Table 6.
Examples of COGs conserved in euryarchaea but missing in A. pernix
| COG number | Phylogenetic pattern* | Function | Comments |
| 0101 | amtks-yqvdcebrhujwgpolinx | Pseudouridylate synthase (tRNA psi55) | This RNA modification enzyme hitherto has been considered ubiquitous and essential [54] |
| 1549 | amtks- - - - - - - - - - - - - - - - - - - - | Archaeosine tRNA-ribosyltransferase, contains PUA domain | See text |
| 2036 | amtks-y- - - - - - - - - - - - - - - - - - | Histones H3 and H4 | In the crenarchaeon Sulfolobus solfataricus, the role of histones in maintaining DNA supercoiling appears to be relegated to the DNA-binding protein Sso7d [55]. However, A. pernix does not encode an ortholog of this protein, and the mechanism of chromatin packaging remains unclear |
| 1933 | amtks- - - - - - - - - - - - - - - - - - - - | Unique archaeal DNA polymerase, large subunit | This DNA polymerase is highly conserved among the euryarchaea but so far has not been seen in other taxa [15] |
| 1311 | amtks-y- - - - - - - - - - - - - - - - - - | Small subunit of DNA polymerase, predicted phosphatase (calcineurin-like superfamily) | The absence of this subunit, which is represented by (predicted) active phosphatases in archaea and inactivated forms in eukaryotes [37] correlates with the absence of the large subunit |
| 1111 | amtks-y- - - - - - - - - - - - - - - - - | ERCC4-like helicase | A typical archaeal-eukaryotic repair protein, a predicted active helicase in euryarchaea and an inactivated form in eukaryotes [39] |
| 1107 | amtks- - - - - - - - - - - - - - - - - - - - | Archaea-specific RecJ-like exonuclease, ontains DnaJ-type Zn finger domain | |
| 1243 | amtks-y-v- - - - - - - - - - - - - - - - | Transcription elongation factor ELP3 | Consists of an amino-terminal biotin-synthase-like domain and a carboxy-terminal histone acetylase domain (only the biotin-synthase-like domain is represented in some bacteria) |
| 0206 | amtks- -qvdcebrhuj-gpol-nx | Cell division GTPase FtsZ | A central component of bacterial and archaeal cell-division machinery which is homologous (although only weakly similar) and functionally analogous to eukaryotic tubulins [56]. So far, among prokaryotes, FtsZ has been found missing only in Chlamydia [57]. |
| 0455 | amtks- -qvdcebr-uj- - -ol-n- | ATPases involved in chromosome partitioning | There may be a correlation between the absence of FtsZ and the presence of only one chromosome-partitioning ATPase (the ortholog of bacterial Mrp) in A. pernix |
| 1149 | amtks- - -v- - - - - - - - - - - - - - - | MinD superfamily P-loop ATPases containing an inserted ferredoxin domain | |
| 0065 | amtks-yqvdcebrh-j- - - - - -n- | 3-Isopropylmalate dehydratase large subunit | A. pernix does not encode committed enzymes of leucine biosynthesis, indicating that, unlike all other free-living organisms whose genomes have been sequenced so far, it cannot produce leucine. It might depend on other archaea and/or bacteria as the source of leucine, or perhaps synthesize leucine by a distinct, completely uncharacterized pathway |
| 0066 | amtks-yqvdcebrh-j- - - - - -n- | 3-isopropylmalate dehydratase small subunit | |
| 0473 | amtks-yqvdcebrh-j- - - - - -nx | 3-isopropylmalate dehydrogenase | |
| 0119 | amtks-yqvdcebrh-j- - - - - -n- | Isopropylmalate/homocitrate/citramalate synthase | |
| 0015 | amtks-yqvdcebrhuj- - - - - -n- | Adenylosuccinate lyase | Most of the enzyme of the de novo pathway of purine biosynthesis are missing in A. pernix. It appears likely that, in this organism, all purine nucleotides are produced via the salvage pathway. |
| 0104 | amtks-yqvdcebrhuj- - - - - -n- | Adenylosuccinate synthase | |
| 0034 | amtks-yqvdcebrh-j- - - - - -n- | Glutamine phosphoribosyl-pyrophosphate amidotransferase | |
| 0151 | amtks-yqvdcebrhuj- - - - - -n- | Phosphoribosylamine-glycine ligase | |
| 0150 | amtks-yqvdcebrh-j- - - - - -n- | Phosphoribosylamino-imidazol (AIR) synthetase PurM | |
| 0152 | amtks-yqvdcebrh-j- - - - - -nx | Phosphoribosylamino-imidazolesuccino-carboxamide (SAICAR) synthase | |
| 0041 | amtks-yqvdcebrh-j- - - - - -n- | Phosphoribosylcarboxy-aminoimidazole (NCAIR) mutase PurE | |
| 0047 | amtks-yqvdcebrh-j- - - - - -n- | Phosphoribosylformyl-glycinamidine (FGAM) synthase, glutamine amidotransferase | |
| domain | |||
| 0046 | amtks-yqvdcebrh-j- - - - - -n- | Phosphoribosylformyl-glycinamidine (FGAM) synthase, synthetase domain | |
| 0340 | amtks-yqvdcebrhuj- - - -linx | Biotin-(acetyl-CoA carboxylase) ligase | A. pernix apparently does not encode any enzymes of biotin synthesis or biotin-utilizing enzymes |
| 0511 | amtks-yqvdcebrhuj- - - -linx | Biotin carboxyl carrier protein of acetyl-CoA carboxylase | |
| 0157 | amtks-yqv-cebrhu- - - - - - -n- | Nicotinate-nucleotide pyrophosphorylase |
*In the phylogenetic patterns, each letter indicates that a particular genome is represented in the given COG, and a dash indicates the absence of a representative from the corresponding genome. The one-letter code for genomes is as follows: a, Archeoglobus fulgidus; m, Methanococcus jannaschii; t, Methanobacterium thermoautotrophicum; k, Pyrococcus horikoshii; s, Pyrococcus abyssi; z, Aeropyrum pernix; y, Saccharomyces cerevisiae; q, Aquifex aeolicus; v, Thermotoga maritima; d, Deinococcus radiodurans; c, Synechocystis sp; e, Escherichia coli; b, Bacillus subtilis; r, Mycobacterium tuberculosis; h, Haemophilus influenzae; u, Helicobacter pylori; j, Campylobacter jejuni; w, Ureaplasma urealyticum; g, Mycoplasma genitalium; p, Mycoplasma pneumoniae; o, Borrelia burgdorferi; l, Treponema pallidum; i, Chlamydia trachomatis and C. pneumoniae; n, Neisseria meningitidis; x, Rickettsia prowazekii.