Decoding mechanism of non-universal genetic codes in Loligo bleekeri mitochondria.
Non-universal genetic codes are frequently found in animal mitochondrial decoding systems. In squid mitochondria, four codons deviate from the universal genetic code, namely AUA, UGA, and AGA/AGG (AGR) for Met, Trp, and Ser, respectively. To understand the molecular basis for establishing the non-universal genetic code, we isolated and analyzed five mitochondrial tRNAs from a squid, Loligo bleekeri. Primary structures of the isolated tRNAs, including their post-transcriptional modifications, were analyzed by mass spectrometry. tRNA(Met)(AUR) possessed an unmodified cytidine at the first position of the anticodon, suggesting that the AUA codon is deciphered by CAU anticodon via non-canonical A-C pairing. We identified 5-taurinomethyluridine (τm(5)U) at the first position of the anticodon in tRNA(Trp)(UGR). τm(5)U enables tRNA(Trp) to decipher UGR codons as Trp. In addition, 5-taurinomethyl-2-thiouridine (τm(5)s(2)U) was found in mitochondrial tRNAs for Leu(UUR) and Lys in L. bleekeri. This is the first discovery of τm(5)U and τm(5)s(2)U in molluscan mitochondrial tRNAs.
Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Takayuki
T
Ohira
Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Takeo
T
Suzuki
Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Kenjyo
K
Miyauchi
Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. Electronic address: ts@chembio.t.u-tokyo.ac.jp.
Tsutomu
T
Suzuki
Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
Shin-Ichi
SI
Yokobori
Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
Akihiko
A
Yamagishi
Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Hyogo 679-5148, Japan. Electronic address: kim-wata@toyaku.ac.jp.
Kimitsuna
K
Watanabe
D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D000926:Anticodon / Q000235:genetics; D003062:Codon; D003562:Cytidine / Q000235:genetics; D005815:Genetic Code; D049834:Loligo / Q000235:genetics*; D013058:Mass Spectrometry / Q000379:methods; D008928:Mitochondria / Q000378:metabolism*; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000378:metabolism; D017433:Protein Structure, Secondary; D012313:RNA / Q000378:metabolism; D000077278:RNA, Mitochondrial; D012343:RNA, Transfer / Q000378:metabolism
D000596:Amino Acids; D000926:Anticodon; D003062:Codon; D009705:Nucleosides; D000077278:RNA, Mitochondrial; D003562:Cytidine; D012313:RNA; D012343:RNA, Transfer