The natural evolutionary relationships among prokaryotes

Critical Reviews in Microbiology

Volumn 26, Issue 2, 2000, Pages 111-131

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Antibiotic resistance; Archaea; Cell membranes; Diderms; Gram positive bacteria; Monoderms; Prokaryote phylogeny; Three domain proposal; Universal ancestor

Indexed keywords

ECOLOGY; EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; REVIEW; SPECIES DIFFERENCE; STRAIN DIFFERENCE; THEORY;

ARCHAEA; BACTERIA (MICROORGANISMS); CHLAMYDIA; CHLOROBI; CHLOROFLEXI; CYTOPHAGA; DEINOCOCCUS; DEINOCOCCUS-THERMUS; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA; THERMUS;

EID: 0033935581     PISSN: 1040841X     EISSN: None     Source Type: Journal    
DOI: 10.1080/10408410091154219     Document Type: Review

References (130)

1. Schopf, J. W., Microfossils of the early archean apex chert: new evidence fof the antiquity of life. Science., 260, 640, 1993.
2. Knoll, A. H., The early evolution of eukaryotes: A geological perspective. Science., 256, 622, 1992.
3. Margulis, L., Symbiosis in Cell Evolution. W.H. Freeman and Company. New York, 1993, 1.
4. Kasting, J. F., Earth's early atmosphere. Science., 259, 920, 1993.
5. Cloud, P., Beginnings of biospheric evolution and their biogeochemical consequences. Paleobiology., 2, 351, 1976.
6. Zuckerkandl, E. and Pauling, L. Molecules as documents of evolutionary history. J. Theoreti. Biol., 8, 357, 1965.
7. Darwin, C., The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London, 1859.
8. Buchanan, R. E., General Systematic Bacteriology. Williams and Wilkins, Baltimore, 1925.
9. Chatton, E., Titres et travaux scientifiques (1906-1937) de Edouard Chatton, E. Sottano. Sete, France, 1937.
10. Murray, R. G. E., Microbial structure as an aid to microbial classification and taxonomy. Spisy Prirodoved Fak, Univ. J. E. Purkyne Brne., 43, 249, 1968.
11. Kluyver, A. J. and van Niel, C. B., Prospects for a natural system of classification of bacteria. Zentralblatt fur Bakteriologie, Parasitenkunde und Infektionskrankheiten II, 94, 369, 1936.
12. Mayr, E., Systmatics and the Origin of Species. Columbia University Press, New York, 1942.
13. Margulis, L., Origin of Eukaryotic Cells. Yale University Press, New Haven, CT, 1970.
14. Murray, R. G. E., Kingdom Procaryote. Bergey's Manual of Systematic Bacteriology. Sneath, P. H. A., Mair, N. S., Sharpe, M. E., and Holt, J. G., Eds., The Williams and Willkins, Baltimore, 1986, 34.
15. Whittaker, R., H., New concepts of kingdoms of organisms. Science., 163, 150, 1969.
16. Stanier, R. Y., The main outlines of bacterial classification. J. Bacterial., 42, 437, 1941.
17. Stanier, R. Y. and van Niel, C. B., The concept of a bacterium. Archiv fur Mikrobiologie, 42, 17, 1962.
18. Holt, J. G., Krieg, N. R., Sneath, P. H. A., Staley, J. T., and Stanley, T. W., Bergey's Manual of Determinative Bacteriology. The Williams and Wilkins, Baltimore, 1994.
19. Woese, C. R., Bacterial evolution. Microbiol. Rev., 51, 221, 1987.
20. Forterre, P. and Philippe, H., Where is the root or the universal tree of life. Bioexxays. 21, 871, 1999.
21. Woese, C. R., O. Kandler, and Wheelis, M. L., Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA, 87, 4576, 1990.
22. Doolittle, W. F., Phylogenetic classification and the universal tree. Science. 284, 2124, 1999.
23. Olsen, G. J., Woese, C. R., and Overbeek, R., The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol., 176, 1, 1994.
