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Nucleic Acids Research, 1994, Vol. 22, No. 24 5378-5384
© 1994

Articles

Higher-order structure of bovine mitochondrial tRNASerUGA: chemical modification and computer modeling

Yoh-ichi Watanabe+,, Gota Kawai, Takashi Yokogawa1,§, Nobuhiro Hayashi1,ø, Yoshinori Kumazawa1,¶, Takuya Ueda, Kazuya Nishikawa1, Ichiro Hirao1,{ddagger}, Kin-ichiro Miura#, and Kimitsuna Watanabe1,*

Department of Chemistry and Biotechnology, Faculty of Engineering, University of Tokyo Hongo, Tokyo 113 1Department of Biological Sciences, Faculty of Bioscience and Biotechnology Tokyo Institute of Technology, Nagatsuta, Yokohama 227, Japan

*To whom correspondence should be addressed

+Present addresses. Biotechnology Center, Insuwte for Medical Research, Jalan Paliang, 50588 Kuala Lumpur, Malaysia

§Laboratonum für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany

Ølnstnutc for Comprehensive Medical Science. Fujita Health University. Toyoake. Atchi 470-11

¶Department of Earth and Planetaiy Sciences, School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-01.

{ddagger}Luboratory of Pharmaceutical Chemistiy, Tokyo College of Pharmacy, Horinouclu, Hachioji, Tokyo 192-03

#Institute for Bionxilecular Science, Gakushum University. Mejiro. Toshinia-ku, Tokyo 113, Japan

Received August 5, 1994. Revised October 31, 1994. Accepted November 8, 1994.

On the basis of enzymatic probing and phylogenetlc comparison, we have previously proposed that mammalian mitochondrial tRNAsSer (anticodon UGA) possess a slightly altered cloverleaf structure In which only one nucleotide exists between the acceptor stem and D stem (usually two nucleotides) and the anticodon stem consists of six base pairs (usually five base pairs) [Yokogawa et al. (1991) Nucleic Acids Res. 19, 6101-6105]. To ascertain whether such tRNAsSer can be folded Into a normal L-shaped tertiary structure, the higher-order structure of bovine mitochondrial tRNASerUGA was examined by chemical probing using dimethylsulfate and dlethylpyrocarbonate, and on the basis of the results a tertiary structure model was obtained by computer modeling. It was found that a one-base-pair elongation In the anticodon stem was compensated for by multiple-base deletions In the D and extra loop regions of the tRNASerUGA, which resulted In preservation of an L-shaped tertiary structure similar to that of conventional tRNAs. By summarizing the findings, the general structural requirements of mitochondrial tRNAs necessary for their functioning in the mitochondrial translation system are considered.


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