title: Comprehensive phylogenetic analysis of evolutionarily conserved rRNA adenine dimethyltransferase suggests diverse bacterial contributions to the nucleus-encoded plastid proteome.
abstract: The KsgA/Dim1 protein family of rRNA adenine dimethyltransferase (rAD) is well conserved throughout evolution. This protein family has been recognized to play multiple additional roles: as a mitochondrial transcription factor (mtTFB); as a yeast pre-rRNA cleavage enzyme (Dim1p); and as a chloroplast developmental protein (PFC1). Comprehensive phylogenetic analysis of rAD led to three main findings. First, rAD sequences were grouped by three domains of life, bacteria, archaea, and eukaryotes. Second, mtTFB shows alpha-proteobacterial endosymbiotic ancestry. Third, plastid-targeted rADs do not show cyanobacterial affiliation. Instead, plastid-targeted homologs from chlorophytes/land plants were clustered with chlamydiae, while those from rhodophytes/red algal lineage grouped with the bacteroides/chlorobi group. These unusual two-bacterial ancestries of plastid-targeted rAD suggest that bacterial genes influenced the evolution of the proteome of eukaryotic plastids in a complex way, involving more diverse bacterial groups than previously believed, and underscoring the importance of eukaryotic acquisition of bacterial functions.
authors.affiliation: Department of Biostatistics and Epidemiology, School of Public Health, Seoul National University, 28 Yeongeon-Dong, Jongro-Gu, Seoul 110-460, Republic of Korea.
authors.forename: Ae Kyung
authors.initials: AK
authors.lastname: Park
authors.forename: Ho
authors.initials: H
authors.lastname: Kim
authors.forename: Hyung Jong
authors.initials: HJ
authors.lastname: Jin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001499:Bayes Theorem; D005075:Biological Evolution; D017124:Conserved Sequence; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D006801:Humans; D016013:Likelihood Functions; D008780:Methyltransferases / Q000235:genetics*; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D020543:Proteome / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D020543:Proteome; D012335:RNA, Ribosomal; D008780:Methyltransferases; C047346:16S rRNA (adenine(1518)-N(6)-adenine(1519)-N(6))-dimethyltransferase