Decoding Mechanism of Non-universal Genetic Codes in Loligo bleekeri Mitochondria

• Published in: The Journal of biological chemistry 2013-03, Vol.288 (11), p.7645-7652
• Main Authors: Ohira, Takayuki, Suzuki, Takeo, Miyauchi, Kenjyo, Suzuki, Tsutomu, Yokobori, Shin-ichi, Yamagishi, Akihiko, Watanabe, Kimitsuna
• Format: Article
• Language: English
• Subjects: Amino Acids - chemistry; Animals; Anticodon - genetics; Codon; Cytidine - genetics; Decoding Mechanism; Genetic Code; Loligo - genetics; Mass Spectrometry (MS); Mass Spectrometry - methods; Mitochondria; Mitochondria - metabolism; Models, Genetic; Non-universal Genetic Code; Nucleic Acid Conformation; Nucleosides - metabolism; Protein Structure, Secondary; Protein Synthesis; RNA; RNA - metabolism; RNA Modification; RNA, Mitochondrial; RNA, Transfer - metabolism; Transfer RNA (tRNA)
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M112.439554

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. tRNAMet(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 (τm5U) at the first position of the anticodon in tRNATrp(UGR). τm5U enables tRNATrp to decipher UGR codons as Trp. In addition, 5-taurinomethyl-2-thiouridine (τm5s2U) was found in mitochondrial tRNAs for Leu(UUR) and Lys in L. bleekeri. This is the first discovery of τm5U and τm5s2U in molluscan mitochondrial tRNAs. Background: Non-universal genetic codes are frequently found in animal mitochondrial decoding systems. Results: Five mitochondrial tRNAs from Loligo bleekeri were isolated and analyzed by mass spectrometry. Conclusion: AUA codon is deciphered as Met by CAU anticodon of tRNAMet(AUR), UGA codon is deciphered as Trp by τm5UCA anticodon of tRNATrp(UGR). Significance: AUA codon is deciphered by unmodified CAU anticodon through non-canonical A-C pairing.