The phylogeny of proteobacteria: Relationships to other eubacterial phyla and eukaryotes

FEMS Microbiology Reviews

Volumn 24, Issue 4, 2000, Pages 367-402

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Aquifex; Chlamydia Cytophaga; Evolutionary direction; Mitochondrial origin; Origin of eukaryotic cell; Prokaryote taxonomy; Protein signature; Proteobacterial subdivision; Purple bacteria and relatives

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING);

AMINO ACID SEQUENCE; CHLAMYDIA; CYANOBACTERIUM; DEINOCOCCACEAE; EVOLUTION; FLEXIBACTERACEAE; MITOCHONDRION; MOLECULAR GENETICS; NONHUMAN; PHENOTYPE; PHYLOGENY; PROKARYOTE; PROTEOBACTERIA; REVIEW; SEQUENCE HOMOLOGY; SPIROCHAETA; TAXONOMY; THERMUS;

ADENOSINE TRIPHOSPHATASES; ALANINE-TRNA LIGASE; AMINO ACID SEQUENCE; ATP-DEPENDENT PROTEASES; BACTERIAL PROTEINS; CARRIER PROTEINS; CHAPERONIN 60; DNA TOPOISOMERASES, TYPE II; ESCHERICHIA COLI PROTEINS; EUKARYOTIC CELLS; GENE DELETION; HEAT-SHOCK PROTEINS; HSP70 HEAT-SHOCK PROTEINS; LIGASES; MEMBRANE TRANSPORT PROTEINS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHOSPHORIBOSYL PYROPHOSPHATE; PHYLOGENY; PROTEOBACTERIA; PYROPHOSPHATASES; RIBOSOMAL PROTEINS; SEQUENCE ALIGNMENT; SERINE ENDOPEPTIDASES; SUCCINATE-COA LIGASES; SULFURTRANSFERASES; TERMINOLOGY; UDPGLUCOSE 4-EPIMERASE; VALINE-TRNA LIGASE;

AQUIFEX; BACTERIA (MICROORGANISMS); CHLAMYDIA; CHLOROBI; CHLOROFLEXI; CYANOBACTERIA; CYTOPHAGA; DEINOCOCCACEAE; DEINOCOCCUS; DEINOCOCCUS-THERMUS; EUKARYOTA; FLEXIBACTERACEAE; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA; SPIROCHAETA; THERMUS; UNCULTURED ALPHA PROTEOBACTERIUM;

EID: 0033823160     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6445(00)00031-0     Document Type: Review

References (187)

1. Stackebrandt E., Murray R.G.E., Trüper H.G. Proteobacteria classis nov., a name for the phylogenetic taxon that includes the 'purple bacteria and their relatives'. Int. J. Syst. Bacteriol. 38:1988;321-325.
2. Stackebrandt, E. (1992) Unifying phylogeny and phenotypic diversity. In: The Prokaryotes (Balows, A., Truper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 19-47. Springer-Verlag, New York.
3. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271.
4. Holt, J.G., Krieg, N.R., Sneath, P.H.A., Staley, J.T. and Stanley, T.W. (1994) Bergey's Manual of Determinative Bacteriology. Williams and Wilkins, Baltimore, MD.
5. Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H. (1992) The Prokaryotes. Springer-Verlag, New York.
6. Holt, J.G. (Ed. in Chief) (1984) Bergey's Manual of Systematic Bacteriology. Williams and Wilkins, Baltimore, MD.
7. Collier, L., Balows, A. and Sussman, M. (1998) Topley and Wilson's Microbiology and Microbial Infections, Vol. 2, Systematic Bacteriology. Arnold, London.
8. Zinder, S.H. (1998) Bacterial diversity. In: Topley and Wilson's Microbiology and Microbial Infections, Vol. 2, Systematic Bacteriology (Balows, A. and Duerden, B.I., Eds.), pp. 125-147. Arnold, London.
