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

Volumn 54, Issue 2, 1998, Pages 91-104

  Gupta, Radhey S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Archaebacteria; Cell structure; Eukaryotic cell origin; Gram negative bacteria; Gram positive bacteria; Prokaryote phylogeny

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA;

EID: 0032189747     PISSN: 00405809     EISSN: None     Source Type: Journal    
DOI: 10.1006/tpbi.1998.1376     Document Type: Review

References (69)

1. Baldauf, S. L., Palmer, J. D., and Doolittle, W. F. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny, Proc. Natl. Acad. Sci. USA 93, 7749-7754.
2. Belfort, M., and Weiner, A. 1997. Another bridge between kingdoms: tRNA splicing in archaea and eukaryotes, Cell 89, 1003-1006.
3. Benachenhou-Lahfa, N., Forterre, P., and Labedan, B. 1993. 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, 335-346.
4. Brown, J. R., Masuchi, Y., Robb, F. T., and Doolittle, W. F. 1994. Evolutionary relationships of bacterial and archaeal glutamine synthetase genes, J. Mol. Evol. 38, 566-576.
5. Brown, J. R., and Doolittle, W. F. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications, Proc. Natl. Acad. Sci. USA 92, 2441-2445.
6. Brown, J. R., and Doolittle, W. F. 1997. Archaea and the prokaryote-to-eukaryote transition, Microbiol. Rev. 61, 456-502.
7. Bui, E. T., Bradley, P. J., and Johnson, P. J. 1996. A common evolutionary origin for mitochondria and hydrogenosomes, Proc. Natl. Acad. Sci. USA 93, 9651-9656.
8. 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., and Venter, J. C. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii, Science 273, 1058-1073.
9. Cavalier-Smith, T. 1987. The origin of eukaryotic and archaebacterial cells, Ann. N. Y. Acad. Sci. 503, 17-54.
10. Cavalier-Smith, T. 1992. Origins of secondary metabolism, Ciba Found. Symp. 171, 64-80.
11. Chatton, E. 1937. "Titres et Travaux Scientifiques (1906-1937) de Edouard Chatton," E. Sottano, Sete, France.
12. Dennis, P. P. 1997. Ancient ciphers: Translation in Archaea, Cell 89, 1007-1010.
13. Doolittle, R. F. 1995. Of archae and eo: What's in a name? Proc. Natl. Acad. Sci. USA 92, 2421-2423.
14. Doolittle, R. F., Feng, D. F., Tsang, S., Cho, G., and Little, E. 1996. Determining divergence times of the major kingdoms of living organisms with a protein clock, Science 271, 470-477.
15. Edgell, D. R., and Doolittle, W. F. 1997. Archaea and the origin(s) of DNA replication proteins, Cell 89, 995-998.
16. 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., and Merrick, J. M. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science 269, 496-512.
17. Forterre, P. 1997. Protein versus rRNA: Problems in rooting the universal tree of life, ASM News 63, 89-95.
18. 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., and Kelley, J. M. 1995. The minimal gene complement of Mycoplasma genitalium, Science 270, 397-403.
19. Germot, A., Philippe, H., and Le Guyader, H. 1996. Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggest a very early mitochondrial endosymbiosis in eukaryotes, Proc. Natl. Acad. Sci. USA 93, 14614-14617.
20. Gogarten, J. P., Kibak, H., Dittrich, P., Taiz, L., Bowman, E. J., Bowman, B. J., Manolson, M. F., Poole, R. J., Date, T., and Oshima, T. 1989. Evolution of the vacuolar H + -ATPase: Implications for the origin of eukaryotes, Proc. Natl. Acad. Sci. USA 86, 6661-6665.
21. Golding, G. B., and Gupta, R. S. 1995. Protein-based phylogenies support a chimeric origin for the eukaryotic genome, Mol. Biol. Evol. 12, 1-6.
22. Gram, C. 1884. Ueber die isolierte farbung der Schizomyceten in Schnitt und Trockenpraparaten, Fortschr. Med. 2, 185-189.
23. Gray, M. W. 1992. The endosymbiont hypothesis revisited, Int. Rev. Cytol. 141, 233-357.
24. 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.
25. Gupta, R. S. 1995. Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species, Mol. Biol. Evol. 12, 1063-1073.
26. Gupta, R. S. 1997. Protein phylogenies and signature sequences: Evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes, Antonie van Leeuwenhoek 72, 49-61.
27. 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.
28. Gupta, R. S. 1998. Protein phylogenies and signature sequences: A reappraisal of the evolutionary relationships between archaebacteria, eubacteria, and eukaryotes, Microbiol. Rev., submitted.
29. Gupta, R. S., and Golding, G. B. 1993. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes, J. Mol. Evol. 37, 573-582.
30. Gupta, R. S., and Golding, G. B. 1996. The origin of the eukaryotic cell, Trends Biochem. Sci. 21, 166-171.
31. Gupta, R. S., and Singh, B. 1992. 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, 4594-4605.
32. 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.
33. Hashimoto, T., and Hasegawa, M. 1996. Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G, Adv. Biophys. 32, 73-120.