24. Poole, A., Jeffares, D., and Penny, D., Early evolution: prokaryotes, the new kids on the block. Bioessays, 21, 880, 1999.
25. Koonin, E. V., Mushegian, A. R., Galperin, M. Y., and 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, 619, 1997.
26. Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., and Miyata, T., Evolutionary relationship of archaebacteria, eubacteria. and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA, 86, 9355, 1989.
27. Karlin, S., Mrazek, J., and Campbell, A. M., Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol., 179, 3899, 1997.
28. Rivera, M. C. and Lake, J. A., Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science, 257, 74, 1992.
29. 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., Report of the Ad Hoc Committee on approaches to taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol., 40, 213, 1990.
30. Woese, C. R., Prokaryote systematics: the evolution of a science. The Prokaryotes. Balows, A., Truper, H. G., Dworkin, M., Harder, W., and Schleifer K. H., Eds., Springer-Verlag, New York, 1992, 3.
31. Olsen, G. J. and Woese, C. R., Ribosomal RNA: a key to phylogeny. FASEB J., 7, 113, 1993.
32. Morowitz, H. J., Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. Yale University Press, New Haven, 1992, 1,
33. Deamer, D. W., The first living systems: a bioenergetic perspective. Microbiol. Mol. Biol. Rev., 61, 239, 1997.
34. Oparin, A. I., Evolution of the concepts of the origin of life. 1924-1972. Orig. Life, 7, 3. 1976.
35. Atlas, R. M., Microbiology: Fundamentals and Applications. Macmillan, New York, 1988, 1.
36. Mayr, E., Two empires or three? Proc. Natl. Acad. Sci. USA, 95, 9720, 1998.
37. Allsopp, A., Phylogenetic relationships of the prokaryota and the origin of the eucaryotic cell. New Phytology, 68, 591, 1969.
38. Truper, H. G. and Schleifer, K. H., Prokaryote characterization and identification. In: The Prokaryotes. Balows, A.,A., Truper, A., Dworkin, M., Harder, W., and H. Schleifer K., Eds., Springer-Verlag, New York, 1992, 126.
39. Wright, A. and Tipper, D. J., The outer membrane of Gram-negative bacteria. In: The Bacteria, Vol VII. Sokatch J. R. and Ornston L. N., Eds., Academic Press, New York, 1979, 427.
40. Stanier, R. Y., Adelberg, E. A., and Ingraham, J. L., The Microbial World. Prentice-Hall Inc., New Jersey, 1976, 1.
41. Gupta, R. S., Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria. eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev., 62, 1435, 1998.
42. 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, 695, 1998.
43. 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. Theoretical Population Biology, 54, 91, 1998.
44. Cavalier-Smith, T., A revised six-kingdom system of life. Biol. Rev. Cambridge Philosophic. Soc., 73, 203, 1998.
45. Lyell, C., Principles of Geology. D. Appleton & Co. New York, 1872.
46. Woese, C. R. and Fox, G. E., Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA. 74, 5088, 1977.
47. Kandler, O. and Konig, H., Cell envelopes of archaea: structure and chemistry. In: The Biochemistry of Archaea (Archaebacteria). Kates, M., Kushner, D. J., and Matheson A. T., Eds., Elsevier Science Publishers B.V., New York, 1993, 223.
48. Zillig, W., Schnabel, R., and R., Stetter, R., Archaebacteria and the origin of the eukaryotic cytoplasm. Curr. Topic. Microbiol. Immunol., 114, 1, 1985.
49. Bock, A. and Kandler, O., Antibiotic sensitivity of Archaebacteria. In: The Bacteria, vol. VIII (Archaebacteria). Woese, C. R., and Wolfe, R. S., Eds., Academic Press, New York, 1985, 525.
50. Mayr, E., A natural system of organisms. Nature, 348, 491, 1990.