9. Woese, C.R. (1991) The use of ribosomal RNA in reconstructing evolutionary relationships among bacteria. In: Evolution at Molecular Level (Selander, R.K., Clark, A.G. and Whittmay, T.S., Eds.), pp. 1-24 Sinauer, Sunderland, MA.
10. Olsen G.J., Woese C.R., Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1994;1-6.
11. Pfennig N., Trüper H.G. Taxonomy of phototrophic green and purple bacteria: a review. Ann. Microbiol. (Paris). 134B:1983;9-20.
12. Zavarzin G.A., Stackebrandt E., Murray R.G.E. A correlation of phylogenetic diversity in the Proteobacteria with the influences of ecological forces. Can. J. Microbiol. 37:1991;1-6.
13. Trüper H.G. Phototrophic bacteria (an incoherent group of prokaryotes). A taxonomic versus phylogenetic survey. Microbiologia. 3:1987;71-89.
14. Margulis, L. (1970) Origin of Eukaryotic Cells. Yale University Press, New Haven, CT.
15. Margulis, L. (1993) Symbiosis in Cell Evolution. Freeman, New York.
16. Gray M.W. The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141:1992;233-357.
17. Gray M.W., Doolittle W.F. Has the endosymbiont hypothesis been proven? Microbiol. Rev. 46:1982;1-42.
18. 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. Report of the Ad Hoc Committee on approaches to taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol. 40:1990;213-215.
19. Fox G.E., Stackebrandt E., Hespell R.B., Gibson J., Maniloff J., Dyer T.A., Wolfe R.S., Balch W.E., Tanner R.S., Magrum L.J., Zablen L.B., Blakemore R., Gupta R., Bonen L., Lewis B.J., Stahl D.A., Luehrsen K.R., Chen K.N., Woese C.R. The phylogeny of prokaryotes. Science. 209:1980;457-463.
20. Woese C.R., Stackebrandt E., Macke R.J., Fox G.E. A phylogenetic definition of the major eubacterial taxa. Syst. Appl. Microbiol. 6:1985;143-151.
21. Schleifer K.H., Stackebrandt E. Molecular systematics of prokaryotes. Annu. Rev. Microbiol. 37:1983;143-187.
22. Stackebrandt, E. and Liesack, W. (1993) Nucleic acids and classification. In: Handbook of New Bacterial Systematics (Goodfellow, M. and O'Donnell, A.G., Eds.), pp. 151-194. Academic Press, New York.
23. De Ley, J. (1992) The proteobacteria: ribosomal RNA cistron similarities and bacterial taxonomy. In: The Prokaryotes (Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 2111-2140. Springer-Verlag, New York.
24. Woese, C.R. (1992) Prokaryote systematics: the evolution of a science. In: The Prokaryotes (Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 3-18. Springer-Verlag, New York.
25. Woese C.R., Weisburg W.G., Hahn C.M., Paster B.J., Zablen L., Lewis B.J., Macke T.J., Ludwig W., Stackebrandt E. The phylogeny of purple bacteria: the gamma subdivision. Syst. Appl. Microbiol. 6:1985;25-33.
26. 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. The phylogeny of purple bacteria: the alpha subdivision. Syst. Appl. Microbiol. 5:1984;315-326.
27. Woese C.R., Weisburg W.G., Paster B.J., Hahn C.M., Tanner R.S., Krieg N.R., Koops H.-P., Harms H., Stackebrandt E. The phylogeny of purple bacteria: the beta subdivision. Syst. Appl. Microbiol. 5:1984;327-336.
28. Jarvis B.D.W., Gillis M., De Ley J. Intra and intergeneric similarities between the ribosomal ribonucleic acid cistrons of Rhizobium and Bradyrhizobium species and some related bacteria. Int. J. Syst. Bacteriol. 36:1986;129-138.