34. 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 & Wilkins, Baltimore.
35. Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., and Miyata, T. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes, Proc. Natl. Acad. Sci. USA 86, 9355-9359.
36. Kandler, O., and Konig, H. 1993. Cell envelopes of archaea: Structure and chemistry, in "The Biochemistry of Archaea (Archaebacteria)" (M. Kates, D. J. Kushner, and A. T. Matheson, Eds.), p. 223, Elsevier, Amsterdam/New York.
37. Karlin, S., Weinstock, G. M., and Brendel, V. 1995. Bacterial classifications derived from recA protein sequence comparisons, J. Bacteriol. 177, 6881-6893.
38. Karlin, S., Mrazek, J., and Campbell, A. M. 1997. Compositional biases of bacterial genomes and evolutionary implications, J. Bacteriol. 179, 3899-3913.
39. 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., and Loftus, B. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus, Nature 390, 364-NIL7.
40. Klenk, H. P., and Zillig, W. 1994. DNA-dependent RNA polymerase subunit B as a tool for phylogenetic reconstructions: Branching topology of the archaeal domain, J. Molec. Evol. 38, 402-432.
41. Koonin, E. V., Mushegian, A. R., Galperin, M. Y., and Walker, D. R. 1997. 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, 619-637.
42. Lake, J. A., and Rivera, M. C. 1994. Was the nucleus the first endosymbiont? Proc. Natl. Acad. Sci. USA 91, 2880-2881.
43. Langer, D., Hain, J., Thuriaux, P., and Zillig, W. 1995. Transcription in archaea: similarity to that in eucarya, Proc. Natl. Acad. Sci. USA 92, 5768-5772.
44. Margulis, L. 1970. "Origin of Eukaryotic Cells," Yale Univ. Press, New Haven, CT.
45. Margulis, L. 1993. "Symbiosis in Cell Evolution," Freeman, New York.
46. Margulis, L. 1996. Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life, Proc. Natl. Acad. Sci. USA 93, 1071-1076.
47. Martin, W., and Muller, M. 1998. The hydrogenosome hypothesis for the first eukaryote, Nature 392, 37-41.
48. Mayr, E. 1990. A natural system of organisms, Nature 348, 491.
49. Murray, R. G. E. 1968. Microbial structure as an aid to microbial classification and taxonomy, Spisy Prirodoved Fak. Univ. J. E. Purkyne Brne 43, 249-252.
50. Murray, R. G. E. 1986a. Kingdom Procaryote, in "Bergey's Manual of Systematic Bacteriology" (P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt, Eds.), p. 34, Williams & Willkins, Baltimore.
51. Murray, R. G. E. 1986b. The higher taxa, or, a place for everything...? in "Bergey's Manual of Systematic Bacteriology" (P. H. A. Sneath, N. S. Mair, M. E. Sharpe, and J. G. Holt, Eds.), p. 31, Williams & Wilkins, Baltimore.
52. Olsen, G. J., and Woese, C. R. 1993. Ribosomal RNA: a key to phylogeny, FASEB J. 7, 113-123.
53. Olsen, G. J., and Woese, C. R. 1996. Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii? Trend. Genet. 12, 377-379.
54. Olsen, G. J., and Woese, C. R. 1997. Archaeal genomics: An overview, Cell 89, 991-994.
55. Pace, N. R. 1991. Origin of life - Facing up to the physical setting, Cell 65, 531-533.
56. Popper, K. 1968. "The Logic of Scientific Discovery," Hutchison, London.
57. Puhler, G., Leffers, H., Gropp, F., Palm, P., Klenk, H. P., Lottspeich, F., Garrett, R. A., and Zillig, W. 1989. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome, Proc. Natl. Acad. Sci. USA 86, 4569-4573.
58. Reeve, J. N., Sandman, K., and Daniels, C. J. 1997. Archaeal histones, nucleosomes, and transcription initiation, Cell 89, 999-1002.
59. Rivera, M. C., and Lake, J. A. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives, Science 257, 74-76.
60. Schopf, J. W. 1978. The evolution of the earliest cells, Sci. Am. 239, 110-120.
61. 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., and Bush, D. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum DeltaH: Functional analysis and comparative genomics, J. Bacteriol. 179, 7135-7155.
62. Stanier, R. Y., Adelberg, E. A., and Ingraham, J. L. 1976. "The Microbial World," Prentice-Hall, New York.
63. Tiboni, O., Cammarano, P., and Sanangelantoni, A. M. 1993. 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, 2961-2969.
64. TIGR Microbial Database Website, 1998. http://www.tigr.org/tdb/ mdb/mdb.html.
65. Tipper, D. J., and Wright, A. 1979. The structure and biosynthesis of bacterial cell walls, in "The Bacteria" (J. R. Sokatch, and L. N. Ornston, Eds.), Vol. VII, p. 291, Academic Press, New York.
66. Woese, C. R. 1987. Bacterial evolution, Microbiol. Rev. 51, 221-271.
67. Woese, C. R., Kandler, O., and 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.
68. Woese, C. R. 1992. Prokaryote systematics: the evolution of a science, in "The Prokaryotes" (A. Balows, H. G Truper, M. Dworkin, W. Harder, and K. H. Schleifer, Eds.), p. 3, Springer-Verlag, New York.
69. Zillig, W., Klenk, H. P., Palm, P., Leffers, H., Puhler, G., Gropp, F., and Garrett, R. A. 1989. Did eukaryotes originate by a fusion event? Endocytobiosis Cell Res. 6, 1-25.