51. Margulis, L. and Guerrero, R., New Scientist. 132, 46, 1991.
52. Rothschild, L. J., Ragan, M. A., Coleman, A. W., Heywood, P., and Gerbi, S. A., Are rRNA sequence comparisons the Rosetta stone of phylogenetics? Cell, 47, 640, 1986.
53. Tiboni, O., Cammarano, P., and Sanangelantoni, A. M., Cloning and sequencing of the gene coding glutamine synthetase I from the archaeum Pyrococcus woesi: anomalous phylogenies inferred from analysis of archael and bacterial glutamine synthetase I sequence. J. Bacteriol., 175, 2961, 1993.
54. Benachenhou-Lahfa, N., Forterre, P., and Labedan, B., Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J. Mol. Evol., 36, 335, 1993.
55. Gupta, R. S. and Singh, B., Phylogenetic analysis of 70-kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr. Biol., 4, 1104, 1994.
56. Gupta, R. S. and 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, 4594, 1992.
57. Gupta, R. S. and Golding, G. B., Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. J. Mol. Evol., 37, 573, 1993.
58. Forterre, P., Protein versus rRNA: problems in rooting the universal tree of life. ASM News. 63, 89, 1997.
59. Brown, J. R., Masuchi, Y., Robb, F. T., and Doolittle, W. F., Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J. Mol. Evol., 38, 566, 1994.
60. Gupta, R. S., Aitken, K., Falah, M., and 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, 2895, 1994.
61. Anon. 1998. TIGR Microbial Database, http:/ www.tigr.org/tdb/mdb/mdb.html.
62. Pennisi, E., Is it time to uproot the tree of life? Science, 284, 1305, 1999.
63. Pennisi, E., Genome data shake tree of life. Science, 280, 672, 1998.
64. Woese, C. R., The universal ancestor. Proc. Natl. Acad. Sci. USA. 95, 6854, 1998.
65. Olsen, G. J. and Woese, C. R., Archaeal genomics: an overview. Cell. 89, 991, 1997.
66. Dennis, P. P., Ancient ciphers: translation in Archaea. Cell, 89, 1007, 1997.
67. Rivera, M., Jain, R., Moore, J. E., and Lake, J. A., Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA, 95, 6239, 1999.
68. Edgell, D. R. and Doolittle, W. F., Archaea and the origin(s) of DNA replication proteins. Cell, 89, 995, 1997.
69. Reeve, J. N., Sandman, K., and Daniels, C. J., Archaeal histones, nucleosomes, and transcription initiation. Cell, 89, 999, 1997.
70. Belfort, M. and Weiner, A., Another bridge between kingdoms: tRNA splicing in archaea and eukaryotes. Cell, 89, 1003, 1997.
71. Brown, J. R. and Doolittle, W. F., Archaea and the prokaryote-to-eukaryote transition. Microbiol. Rev., 61, 456, 1997.
72. Jain, R., Rivera, M., and Lake, J. A., Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA, 96, 3801, 1999.
73. Martin, W., Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays, 21, 99, 1999.
74. Kandler, O., The early diversification of life and the origin of the three domains: a proposal. Thermophiles: The keys to molecular evolution and the origin of life? Wiegel J. and Adams W. W., Eds., Taylor and Francis, Athens, 1998, 19.
75. Koonin, E. V. and Galperin, M. Y., Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr. Opin. Genet. Dev., 7, 757, 1997.
76. Smith, M. W., Feng, D. F., and Doolittle, R. F., Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci., 17, 489, 1992.
77. Syvanen, M., Horizontal gene transfer: evidence and possible consequences. Ann. Rev., Genet., 28, 237, 1994.
78. Doolittle, W. F., You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. TIG, 14, 307, 1998.
79. Hilario, E. and Gogarten, J. P., Horizontal transfer of ATPase genes - the tree of life becomes a net of life. Biosystems, 31, 111, 1993.