29. De Ley J., Segers P., Kersters K., Mannheim W., Lievens A. Intra- and intergeneric similarities of the Bordetella ribosomal ribonucleic acid cistrons: proposal for a new family, Alcaligenaceae. Int. J. Syst. Bacteriol. 36:1986;405-414.
30. Gupta R.S. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 62:1998;1435-1491.
31. Gupta R.S. What are archaebacteria: Life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol. Microbiol. 29:1998;695-708.
32. Gupta R.S., Mukhtar T., Singh B. Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol. Microbiol. 32:1999;893-906.
33. Felsenstein J. Numerical methods for inferring evolutionary trees. Q. Rev. Biol. 57:1982;379-404.
34. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:1988;521-565.
35. Fitch W.M., Margoliash E. Construction of phylogentic trees: a method based on mutational distances as estimated from cytochrome c sequences is of general applicability. Science. 155:1967;279-284.
36. Lecointre G., Philippe H., Van Le H.L., Le Guyader H. Species sampling has a major impact on phylogenetic inference. Mol. Phylogen. Evol. 2:1993;205-224.
37. Felsenstein J. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:1978;401-410.
38. Fitch W.M. Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20:1971;406-416.
39. Hasegawa M., Fujiwara M. Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol. Phylogen. Evol. 2:1993;1-5.
40. Hasegawa M., Hashimoto T. Ribosomal RNA trees misleading? Nature. 361:1993;23.
41. Lake J.A. The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol. 8:1991;378-385.
42. Lake J.A. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. USA. 91:1994;1455-1459.
43. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:1989;170-179.
44. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
45. Swofford, D.L. and Olsen, G.L. (1990) Phylogeny reconstruction. In: Molecular Systematics (Hillis, D. and Moritz, C., Eds.), pp. 411-501. Sinauer, Sunderland, MA.
46. Tateno Y., Takezei N., Nei M. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 12:1994;261-277.
47. Foster P.G., Hickey D.A. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:1999;284-290.
48. Rivera M.C., Lake J.A. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science. 257:1992;74-76.
49. Meyer T.E., Cusanovich M.A., Kamen M.D. Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees. Proc. Natl. Acad. Sci. USA. 83:1986;217-220.
50. Gupta R.S., Singh B. Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model for the evolution of the HSP70 gene. J. Bacteriol. 174:1992;4594-4605.
51. Baldauf S.L., Palmer J.D. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA. 90:1993;11558-11562.
52. Brown J.R., Doolittle W.F. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Rev. 61:1997;456-502.
53. Maidak B.L., Olsen G.J., Larsen N., Overbeek R., McCaughey M.J., Woese C.R. The Ribosomal Database Project (RDP). Nucleic Acids Res. 24:1996;82-85.
54. Smith M.W., Feng D.F., Doolittle R.F. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17:1992;489-493.
55. Aravind L., Tatusov R.L., Wolf Y.I., Walker D.R., Koonin E.V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:1998;442-444.
56. Koonin E.V., Mushegian A.R., Galperin M.Y., Walker D.R. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 25:1997;619-637.
57. Pennisi E. Genome data shake tree of life. Science. 280:1998;672-674.
58. Syvanen M. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28:1994;237-261.
59. Doolittle W.F. Phylogenetic classification and the universal tree. Science. 284:1999;2124-2128.
60. Gribaldo S., Lumia V., Creti R., De Macario E.C., Sanangelantoni A., Cammarano P. Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J. Bacteriol. 181:1999;434-443.
61. Lorenz M.G., Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:1994;563-602.
62. Pennisi E. Is it time to uproot the tree of life? Science. 284:1999;1305-1307.
63. Lawrence J.G., Ochman H. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA. 95:1998;9413-9417.
64. Koonin E.V., Galperin M.Y. Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr. Opin. Genet. Dev. 7:1997;757-763.
65. Jain R., Rivera M., Lake J.A. Horizontal gene transfer among genomes: The complexity hypothesis. Proc. Natl. Acad. Sci. USA. 96:1999;3801-3806.
