title: Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes.
abstract: 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 C are 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 strand-encoded 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.
authors.affiliation: Department of Industrial Chemistry, Faculty of Engineering, University of Tokyo, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Asakawa
authors.forename: Y
authors.initials: Y
authors.lastname: Kumazawa
authors.forename: T
authors.initials: T
authors.lastname: Araki
authors.forename: H
authors.initials: H
authors.lastname: Himeno
authors.forename: K
authors.initials: K
authors.lastname: Miura
authors.forename: K
authors.initials: K
authors.lastname: Watanabe
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001001:Anura; D001482:Base Composition; D001483:Base Sequence; D002645:Chickens; D003062:Codon; D004261:DNA Replication; D004272:DNA, Mitochondrial / Q000737:chemistry*; D004330:Drosophila; D005796:Genes; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D012343:RNA, Transfer / Q000737:chemistry; D013215:Starfish / Q000235:genetics*
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial; D012343:RNA, Transfer