title: Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems.
abstract: A systematic comparative genomic analysis of all archaeal membrane proteins that have been projected to the last archaeal common ancestor gene set led to the identification of several novel components of predicted secretion, membrane remodeling, and protein glycosylation systems. Among other findings, most crenarchaea have been shown to encode highly diverged orthologs of the membrane insertase YidC, which is nearly universal in bacteria, eukaryotes, and euryarchaea. We also identified a vast family of archaeal proteins, including the C-terminal domain of N-glycosylation protein AglD, as membrane flippases homologous to the flippase domain of bacterial multipeptide resistance factor MprF, a bifunctional lysylphosphatidylglycerol synthase and flippase. Additionally, several proteins were predicted to function as membrane transporters. The results of this work, combined with our previous analyses, reveal an unexpected diversity of putative archaeal membrane-associated functional systems that remain to be functionally characterized. A more general conclusion from this work is that the currently available collection of archaeal (and bacterial) genomes could be sufficient to identify (almost) all widespread functional modules and develop experimentally testable predictions of their functions.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: makarova@ncbi.nlm.nih.gov.
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D001105:Archaea / Q000502:physiology*; D019843:Archaeal Proteins / Q000378:metabolism*; D005075:Biological Evolution; D055028:Comparative Genomic Hybridization; D003198:Computer Simulation; D017124:Conserved Sequence; D019143:Evolution, Molecular; D019766:Genes, Archaeal / Q000235:genetics*; D006031:Glycosylation; D008565:Membrane Proteins / Q000378:metabolism*; D010802:Phylogeny; D011487:Protein Conformation
chemical_list: D019843:Archaeal Proteins; D008565:Membrane Proteins
keywords: Archaeal genomes; Gene neighborhoods; Membrane proteins; arCOGs