Archaeal Ubiquitin-Like Proteins: Functional Versatility and Putative Ancestral Involvement in tRNA Modification Revealed by Comparative Genomic Analysis
Table 1
Components of Ubl-related pathways in archaea predicted in this paper.
Reference arCOG
Representative of the reference arCOG
arCOGs identified by genomic context analysis
Lineage
Comment
Genomic associations of genes for UBL (-grasp) proteins
arCOG00540
70606476
arCOG01885 arCOG07188 arCOG00286
Sulfolobales
Predicted operon contains genes for 30 S ribosomal protein S17e, small uncharacterized protein, and a distinct membrane-associated HerA-like ATPase of the SSO0283 family. Thermosome beta subunit is a divergently encoded gene located within a conserved region which includes a variety of informational genes.
arCOG00537
18313032
arCOG05553
Thermoproteales
Membrane protein
arCOG00535
15791089
arCOG04721
Halobacteria
GNAT N-acetyltransferase
arCOG00535
15679735
arCOG00042
Many diverse archaea
tRNA(Ile)-lysidine synthase MesJ
arCOG00535
70607385
arCOG03852
Sulfolobales
Uncharacterized protein
Genomic associations of arCOG06308 (TBP-like fold protein with [GG] C-terminal motif)
arCOG06308
76801892
arCOG06307
Halobacteria
Two small uncharacterized proteins and MoaD-like Ubl protein
arCOG06309
arCOG00536
Genomic associations of arCOG08988 (uncharacterized protein with [CC] C-terminal motif)
arCOG08988
257373014
arCOG04404
Halobacteria
ComK-like protein, in bacteria, is involved in regulation of competence; in archaea, its role is unclear [34].
Genomic associations of genes for E1-like enzymes (ThiF/MoeB)
arCOG01677
15679158
arCOG04863
Methanococcales
First two genes are distant CinA C-terminal domain homologs; next is an NAD-binding domain containing protein and an NIF3 homolog.
arCOG04865
arCOG04864
arCOG04454
Genomic associations of genes for the Jab protease
arCOG01139
257387955
arCOG01222
Many diverse archaea
Cytidylyltransferase family protein
The table lists genes (arCOGs) that are consistently found within genomic neighborhoods of genes that encode components of Ubl-related pathways. On the basis of theses associations and, in some cases, their domain content as well, the protein products of these neighboring genes are predicted to be functionally related to Ubl systems as well.
