title: Multiple conversion between the genes encoding bacterial class-I release factors.
abstract: Bacteria require two class-I release factors, RF1 and RF2, that recognize stop codons and promote peptide release from the ribosome. RF1 and RF2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. This scenario expects that the two RF gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. However, we here report two independent cases of conversion between RF1 and RF2 genes (RF1-RF2 gene conversion), which were severely examined by procedures incorporating the maximum-likelihood phylogenetic method. In both cases, RF1-RF2 gene conversion was predicted to occur in the region encoding nearly entire domain 3, of which functions are common between RF paralogues. Nevertheless, the 'direction' of gene conversion appeared to be opposite from one another-from RF2 gene to RF1 gene in one case, while from RF1 gene to RF2 gene in the other. The two cases of RF1-RF2 gene conversion prompt us to propose two novel aspects in the evolution of bacterial class-I release factors: (i) domain 3 is interchangeable between RF paralogues, and (ii) RF1-RF2 gene conversion have occurred frequently in bacterial genome evolution.
authors.affiliation: Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.|Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
authors.forename: Sohta A
authors.initials: SA
authors.lastname: Ishikawa
authors.affiliation: Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan.|Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan.
authors.forename: Ryoma
authors.initials: R
authors.lastname: Kamikawa
authors.affiliation: Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.|Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Inagaki
mesh_terms: D020816:Amino Acid Motifs; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001499:Bayes Theorem; D041862:Chloroflexi / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D010454:Peptide Termination Factors / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000145:classification / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000145:classification / Q000235:genetics; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D016963:Thermus thermophilus / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D010454:Peptide Termination Factors; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; C489005:prfA protein, E coli; C489006:prfB protein, E coli