title: S. cerevisiaeTrm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates.
abstract: The 3-methylcytidine (m3C) modification is ubiquitous in eukaryotic tRNA, widely found at C32in the anticodon loop of tRNAThr, tRNASer, and some tRNAArgspecies, as well as in the variable loop (V-loop) of certain tRNASerspecies. In the yeastSaccharomyces cerevisiae, formation of m3C32requires Trm140 for six tRNA substrates, including three tRNAThrspecies and three tRNASerspecies, whereas inSchizosaccharomyces pombe, two Trm140 homologs are used, one for tRNAThrand one for tRNASerThe occurrence of a single Trm140 homolog is conserved broadly among Ascomycota, whereas multiple Trm140-related homologs are found in metazoans and other fungi. We investigate here howS. cerevisiaeTrm140 protein recognizes its six tRNA substrates. We show that Trm140 has two modes of tRNA substrate recognition. Trm140 recognizes G35-U36-t6A37of the anticodon loop of tRNAThrsubstrates, and this sequence is an identity element because it can be used to direct m3C modification of tRNAPheHowever, Trm140 recognition of tRNASersubstrates is different, since their anticodons do not share G35-U36and do not have any nucleotides in common. Rather, specificity of Trm140 for tRNASeris achieved by seryl-tRNA synthetase and the distinctive tRNASerV-loop, as well as by t6A37and i6A37We provide evidence that all of these components are important in vivo and that seryl-tRNA synthetase greatly stimulates m3C modification of tRNASer(CGA)and tRNASer(UGA)in vitro. In addition, our results show that Trm140 binding is a significant driving force for tRNA modification and suggest separate contributions from each recognition element for the modification.
authors.affiliation: Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
authors.forename: Lu
authors.initials: L
authors.lastname: Han
authors.affiliation: Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Marcus
authors.affiliation: Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
authors.forename: Sonia
authors.initials: S
authors.lastname: D'Silva
authors.affiliation: Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
authors.forename: Eric M
authors.initials: EM
authors.lastname: Phizicky
mesh_terms: D000926:Anticodon / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D003562:Cytidine / Q000031:analogs & derivatives* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D008840:Microfilament Proteins / Q000235:genetics / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D014176:Protein Biosynthesis; D000072417:Protein Domains; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012362:RNA, Transfer, Ser / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012363:RNA, Transfer, Thr / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity; D012359:tRNA Methyltransferases / Q000235:genetics / Q000378:metabolism*
chemical_list: C110542:ABP140 protein, S cerevisiae; D000926:Anticodon; D008840:Microfilament Proteins; D012360:RNA, Transfer, Phe; D012362:RNA, Transfer, Ser; D012363:RNA, Transfer, Thr; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; C043208:3-methylcytidine; D003562:Cytidine; D012359:tRNA Methyltransferases
keywords: 3-methylcytidine; anticodon loop; methyltransferase; modification; specificity; tRNA