Table 3

Examples of computational and experimental discovery of unexpected functions in archaea.

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K.S.M. and E.V.K., unpublished observations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K.S.M. and E.V.K., unpublished observations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K.S.M. and E.V.K., unpublished observations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[143] and K.S.M. and E.V.K., unpublished observations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]

Makarova and Koonin Genome Biology 2003 4:115   doi:10.1186/gb-2003-4-8-115