66. Woese C.R. The universal ancestor. Proc. Natl. Acad. Sci. USA. 95:1998;6854-6859.
67. Philippe H., Budin K., Moreira D. Horizontal transfers confuse the prokaryotic phylogeny based on the HSP70 protein family. Mol. Microbiol. 31:1999;1007-1009.
68. Cohan F.M. The role of genetic exchange in bacterial evolution. ASM News. 62:1996;631-636.
69. Cohan F.M. Genetic exchange and evolutionary divergence in prokaryotes. Science. 264:1994;382-388.
70. Mazodier P., Davies J. Gene transfer between distantly related bacteria. Annu. Rev. Genet. 25:(147-71):1991;147-171.
71. Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science. 264:1994;375-382.
72. Spratt B.G. Resistance to antibiotics mediated by target alterations. Science. 264:1994;388-393.
73. Cavalier-Smith T. Origins of secondary metabolism. Ciba Found. Symp. 171:1992;64-80.
74. Olsen G.J., Woese C.R. Ribosomal RNA: a key to phylogeny. FASEB J. 7:1993;113-123.
75. Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA. 87:1990;4576-4579.
76. Ludwig W., Schleifer K.H. Phylogeny of Bacteria beyond the 16S rRNA Standard. ASM News. 65:1999;752-757.
77. Gupta R.S. Life's third domain (Archaea): An established fact or an endangered paradigm? A new proposal for classification of organisms based on protein sequences and cell structure. Theor. Popul. Biol. 54:1998;91-104.
78. Cavalier-Smith T. A revised six-kingdom system of life. Biol. Rev. Cambridge Phil. Soc. 73:1998;203-266.
79. Gupta R.S., Soltys B.J. Technical comments: www.sciencemag.org/cgi/content//full/286/5444/1443a. Science. 286:1999;1443a.
80. Gupta, R.S. (2000) The natural evolutionary relationships among prokaryotes. CRC Crit. Rev. Microbiol. (in press).
81. Wang J.C. DNA topoisomerases. Annu. Rev. Biochem. 65:1996;635-692.
82. Wright, A. and Tipper, D.J. (1979) The outer membrane of Gram-negative bacteria. In: The Bacteria, Vol. VII (Sokatch, J.R. and Ornston, L.N., Eds.), pp. 427-485. Academic Press, New York.
83. Gupta, R.S. (1996) Evolutionary relationships of chaperonins. In: The Chaperonins (Ellis, R.J., Ed.), pp. 27-64. Academic Press, New York.
84. Gupta R.S. Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol. Microbiol. 15:1995;1-11.
85. Rusanganwa E., Gupta R.S. Cloning and characterization of multiple groEL chaperonin-encoding genes in Rhizobium meliloti. Gene. 126:1993;67-75.
86. Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:1996;109-136.
87. Gupta R.S., Bustard K., Falah M., Singh D. 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. 179:1997;345-357.
88. Pascarella S., Argos P. Analysis of insertion/deletions in protein structures. J. Mol. Biol. 224:1992;461-471.
89. Gupta R.S., Johari V. Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-Thermus group and Cyanobacteria. J. Mol. Evol. 46:1998;716-720.
90. Erickson H.P. FtsZ, a tubulin homologue in prokaryote cell division. Trends Cell Biol. 7:1997;362-367.
91. Gupta R.S., Soltys B.J. Prokaryotic homolog of tubulin? Consideration of FtsZ and glyceraldehyde 3-phosphate dehydrogenase as probable candidates. Biochem. Mol. Biol. Int. 38:1996;1211-1221.
92. Lutkenhaus J., Addinall S.G. Bacterial cell division and the Z ring. Annu. Rev. Biochem. 66:1997;93-116.
93. Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Venter J.C. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 273:1996;1058-1073.
94. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.F., Dougherty B.A., Merrick J.M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
95. Tomb J.F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.P., Gill S., Dougherty B.A., Nelson K., Quackenbush J., Zhou L., Kirkness E.F., Peterson S., Loftus B., Richardson D., Dodson R., Khalak H.G., Glodek A., McKenney K., Fitzgerald L.M., Lee N., Adams M.D., Venter J.C., et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 388:1997;539-547.
96. Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1462.
97. Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.M., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D., Hoang L., Keagle P., Lumm W., Pothier B., Qiu D.Y., Spadafora R., Vicaire R., Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D. Complete genome sequence of Methanobacterium thermoautotrophicum DeltaH: Functional analysis and comparative genomics. J. Bacteriol. 179:1997;7135-7155.
98. Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessières P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.K., Codani J.J., Connerton I.F. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature. 390:1997;249-256.
99. Fraser C.M., Casjens S., Huang W.M., Sutton G.G., Clayton R., Lathigra R., White O., Ketchum K.A., Dodson R., Hickey E.K., Gwinn M., Dougherty B., Tomb J.F., Fleischmann R.D., Richardson D., Peterson J., Kerlavage A.R., Quackenbush J., Salzberg S., Hanson M., Van Vugt R., Palmer N., Adams M.D., Gocayne J. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390:1997;580-586.
100. Klenk H.P., Clayton R.A., Tomb J.F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G., Gill S., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 390:1997;364-370.
101. Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R., Feldman R.A., Short J.M., Olsen G.J., Swanson R.V. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 392:1998;353-358.
102. Stephens R.S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R.L., Zhao Q.X., Koonin E.V., Davis R.W. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 282:1998;754-759.
103. Andersson S.G.E., Zomorodipour A., Andersson J.O., Sicheritz-Pontén T., Alsmark U.C.M., Podowski R.M., Näslund A.K., Eriksson A.S., Winkler H.H., Kurland C.G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 396:1998;133-140.
104. Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takayima M., Ohfuku Y., Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Kikuchi H. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:1998;55-76.
105. Fraser C.M., Norris S.J., Weinstock C.M., White O., Sutton G.G., Dodson R., Gwinn M., Hickey E.K., Clayton R., Ketchum K.A., Sodergren E., Hardham J.M., McLeod M.P., Salzberg S., Peterson J., Khalak H., Richardson D., Howell J.K., Chidambaram M., Utterback T., McDonald L., Artiach P., Bowman C., Cotton M.D. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science. 281:1998;375-388.
106. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornby T., Jagels K. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393:1998;537-538.
107. Nelson K.E., Clayton R., Gill S., Gwinn M., Dodson R., Haft D.N., Hickey E.K., Peterson J., Nelson W.C., Ketchum K.A., McDonald L., Utterback T., Malek J., Linher K., Garrett M.M., Stewart A., Cotton M.D., Pratt M.S., Phillps C., Richardson D., Heidelberg J., Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S., Smith H.O., Venter J.C., Fraser C.M. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
108. Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A., Fleischmann R.D., Bult C.J., Kerlavage A.R., Sutton G., Kelley J.M. The minimal gene complement of Mycoplasma genitalium. Science. 270:1995;397-403.
109. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B.C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:1996;4420-4449.
110. Eisen J.A. 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. 41:1995;1105-1123.
111. Nagel G.M., Doolittle R.F. Evolution and relatedness in two aminoacyl-tRNA synthetase families. Proc. Natl. Acad. Sci. USA. 88:1991;8121-8125.
112. Cusack S., Hartlein M., Leberman R. Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Res. 19:1991;3489-3498.
113. Carter C.W.J. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu. Rev. Biochem. 62:1993;715-748.
114. Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y., Philippsen P., Tettelin H., Oliver S.G. Life with 6000 genes. Science. 274:(546):1996;563-567.
