title: Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs.
abstract: Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNA is unusually variable among lepidosaurian reptiles. Phylogenetic and comparative analyses of cysteine tRNA gene sequences identify eight parallel losses of the D-stem, resulting in D-arm replacement loops. Sampling within the monophyletic Acrodonta provides no evidence for reversal. Slipped-strand mispairing of noncontiguous repeated sequences during replication or direct replication slippage can explain repeats observed within cysteine tRNAs that contain a D-arm replacement loop. These two mechanisms involving replication slippage can account for the loss of the cysteine tRNA D-stem in several lepidosaurian lineages, and may represent general mechanisms by which the secondary structures of mitochondrial tRNAs are altered.
authors.affiliation: Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
authors.forename: J R
authors.initials: JR
authors.lastname: Macey
authors.forename: A
authors.initials: A
authors.lastname: Larson
authors.forename: N B
authors.initials: NB
authors.lastname: Ananjeva
authors.forename: T J
authors.initials: TJ
authors.lastname: Papenfuss
mesh_terms: D000818:Animals; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D000077278:RNA, Mitochondrial; D012350:RNA, Transfer, Cys / Q000737:chemistry* / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D012104:Reptiles / Q000145:classification / Q000235:genetics; D017384:Sequence Deletion; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial; D000077278:RNA, Mitochondrial; D012350:RNA, Transfer, Cys; D012313:RNA