80. Doolittle, W.F., Lateral genomics, Trends in Biochemical Sciences., 24, M5, 1999.
81. Gogarten, J. P. and L. Olendzenski., Orthologs, paralogs and genome comparisons. Current Opinion in Genetics and Development., 9, 630, 1999.
82. Stiller, J. W. and Hall, B. D., Technical comments: w w w.sciencemag.org/cgi/content/ full/286/5444/1443a. Science, 286, 1443a, 1999.
83. Gupta, R. S. and Soltys, B. J., Technical comments: www.sciencemag.org/cgi/content/ full/286/5444/1443a. Science 286, 1443a, 1999.
84. Gupta, R. S., The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes, FEMS Microbiol. Rev., 24, (in press), 2000.
85. Gupta, R. S., Evolutionary relationships among bacteria: Does 16S rRNA provide all the answers, ASM News, 66, 189, 2000.
86. Puhler, G., Leffers, H., Gropp, F., Palm, P., Klenk, H. P., Lottspeich R., Garrett, R. A., and Zillig, W., Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc. Natl. Acad. Sci. USA, 86, 4569, 1989.
87. Doolittle, W. F., What are the archaebacteria and why are they important? Biochem. Soc. Symp., 58:1-6, 1, 1992.
88. Cavalier-Smith, T., The origin of eukaryotic and archaebacterial cells. Ann. N. Y. Acad. Sci., 503: 17-54, 17, 1987.
89. Feng, D. F., Cho, G., and Doolittle, R. F., Determining divergence times with a protein clock: update and reevaluation. Proc. Natl. Acad. Sci. USA, 94, 13028, 1997.
90. Karlin, S., Brocchieri, L., Mrazek, J., Campbell, A. M., and Spormann, A. M., A chimeric prokaryotic ancestory of mitochondria and primitive eukaryotes. Proc. Natl. Acad. Sci. USA, 96, 9190, 1999.
91. Margulis, L., Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl. Acad. Sci. USA, 93, 1071, 1996.
92. Ribeiro, S. and Golding, G. B., The mosaic nature of the eukaryotic nucleus. Mol. Biol. Evol., 15, 779, 1998.
93. Gupta, R. S. and Golding, G. B., The origin of the eukaryotic cell. Trends Biochem. Sci., 21, 166, 1996.
94. Gupta, R. S., Origin of eukaryotic cells: was metabolic symbiosis based on hydrogen the driving force? Trends Biochem. Sci, 24, 423, 1999.
95. Hashimoto, T. and Hasegawa, M., Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors lalpha/Tu and 2/G. Adv. Biophvsics., 32: 73-120, 73, 1996.
96. 92a. Ludwig, W. and K. H. Schleifer., Phylogeny of Bacteria beyond the 16S RRNA Standard, ASM News., 65, 752, 1999.
97. Woese, C. R., The Archaea: their history and significance. In: The Biochemistry of Archaea (Archaebaderia). Kates, M., Kushner, D. J., and Matheson A. T., Eds., Elsevier Science Publishers B.V., New York, 1993, vii.
98. Woese, C. R., 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., Sinauer Associates Inc., Sunderland, MA, 1991, 1
99. Lawrence, J. G. and Ochman, H., Molecular archaeology of the Excherichia colt genome. Proc. Natl. Acad. Sci. USA, 95, 9413, 1998.
100. Baldauf, S. L., Palmer, J. D., and 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, 7749, 1996.
101. Gupta, R. S. and 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, 716, 1998.
102. Gupta, R. S., Protein phytogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek, 72. 49, 1997.
103. Gupta, R. S., Mukhtar, T., and Singh, B., Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlombium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol. Microbiol., 32, 893, 1999.
104. Gupta, R. S., Bustard, K., Falah, M., and 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. Bacteriaol., 179, 345, 1997.
