Archaea are widely regarded as one of the three main domains of life [1-4], although their origin is a subject of debate [5-11]. They were earlier believed to inhabit only extreme environments such as extremely hot, or hot and acidic, extremely saline, or very acidic or alkaline conditions [12], but recent studies indicate that they are widespread in different environments [13]. The archaea also include methanogens, which grow under strictly anaerobic and often thermophilic conditions, and are the only organisms that derive all of their metabolic energy by reduction via methanogenesis. The archaeal species branch distinctly from all other organisms in phylogenetic trees based on 16S rRNA and many other gene/protein sequences [3,14-17]. In addition, several additional characteristics such as the presence of branched-chain ether-linked lipids in their cell membrane, lack of peptidoglycan in their cell wall, characteristic subunit pattern of RNA polymerase, presence of modified bases in tRNA, presence of a unique form of DNA polymerase, have also been indicated as defining characteristics of archaea [1,12]. However, many of these features are either not shared by all archaea or they are also present in various eukaryotes or some thermophilic bacteria [18,19].

The Three Domain Hypothesis

The phylogenetic analyses of Archaea have led to their division into two major groups or phyla designated as Crenarchaeota and Euryarchaeota[1,9,14,16,20,21]. The species from both these groups, particularly Euryarchaeota, are highly diverse in terms of their metabolism and physiology. Based on their metabolic and physiological characteristics and other unique features, five functionally distinct groups within Euryarchaeota are currently recognized: methanogens, sulfate reducers, extreme halophiles, cell wall-less archaea, and extremely thermophilic sulfur metabolizing archaea [9,16,22]. Some of these groups, such as methanogens, are polyphyletic in different phylogenetic trees [9,23]. However, the sets of genes or proteins that are unique to these different functional groups and distinguish them from all others remain to be identified. In recent years, complete genomes of many archaeal species have been sequenced (see Table 1) and their comparative analyses is providing valuable information regarding different genes/proteins that are distinctive characteristics of various functional groups within Archaeaand also their relationships to Bacteria and Eukaryotes. A few aspects of Archaea will be considered here:

1. Phylogenetic Trees
2. Signature Proteins for Archaea and its various subgroups
3. Evolutionary Relationships of Archaea and Bacteria
4. Conserved Indels

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Selected References:

1. 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 U S A 87, 4576-4579.
2. Kandler, O. (1998). The early diversification of life and the origin of the three domains: A proposal. In "Thermophiles: The keys to molecular evolution and the origin of life?" (J. Wiegel and W. W. Adams, Eds.), Taylor and Francis, Athens.
3. Olsen, G. J. and Woese, C. R. (1997). Archaeal genomics:  An overview. Cell 89, 991-994.
4. Edgell, D. R. and Doolittle, W. F. (1997). Archaea and the origin(s) of DNA replication proteins. Cell 89, 995-998.
5. Gupta, R. S. (1998). 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, 695-708.
   
6. Mayr, E. (1998). Two empires or three? Proc.Natl.Acad.Sci.USA 95, 9720-9723.
   
7. Gupta, R. S. (2000). The Natural Evolutionary Relationships Among Prokaryotes. Crit.Rev.Microbiol. 26, 111-131. [PDF]
8. Cavalier-Smith, T. (2002). The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int.J.Syst.Evol.Microbiol. 52, 7-76.
9. Gribaldo, S. and Brochier-Armanet, C. (2006). The origin and evolution of Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci 361, 1007-1022.
10. Gupta, R. S. (2005). Molecular Sequences and the Early History of Life. In "Microbial Phylogeny and Evolution: Concepts and Controversies" (J. Sapp, Ed.), Oxford University Press, New York. [PDF]
11. Lake, J. A., Herbold, C. W., Rivera, M. C., Servin, J. A., and Skophammer, R. G. (2007). Rooting the tree of life using nonubiquitous genes. Mol.Biol.Evol. 24, 130-136.
12. Woese, C. R. (1987). Bacterial Evolution. Microbiol Rev 51, 221-266.
13. Schleper, C., Jurgens, G., and Jonuscheit, M. (2005). Genomic studies of uncultivated archaea. Nat.Rev.Microbiol. 3, 479-488.
14. Olsen, G. J., Woese, C. R., and Overbeek, R. (1994). The winds of (evolutionary) change: breathing new life into microbiology. J.Bacteriol. 176, 1-6.
15. Brown, J. R. and Doolittle, W. F. (1997). Archaea and the prokaryote-to-eukaryote transition. Microbiol.Rev. 61, 456-502.
16. Ludwig, W. and Klenk, H. P. (2001). Overview:A phylogenetic backbone and taxonomic framework for prokaryotic systamatics. In "Bergey's Manual of Systematic Bacteriology" (Boone D.R. and Castenholz R.W., Eds.), Springer-Verlag, Berlin.
17. 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.
18. Walsh, D. A. and Doolittle, W. F. (2005). The real 'domains' of life. Curr Biol 15, R237-R240.
19. Gao, B. and Gupta, R. S. (2007). Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 8, 86. [PDF]
20. Makarova, K. S., Aravind, L., Galperin, M. Y., Grishin, N. V., Tatusov, R. L., Wolf, Y. I., and Koonin, E. V. (1999). Comparative genomics of the archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell. Genome Res 9, 608-628.
21. Bapteste, E., Brochier, C., and Boucher, Y. (2005). Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1, 353-363.
22. Brochier, C., Forterre, P., and Gribaldo, S. (2005). An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol Biol 5.
23. Woese, C. R. and Olsen, G. J. (1986). Archaebacterial Phylogeny - Perspectives on the Urkingdoms. Syst Appl Microbiol 7, 161-177.

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Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (April 2007). http://www.bacterialphylogeny.com/index.html