eukaryotic organelles. FEBS Letters 341, 146-151.
104. Viale, A.M., Arakaki, A.K., Soncini, F.C., and Ferreyra, R.G. 1994. Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int. J. Syst. Bacteriol 44, 527-533.
105. Wang, E.T., van Berkum, P., Beyene, D., Sui, X.H., Dorado, O., Chen, W.X., and Martinez-Romero, E. 1998. Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae. Int. J. Syst. Bacteriol. 48 Pt. 3, 687-699.
106. Woese, C.R., Stackebrandt, E., Macke, R.J., and Fox, G.E. 1985. A phylogenetic definition of the major eubacterial taxa. System. Appl. Microbiol. 6, 143-151.
107. 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., and Fox, G.E. 1984 The phylogeny of purple bacteria: The alpha subdivision. System. Appl. Microbiol. 5, 315-326.
108. Wolf, Y.I., Aravind, L., and Koonin, E.V. 1999. Rickettsiae and Chlamydiae-evidence of horizontal gene transfer and gene exchange. Trends Genet 15, 173-175.
109. Wood, D.W., Setubal, J.C., Kaul, R., Monks, D.E. Kitajima, J. P., Okura, V. K., Zhou, Y., Chen, L., Wood, G. E., Almeida, N. F., Jr., Woo, L., Chen, Y., Paulsen, I. T., Eisen, J. A., Karp, P. D., Bovee, D., Sr., Chapman, P., Clendenning, J., Deatherage, G., Gillet, W., Grant, c., Kutyavin, T., Levy, R., Li, M. J., McClelland, E., Palmieri, A., Raymond, C., Rouse, G., Saenphimmachak, C., Wu, Z., Romero, P., Gordon, D., Zhnag, S., Yoo, H., Tao, Y., Biddle, P., Jung, M., Krespan, W., Perry, M., Gordon-Kamm, B., Lioa, L., Kim, S., Hendrick, C., Zhao, Z. Y., Dolan, M., Chumley, F., Tingey, S. V., Tomb, J. F., Godon, M. P., Olson, M. V., and Nester, E. W., 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294, 2317-2323.
110. Young, J.M., Kuykendall, L.D., Martinez-Romero, E., Kerr, A., and Sawada, H. 2001. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis. Int. J. Syst. Evol. Microbiol. 51, 89-103.
111. Yu, X.J. and D. H. Walker. 2003. The Order Rickettsiales. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, ed. M. e. al. Dworkin. Springer-Verlag, New York.
112. Yu, X.J., Zhang, X.F., McBride, J.W., Zhang, Y., and Walker, D.H. 2001. Phylogenetic relationships of Anaplasma marginale and 'Ehrlichia platys' to other Ehrlichia species determined by GroEL amino acid sequences. Int. J. Syst. Evol. Microbiol. 51, 1143-1146.
113. Yurkov, V.V., and Beatty, J.T. 1998. Aerobic anoxygenic phototrophic bacteria. Microbiol. Mol. Biol. Rev. 62, 695-724.