105. Murray, R. G. E., Family II. Deinococcaceae Brooks and Murray 1981, 356VP. In: Bergey's Manual of Systematic Bacteriology. Sneath. P. H. A., Mair, N. S., Sharpe, M. E., and Holt J. G., Eds., The Williams and Wilkins. Baltimore, 1986, 1035.
106. Nikaido, H., Prevention of drug access to bacterial targets: permeability barriers and active efflux. Science, 264, 382, 1994.
107. Nikaido, H., Kim, S-H., and Rosenberg, E. Y., Physical organization of lipids in the cell wall of Mycobacterium chelonae. Mol. Microbiol., 8, 1025, 1993.
108. Brennan, P. J. and Nikaido, H., The envelope of mycobacteria. Annu. Rev. Biochem., 64, 29, 1995.
109. Blankenship, R. E., Origin and early evolution of photosynthesis. Photosynth. Re., 33, 91, 1992.
110. Olson, J. M. and Pierson, B. K., Evolution of reaction centers in photosynthetic prokaryotes. Int. Rev. Cytol., 108, 209, 1987.
111. Asai, T., Zaporojets, D., Squires, C., and 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, 1971, 1999.
112. Nomura, M., Engineering of bacterial ribosomes: replacement of all seven Escherichia coli rRNA operons by a single plasmid-encoded operon. Proc. Null. Acad. Sci. U. S. A., 96, 1820, 1999.
113. Nomura, M., P. Traub, and H. Bechmann., Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins, Nature., 279, 793, 1968.
114. Higo, K., W. Held, L. Kahan, and M. Nomura., Functional correspondence between 30S rihosomal proteins of Escherichia coli and Baciluus stearothermphilus, Proc. Natl. Acad. Sci U. S. A., 70, 944, 1973.
115. O'Neil, D.M., L.S. Baron, and P. S. Sypherd., Chromosomal location of ribosomal protein cistrons determined by intergeneric bacterial mating, J. Bacteriol. 99, 242, 1969.
116. Yap, W. H., Zhang, Z., and Wang, Y., Dis tinct 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, 5201, 1999.
117. Grogan, D. W., Exchange of genetic information at extremely high temperatures in the Archaeon Sulfolobus acidocaldarius. J. Bacteriol., 178, 3207, 1996.
118. Noll, K. M. and Vargas, M., Recent advances in genetic analyses of hyperthermophilic Archaea and Bacteria. Arch. Microbiol., 168, 73, 1997.
119. Sowers, K. R. and Schreier, H. J., Gene transfer systems for the Archaea. Trends Microbiol., 7, 212, 1999.
120. Neu, H. C., The crisis in antibiotic resistance. Science, 251, 1064, 1992.
121. Davies, J., Inactivation of antibiotics and the dissemination of resistance genes. Science. 264, 375, 1994.
122. Spratt, B. G., Resistance to antibiotics mediated by target alterations. Science. 264, 388, 1994.
123. Cavalier-Smith, T., Origins of secondary metabolism. Ciba Foundation Symp., 171, 64, 1992.
124. Forterre, P., Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol. Microbiol., 33, 457, 1999.
125. Mazodier, P. and Davies, J., Gene transfer between distantly related bacteria. Ann. Rev. Genet., 25:147-71, 147, 1991.
126. Lewis, K., Hooper, D. C., and Ouellette, M., Multidrug resistance pumps provide broad defense. ASM News., 63, 605, 1997.
127. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., A. M., Alloni, A. M., 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., and Connerton, I. F., The complete genome sequence of the Grampositive bacterium Bacillus subtilis. Nature, 390, 249, 1997.
128. Woese, C. R., Default taxonomy: Ernst Mayr's view of the microbial world. Proc. Natl. Acad. Sci. USA, 95, 11043, 1998.
129. Laporte, L. F., Earliest traces of life. In: The Fossil Record and Evolution. Laporte L., Ed., W.H., Freeman and Company, San Francisco. 1982, 44.
130. Woese, C. R., There must be a prokaryote somewhere: microbiology's search for itself. Microbiol. Rev., 58, 1, 1994.