115. 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.
116. Viale A.M., Arakaki A.K. The chaperone connection to the origins of the eukaryotic organelles. FEBS Lett. 341:1994;146-151.
117. Yang D., Oyaizu Y., Oyaizu H., Olsen G.J., Woese C.R. Mitochondrial origins. Proc. Natl. Acad. Sci. USA. 82:1985;4443-4447.
118. Forterre P., Benachenhou-Lahfa N., Labedan B. Universal tree of life. Nature. 362:1993;795.
119. Gray M.W., Burger G., Lang B.F. Mitochondrial evolution. Science. 283:1999;1476-1481.
120. Falah M., Gupta R.S. 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. 176:1994;7748-7753.
121. Boorstein W.R., Ziegelhoffer T., Craig E.A. Molecular evolution of the HSP70 multigene family. J. Mol. Evol. 38:1994;1-17.
122. Gupta R.S., Golding G.B. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J. Mol. Evol. 37:1993;573-582.
123. TIGR Microbial Database Website. http://www.tigr.org/tdb/mdb/mdb.html .
124. Seaton B.L., Vickery L.E. A gene encoding a DnaK/hsp70 homolog in Escherichia coli. Proc. Natl. Acad. Sci. USA. 91:1994;2066-2070.
125. Kawula T.H., Lelivelt M.J. Mutations in a gene encoding a new Hsp70 suppress rapid DNA inversion and bgl activation, but not proU derepression, in hns-1 mutant Escherichia coli. J. Bacteriol. 176:1994;610-619.
126. Gupta R.S. Hsp70 sequences and the phylogeny of prokaryotes. Mol. Microbiol. 31:1999;1009-1010.
127. Gupta R.S., Singh B. Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr. Biol. 4:1994;1104-1114.
128. Gupta R.S., Golding G.B. The origin of the eukaryotic cell. Trends Biochem. Sci. 21:1996;166-171.
129. Abeles, R.H., Frey, P.A. and Jencks, W.P. (1992) Biochemistry, p. 1. Jones and Bartlett, Boston, MA.
130. Lahti R., Pitkaranta T., Valve E., Ilta I., Kukko-Kalske E., Heinonen J. Cloning and characterization of the gene encoding inorganic pyrophosphatase of Escherichia coli K-12. J. Bacteriol. 170:1988;5901-5907.
131. Langer T., Neupert W. Regulated protein degradation in mitochondria. Experientia. 52:1996;1069-1076.
132. Wang N., Gottesman S., Willingham M.C., Gottesman M.E., Maurizi M.E. A human mitochondrial ATP-dependent protease that is highly homologous to bacterial Lon protease. Proc. Natl. Acad. Sci. USA. 90:1993;11247-11251.
133. Wigley D.B. Structure and mechanism of DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct. 24:1995;185-208.
134. Luttinger A.L., Springer A.L., Schmid M.B. A cluster of genes that affects nucleoid segregation in Salmonella typhimurium. New Biol. 3:1991;687-697.
135. Ward E., Newton A. Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Mol. Microbiol. 26:1997;897-910.
136. den Blaauwen T., Driessen A.J. Sec-dependent preprotein translocation in bacteria. Arch. Microbiol. 165:1996;1-8.
137. Economou A. Bacterial preprotein translocase: mechanism and conformational dynamics of a processive enzyme. Mol. Microbiol. 27:1998;511-518.
138. Sanyal I., Gibson K.J., Flint D.H. Escherichia coli biotin synthase: an investigation into the factors required for its activity and its sulfur donor. Arch. Biochem. Biophys. 326:1996;48-56.
139. Ohsawa I., Speck D., Kisou T., Hayakawa K., Zinsius M., Gloeckler R., Lemoine Y., Kamogawa K. Cloning of the biotin synthetase gene from Bacillus sphaericus and expression in Escherichia coli and Bacilli. Gene. 80:1989;39-48.
