From: Comparative genomics of archaea: how much have we learned in six years, and what's next?
COG numbers [37,38] | Function and comments | References |
---|---|---|
Computational predictions | ||
0012, 1325, 1603, 1369, 0638, 1500, 1097, 689, 2123, 1996, 2136, 2892, 0618, 1782, 1096, 3286, 1761 and more | Archaeal exosome. Orthologs of eukaryotic exosome subunits form the largest conserved superoperon in archaea, after the ribosomal superoperon, suggesting the existence of a physical complex | [88] |
1769, 1336, 3337, 1583, 1367, 1604, 1517, 1857, 1688, 1203, 1468, 1518, 2254, 1343, 1353, 1421, 1337, 1567, 1332, 4343 | DNA repair system represented primarily in thermophiles | [59] |
0358 | Bacterial-type DNA primase (DnaG orthologs) | [24] |
1311 | Small subunit of euryarchaeal DNA polymerase II, predicted PHP family phosphohydrolase (probably phosphatase); eukaryotic homologs appear to be inactivated | [123] |
1833 | Uri superfamily endonuclease. | [136] |
1628 | Endonuclease V homologs. | K.S.M. and E.V.K., unpublished observations |
1679,1786 | Aconitase catalytic core and an interacting 'swiveling domain' | K.S.M. and E.V.K., unpublished observations |
1711 | Possible subunit of the DNA replication machinery | K.S.M. and E.V.K., unpublished observations |
1310 | Zn2+-dependent hydrolase homologous to the eukaryotic ubiquitin isopeptidase contained in the proteasome and COP9 signalosome | [137,138] |
Computational predictions validated by experiments | ||
1708 | 'Minimal' nucleotidyltransferases | [100,139] |
1830 | Fructose-1,6-bisphosphate aldolases (DhnA family) | [76,77] |
1351 | Thymidylate synthase | [61,64] |
1685 | Shikimate kinase (predicted on the basis of operon organization) | [140] |
3635 | Phosphoglycerate mutase | [24,141] |
Experimental discovery of unexpected protein functions in archaea | ||
1384 | Class I lysyl-tRNA synthetase | [62] |
1933 | DNA polymerase II | [104] |
1980 | Fructose 1,6-bisphosphatase | [142] |
1630 | NurA, a novel 5'-3' nuclease encoded next to Rad50 and Mre11 orthologs; present in all sequenced archaeal genomes and some bacteria | [143] and K.S.M. and E.V.K., unpublished observations |
1812 | S-adenosylmethionine synthetase, was identified by mass tags | [144] |
1591 | Holliday junction resolvase | [101] |
1581 | Alba, a major DNA-binding chromatin protein in Crenarchaeota | [106] |
1945 | Pyruvoyl-dependent arginine decarboxylase (PvlArgDC), involved in polyamine biosynthesis | [145] |