Table 2.
Synapomorphies in Euryarchaeota (Examples)
| COG description | Representatives | Unique shared characters nonarchaeal homologs (see also Fig.8) | |||||||||
| Mj | Mt | Af | Ph | ||||||||
| DNA polymerase II large subunit | MJ1630 | MTH1536 | AF1722 | PHBN021 | a highly conserved archaeal enzyme without similarity to any other proteins, with the exception of a C4 Zn finger resembling those in eukaryotic DNA polymerase δ. | ||||||
| DNA polymerase II small subunit, predicted phosphohydrolase of the calcineurin-like superfamily | MJ0702 | MTH1405 | AF1790 | PHBN023 PHAZ021 | Predicted active phosphohydrolase (phosphatase) in archaea and an inactivated form in eukaryotes (Aravind and Koonin 1998a). | ||||||
| Predicted ATP-dependent DNA ligase | MJ0414 | MTH1221 | AF0849 | PHBG013 | very limited similarity to other ATP-dependent DNA ligases except for one fromAquifex aeolicus, probably due to horizontal transfer (Altschul and Koonin 1998). | ||||||
| DNA excision repair enzyme | MJ1505 | MTH1415 | AF0358 | PHAI012 | consists of a typical helicase domain and a nuclease domain as opposed to the apparent eukaryotic orthologs (ERCC4/RAD1) in which the helicase domain appears to be inactivated (Aravind et al. 1999). | ||||||
| DnaG-type primase-like proteins | MJ1206 | MTH891 | AF1899 | PHAN003 | unique domain organization with a N-terminal helicase motif combined with the DnaG-type (Toprim) domain (Aravind et al. 1998). | ||||||
| DNA-directed RNA polymerase subunit (E‘/E") | MJ0396/MJ0397 | MTH264/MTH265 | AF1116/AF1117 | PHBT008/inPH744 | two single domain (S1 and C4 Zn finger domains) proteins in all Euryarchaeota; a fusion in Sulfolobus; only the S1 domain protein is a RNA polymerase subunit in eukaryotes (Fig.8). | ||||||
| DNA-dependent RNA polymerase A‘/A" subunits | MJ1042/MJ1043 | MTH1051/MTH1052 | AF1888/AF1889 | PHCB020/PHCB021 | the split of the largest RNA polymerase subunit gene into two adjacent genes is unique to archaea. Both eukaryotes and bacteria encode highly conserved orthologs of the archaeal A‘ and A" subunits as a single polypeptide (the β‘-subunit in bacteria). | ||||||
| Predicted HTH transcriptional regulators | MJ0188 | MTH1282 | AF1259 | PHCN020 | unique domain organization: two CBS domains fused with an HTH domain. | ||||||
| Archaeosine synthetase (archaea-specific tRNA modification) | MJ1022 | MTH1665 | AF0587 | PHBN035 | two-domain architecture, with an additional, predicted RNA-binding PUA domain, as opposed to bacterial homologs (queuine synthetases) that consist of the enzymatic domain alone (Fig 8; Aravind and Koonin 1999a). | ||||||
| Translation elongation factor EF-1β | MJ0459 | MTH1699 | AF0574 | AP000001 | the archaeal EF-1β is a small protein of ∼120 amino acids whereas all eukaryotic homologs (orthologs?) contain an additional domain homologous to GSTs (Koonin et al. 1994). | ||||||
| ATP-dependent protease Lon | MJ1417 | MTH785 | AF0364 | PHBH031 | only the carboxy-terminal, protease domain is highly conserved in archaea and bacteria; the amino-terminal ATPase domain in the archaeal proteins is distinct from the ATPase domain of Lon. | ||||||
| PilT family ATPase | MJ1533 | MTH246 | AF1951 | PHBP012 | unique domain organization—ATPase + amino-terminal PIN domain. | ||||||
| GMP synthetase subunits—PP-family ATPases and glutamine amidotransferase | MJ1131 | MTH710 | AF0253 | PHAU017 | ATPase (top row) and glutamine amidotransferase (bottom row) moieties of the GMP synthetase are separate polypeptides. Orthologs of each subunit in bacteria and eukaryotes are domains of a single protein. | ||||||
| MJ1575 | MTH709 | AF1320 | PHAU016 | ||||||||
| Predicted enzyme with an ATP-grasp domain and a redox active center | MJ0202 | MTH1744 | AF1104 | PHBQ042 | ortholog with the same domain architecture only in Aquifex; all other homologs are distantly related and lack the redox center. | ||||||
