title: Transfer RNAs with novel cloverleaf structures.
abstract: We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter T-stem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide. In Acidobacteria, tRNAs with 8/4 and 9/3 structures may function as missense and nonsense suppressor tRNAs and/or regulatory noncoding RNAs. In δ-proteobacteria, an additional cysteine tRNA with an 8/4 structure mimics selenocysteine tRNA and may function as opal suppressor. We examined the potential translation function of suppressor tRNA species in Escherichia coli; tRNAs with 8/4 or 9/3 structures efficiently inserted serine, alanine and cysteine in response to stop and sense codons, depending on the identity element and anticodon sequence of the tRNA. These findings expand our view of how tRNA, and possibly the genetic code, is diversified in nature.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA.
authors.forename: Takahito
authors.initials: T
authors.lastname: Mukai
authors.affiliation: Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA.
authors.forename: Oscar
authors.initials: O
authors.lastname: Vargas-Rodriguez
authors.affiliation: Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Englert
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: H James
authors.initials: HJ
authors.lastname: Tripp
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA.|Department of Chemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: Dieter
authors.initials: D
authors.lastname: Söll
mesh_terms: D000926:Anticodon; D001419:Bacteria / Q000235:genetics; D001427:Bacterial Toxins / Q000235:genetics; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012329:RNA, Bacterial / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*; D012345:RNA, Transfer, Amino Acid-Specific / Q000737:chemistry; D012350:RNA, Transfer, Cys / Q000737:chemistry / Q000378:metabolism
chemical_list: D000926:Anticodon; D001427:Bacterial Toxins; D012329:RNA, Bacterial; D012345:RNA, Transfer, Amino Acid-Specific; D012350:RNA, Transfer, Cys; C036928:tRNA, selenocysteine-; D012343:RNA, Transfer