Table 2 The top 15 phyletic patterns in proteins from archaea

Archaeal core, including 200 COGs present in both B^† and E, 34 present in at least one B, 63 present in at least one E, 16 unique for A

CP: Only COG0564, pseudouridylate synthase, 23S RNA-specific pseudouridylate synthase present in all E (in which it has an apparently mitochondrial origin) and B, but not in A. In all A another specific pseudouridylate synthase is present (COG1258)

This pattern reflects a large number of genes acquired via HGT^† in Mac (see [55]), including F₀F₁-type ATP synthase and NADH:ubiquinone oxidoreductase, and a specific signal transduction system based on several apoptosis-related domains

CP: The small number of such COGs indicates that the archaeal core is almost fully conserved in Mac

This pattern reflects a substantial amount of HGT in Hsp; see [125]

This pattern consists of COGs including four methanogens and Afu; these organisms specifically share several metabolic pathways (see [45]). The set includes subunits of coenzyme F420-reducing hydrogenase, formylmethanofuran dehydrogenase, CO dehydrogenase/acetyl-CoA synthase and other enzymes of energy metabolism These might have originally evolved in methanogens and subsequently transferred to Afu.

CP: Sugar ABC transporter and some fatty acid biosynthesis enzymes are missing from methanogens and Afu

This pattern is specific for four methanogens, including unique pathways for coenzyme M biosynthesis and reduction and 14 uncharacterized proteins, many of which are likely to be unique enzymes involved in biosynthesis of other specific coenzymes and their utilization

CP: COG2096, cob(I)alamin adenosyltransferase and COG1058, predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA, for which functional substitutes remain to be identified

A pattern specific for thermophilic methanogens (Mth, Mja and Mka), comprising mostly uncharacterized COGs, it includes a specific membrane complex EhaA-EhaP (approximately 18 components) involved in hydrogen production and possibly electron transfer [45,134]

CP: Specific gene loss: peptide ABC-type transporter, NADH: ubiquinone oxidoreductase, malic enzyme (COG0281), and cysteinyl-tRNA synthetase (COG0215; see text)

This pattern reflects a substantial amount of HGT in Sso, including several enzymes of carbohydrate metabolism (beta-glucosidase, alpha-L-fucosidase, and malto-oligosyl trehalose synthase) [97]

This reflects a substantial amount of HGT in Afu

CP: COG0449, glucosamine 6-phosphate synthetase, which catalyzes the first step in hexosamine metabolism. A functional substitute remains to be identified

A pattern specific for two mesophilic archaea, probably resulting from independent HGT

This pattern includes genes that might have been acquired via HGT in Mja, in particular three enzymes of biotin biosynthesis: pimeloyl-CoA synthetase (COG1424), dethiobiotin synthetase (COG0132), and adenosylmethionine-8-amino-7-oxononanoate aminotransferase (COG0161)

A crenarchaea-specific pattern, including 11 COGs that do not have orthologs outside this lineage. Among genes shared with bacteria but not euryarchaeota are three subunits of aerobic-type CO dehydrogenase and CO dehydrogenase maturation factor. Genes specifically shared with eukaryotes are three ribosomal proteins (S30, S25 and L13E)

CP: Euryarchaea-specific pattern, including two subunits of archaeal DNA polymerase II and ERCC4-like helicase, division GTPase FtsZ (COG0206) and ATP-dependent protease LonB (COG1067) plus six COGs that do not have orthologs outside this lineage

Apparent independent HGT to Mac and Afu

Apparent specific gene loss in the Thermoplasma lineage: two subunits of topoisomerase VI (COG1389, 1697), adenylate cyclase of class 2 (COG1437), and predicted exosome subunits (COG1325, COG1931)

CP: genes apparently acquired via HGT in Thermoplasma, including bacterial nucleoid DNA-binding protein HU (COG0776). See also [96]

Apparent gene loss in Ape, including 9 enzymes of purine biosynthesis [135].

Apparent HGT in Pyrococci. Includes two subunits of allophanate hydrolase (COG1984, 2049), two enzymes of carbohydrate metabolism, β-galactosidase (COG1874) and endoglucanase (COG2730)

CP: Specific gene loss in the Pyrococcus lineage includes five enzymes of heme biosynthesis