140. Zhang S., Sanyal I., Bulboaca G.H., Rich A., Flint D.H. The gene for biotin synthase from Saccharomyces cerevisiase: cloning, sequencing, and complementation of Escherichia coli strains lacking biotin synthase. Arch. Biochem. Biophys. 309:1994;29-35.
141. Hashimoto T., Sanchez L.B., Shirakura T., Müller M., Hasegawa M. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl. Acad. Sci. USA. 95:1998;6860-6865.
142. Kubelik A.R., Turcq B., Lambovitz A.M. The Neurospora crassa cyt-20 gene encodes cytosolic and mitochondrial valyl-tRNA synthetases and may have a second function in addition to protein synthesis. Mol. Cell. Biol. 11:1991;4022-4035.
143. Chatton B., Walter P., Ebel J.P., Lacroute F., Fasiolo F. The yeast VAS1 gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases. J. Biol. Chem. 263:1988;52-57.
144. Viale A.M., Arakaki A.K., Soncini F.C., Ferreyra R.G. Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int. J. Syst. Bacteriol. 44:1994;527-533.
145. Bui E.T., Bradley P.J., Johnson P.J. A common evolutionary origin for mitochondria and hydrogenosomes. Proc. Natl. Acad. Sci. USA. 93:1996;9651-9656.
146. Switzer, R.L. (1999) Phosphoribosylpyrophosphate synthetase and related pyrophosphokinases. In: The Enzymes (Boyer, P.D., Ed.), pp. 607-629. Academic Press, New York.
147. Thoden J.B., Holden H.M. Dramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli. Biochemistry. 37:1998;11469-11477.
148. Saito K., Kurosawa M., Murakoshi I. Determination of a functional lysine residue of a plant cysteine synthase by site-directed mutagenesis, and the molecular evolutionary implications. FEBS Lett. 328:1993;111-114.
149. Bogdanova N., Hell R. Cysteine synthesis in plants: protein-protein interactions of serine acetyltransferase from Arabidopsis thaliana. Plant J. 11:1997;251-262.
150. Aiba A., Mizobuchi K. Nucleotide sequence analysis of genes purH and purD involved in the de novo purine nucleotide biosynthesis of Escherichia coli. J. Biol. Chem. 264:1989;21239-21246.
151. Lang B.F., Burger G., O'Kelly C.J., Cedergreen R., Golding G.B., Lemieux C., Sankoff D., Turmel M., Gray M.W. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature. 387:1997;493-497.
152. Kowalczykowski S.C., Dixon D.A., Eggleston A.K., Lauder S.S., Rehrauer W.M. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58:1994;401-465.
153. Iwabe N., Kuma K., Hasegawa M., Osawa S., Miyata T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA. 86:1989;9355-9359.
154. +-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA. 86:1989;6661-6665.
155. Baldauf S.L., Palmer J.D., Doolittle W.F. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA. 93:1996;7749-7754.
156. Gruber T.M., Eisen J.A., Gish K., Bryant D.A. The phylogenetic relationships of Chlorobium tepidum and Chloroflexus auranticus based upon their RecA sequences. FEMS Microbiol. Lett. 162:1998;53-60.
157. Lloyd A.T., Sharpe P.M. Evolution of the recA gene and the molecular phylogeny of bacteria. J. Mol. Evol. 37:1993;399-407.
158. Karlin S., Weinstock G.M., Brendel V. Bacterial classifications derived from recA protein sequence comparisons. J. Bacteriol. 177:1995;6881-6893.
159. 70-type sigma factors of group 1 and group 2. J. Bacteriol. 179:1997;1734-1747.
160. Klenk H.P., Meier T.D., Durovic P., Schwass V., Lottspeich F., Dennis P.P., Zillig W. RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J. Mol. Evol. 48:1999;528-541.
