Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

C R Woese 1, O Kandler 1, M L Wheelis 1
PMCID: PMC54159  PMID: 2112744

Abstract

Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.

Full text

PDF
4576

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Achenbach-Richter L., Gupta R., Zillig W., Woese C. R. Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution. Syst Appl Microbiol. 1988;10:231–240. doi: 10.1016/s0723-2020(88)80007-9. [DOI] [PubMed] [Google Scholar]
  2. Achenbach-Richter L., Stetter K. O., Woese C. R. A possible biochemical missing link among archaebacteria. Nature. 1987 May 28;327(6120):348–349. doi: 10.1038/327348a0. [DOI] [PubMed] [Google Scholar]
  3. Auer J., Lechner K., Böck A. Gene organization and structure of two transcriptional units from Methanococcus coding for ribosomal proteins and elongation factors. Can J Microbiol. 1989 Jan;35(1):200–204. doi: 10.1139/m89-031. [DOI] [PubMed] [Google Scholar]
  4. 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. The phylogeny of prokaryotes. Science. 1980 Jul 25;209(4455):457–463. doi: 10.1126/science.6771870. [DOI] [PubMed] [Google Scholar]
  5. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
  6. 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 U S A. 1989 Dec;86(23):9355–9359. doi: 10.1073/pnas.86.23.9355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Jones W. J., Nagle D. P., Jr, Whitman W. B. Methanogens and the diversity of archaebacteria. Microbiol Rev. 1987 Mar;51(1):135–177. doi: 10.1128/mr.51.1.135-177.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kimura M., Arndt E., Hatakeyama T., Hatakeyama T., Kimura J. Ribosomal proteins in halobacteria. Can J Microbiol. 1989 Jan;35(1):195–199. doi: 10.1139/m89-030. [DOI] [PubMed] [Google Scholar]
  9. Pühler G., Leffers H., Gropp F., Palm P., Klenk H. P., Lottspeich F., Garrett R. A., Zillig W. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4569–4573. doi: 10.1073/pnas.86.12.4569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. STANIER R. Y., VAN NIEL C. B. The concept of a bacterium. Arch Mikrobiol. 1962;42:17–35. doi: 10.1007/BF00425185. [DOI] [PubMed] [Google Scholar]
  11. Schnabel R., Thomm M., Gerardy-Schahn R., Zillig W., Stetter K. O., Huet J. Structural homology between different archaebacterial DNA-dependent RNA polymerases analyzed by immunological comparison of their components. EMBO J. 1983;2(5):751–755. doi: 10.1002/j.1460-2075.1983.tb01495.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Schwartz R. M., Dayhoff M. O. Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts. Science. 1978 Jan 27;199(4327):395–403. doi: 10.1126/science.202030. [DOI] [PubMed] [Google Scholar]
  13. WHITTAKER R. H. On the broad classification of organisms. Q Rev Biol. 1959 Sep;34:210–226. doi: 10.1086/402733. [DOI] [PubMed] [Google Scholar]
  14. Whittaker R. H., Margulis L. Protist classification and the kingdoms of organisms. Biosystems. 1978 Apr;10(1-2):3–18. doi: 10.1016/0303-2647(78)90023-0. [DOI] [PubMed] [Google Scholar]
  15. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Woese C. R., Fox G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088–5090. doi: 10.1073/pnas.74.11.5088. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Woese C. R., Fox G. E. The concept of cellular evolution. J Mol Evol. 1977 Sep 20;10(1):1–6. doi: 10.1007/BF01796132. [DOI] [PubMed] [Google Scholar]
  18. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Zuckerkandl E., Pauling L. Molecules as documents of evolutionary history. J Theor Biol. 1965 Mar;8(2):357–366. doi: 10.1016/0022-5193(65)90083-4. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES