Superkingdom Archaea

Abstract

The Archaea .

Keywords: Archaea

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"According to rRNA trees, there are two groups within the Archaea: the kingdoms Crenarchaeota and Euryarchaeota. The Crenarchaeota are generally hyperthermophiles or thermoacidophiles (some genera are Desulfurococcus, Pyrodictium, Sulfolobus, Thermofilum and Thermoproteus). The Euryarchaeota span a broader ecological range and include hyperthermophiles (e.g. Pyrococcus and Thermococcus), methanogens (e.g. Methanosacrina), halophiles (e.g. Halobacterium and Haloferax), and even thermophilic methanogens (e.g. Methanobacterium, Methanococcus and Methanothermus). However, it is important to note that microbial species assemblages in extreme environments are not exclusively archaeal as bacteria-specific rRNA signatures can also be amplified from such sites. In addition, through polymerase chain reaction (PCR) amplification of rRNA sequences from water and sediment samples, a plethora of new archaeal species belonging to both kingdoms have been found in mesophilic environments such as temperate marine coastal waters, the Antarctic Ocean, and freshwater lakes, even as marine sponge symbionts. PCR-based surveys of hot springs’ microbiota have also detected novel archaeal rRNA sequences that possibly branch deeper than the Crenarchaeota–Euryarchaeota divergence. These ‘organisms’ have been tentatively assigned to a third archaeal kingdom, the Korarchaeota" (Brown 2002).

"Protein synthesis or translation is also strikingly similar between the Archaea and eukaryotes. Archaea and eukaryotes share several translation factors, not found in Bacteria, although the Archaea have several unique types as well. The close relationship between Archaea and eukaryotes is supported by the phylogenetic analyses of several other translation proteins including elongation factors, ribosomal proteins, aminoacyl-tRNA synthetases and methionine aminopeptidase" (Brown 2002).

"In summary, there are some features that distinguish the Archaea from the Bacteria and eukaryotes, most notably the structure and composition of their membranes. Primarily, the members of the Archaea are unique in having a combination of traits which, until now, were believed to be exclusive to either Bacteria or eukaryotes. However, this picture may change rapidly in light of new information from the wide variety of microorganism genome sequencing projects now in progress" (Brown 2002).

"However, there have been serious challenges to the archaeal tree. Based on different reanalyses of rRNA and elongation factor trees, Lake and co-workers have long advocated that the Archaea are a paraphyletic rather than monophyletic group where the kingdom Crenarchaeota is more closely related to eukaryotes than is the kingdom Euryarchaeota. Locke suggests that the Crenarchaeota be renamed ‘eocytes’. Focusing on the heat-shock protein 70 kilodalton (kDa) subunit (HSP70) Gupta and co-workers have also argued that the Archaea are not a true clade. A number of proteins for which only unrooted trees can be derived suggest that either Archaea and Bacteria (some examples are glutamine synthetase, glutamate dehydrogenase and HSP70) or Bacteria and eukaryotes (some examples are valyl-tRNA synthetase, enolase and glyceraldehyde 3-phosphate dehydrogenase) are interrelated groups, thus challenging the notion of monophyletic domains (i.e. that Archaea, Bacteria and Eukarya are separate groups joined at the base of the tree of life) – the basic tenant of the archaeal tree" (Brown 2002).

References

Brown, James R. 2002 (in press): Universal Tree of Life. In Encyclopedia of Life Sciences. Nature Publishing Group, Macmillan.

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