Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes |
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| Authors: | Shuichi Asakawa Yoshinori Kumazawa Takeyoshi Araki Hyouta Himeno Kin-ichiro Miura Kimitsuna Watanabe |
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| Institution: | (1) Department of Industrial Chemistry, Faculty of Engineering, University of Tokyo, Hongo, Bunkyo-ku, 113 Tokyo, Japan;(2) Department of Biological Sciences, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, 227 Yokohama, Japan;(3) Institute of Space and Astronautical Science, 229 Sagamihara, Kanagawa, Japan;(4) Present address: Department of Molecular and Cell Biology, University of California, 94720 Berkeley, CA, USA |
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| Abstract: | Summary The gene organization of starfish mitochondrial DNA is identical with that of the sea urchin counterpart except for a reported inversion of an approximately 4.6-kb segment containing two structural genes for NADH dehydrogenase subunits 1 and 2 (ND 1 and ND 2). When the codon usage of each structural gene in starfish, sea urchin, and vertebrate mitochondrial DNAs is examined, it is striking that codons ending in T and G are preferentially used more for heavy strand-encoded genes, including starfish ND 1 and ND 2, than for light strand-encoded genes, including sea urchin ND 1 and ND 2. On the contrary, codons ending in A and Care preferentially used for the light strand-encoded genes rather than for the heavy strand-encoded ones. Moreover, G-U base pairs are more frequently found in the possible secondary structures of heavy strandencoded tRNAs than in those of light strand-encoded tRNAs. These observations suggest the existence of a certain constraint operating on mitochondrial genomes from various animal phyla, which results in the accumulation of G and T on one strand, and A and C on the other. |
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| Keywords: | Mitochondrial DNA Gene inversion Nucleotide composition bias Codon usage Starfish Sea urchin Echinoderm |
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