161. Gruber T.M., Bryant D.A. Characterization of the group 1 and group 2 sigma factors of the green sulfur bacterium Chlorobium tepidum and the green non-sulfur bacterium Chloroflexus auranticus. Arch. Microbiol. 170:1998;285-296.
162. Burggraf S., Olsen G.J., Stetter K.O., Woese C.R. A phylogenetic analysis of Aquifex pyrophilus. Syst. Appl. Microbiol. 15:1992;353-356.
163. Asai T., Zaporojets D., Squires C., Squires C.L. An Escherichia coli strain with all chromosomal rRNA operons inactivated: Complete exchange of rRNA genes between bacteria. Proc. Natl. Acad. Sci. USA. 96:1999;1971-1976.
164. Yap W.H., Zhang Z., Wang Y. Distinct types of rRNA operons exist in the genome of the Actinomycete Thermonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181:1999;5201-5209.
165. Gupta R.S. Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek. 72:1997;49-61.
166. Morell V. Life's last domain. Science. 273:1996;1043-1045.
167. Felsenstein J. Confidence limits in phylogenies: an approach using the bootstap. Evolution. 39:1985;783-791.
168. Trüper, H.G. and Pfennig, N. (1992) The family Chlorobiaceae. In: The Prokaryotes (Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 3583-3592. Springer-Verlag, New York.
169. Shah, R.N. (1992) The genus Bacteroides and related taxa. In: The Prokaryotes (Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 3593-3607. Springer-Verlag, New York.
170. Reichenbach, H. (1992) The order Cytophagales. In: The Prokaryotes (Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 3631-3675. Springer-Verlag, New York.
171. Fields, P.I. and Barnes, R.C. (1992) The genus Chlamydia. In: The Prokaryotes (Balows, A., Trüper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), pp. 3691-3709. Springer-Verlag, New York.
172. Zillig W., Schnabel R., Stetter K.O. Archaebacteria and the origin of the eukaryotic cytoplasm. Curr. Topics Microbiol. Immunol. 114:1985;1-18.
173. Doolittle W.F. A paradigm gets shifty. Nature. 392:1998;15-16.
174. Gupta R.S., Aitken K., Falah M., Singh B. Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc. Natl. Acad. Sci. USA. 91:1994;2895-2899.
175. Karlin S., Mrazek J., Campbell A.M. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179:1997;3899-3913.
176. Lake J.A., Rivera M.C. Was the nucleus the first endosymbiont? Proc. Natl. Acad. Sci. USA. 91:1994;2880-2881.
177. Martin W., Muller M. The hydrogenosome hypothesis for the first eukaryote. Nature. 392:1998;37-41.
178. Margulis L. Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl. Acad. Sci. USA. 93:1996;1071-1076.
179. Lopez-Garcia P., Moreira D. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem. Sci. 24:1999;88-93.
180. Rivera M., Jain R., Moore J.E., Lake J.A. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA. 95:1999;6239-6244.
181. Karlin S., Brocchieri L., Mrazek J., Campbell A.M., Spormann A.M. A chimeric prokaryotic ancestory of mitochondria and primitive eukaryotes. Proc. Natl. Acad. Sci. USA. 96:1999;9190-9195.
182. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.G., Murray R.G.E., Stackebrandt E., Starr M.P., Trüper H.G. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:1987;463-464.
183. Stackebrandt E. Phylogenetic relationships vs. phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria. Can. J. Microbiol. 34:1988;552-556.
184. Brown J.R., Doolittle W.F. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA. 92:1995;2441-2445.
185. Stiller J.W., Hall B.D. Technical comments: www.sciencemag.org/cgi/content//full/286/5444/1443a. Science. 286:1999;1443a.
186. Gupta, R.S. (2000) Evolutionary relationships among Bacteria: Does 16S rRNA provide all the answers? ASM News (in press).
187. Felsenstein, J. (1994) PHYLIP, version 3.5, University of Washington, Seattle, WA.