, Volume 22, Issue 3, pp 252-271

The mitochondrial DNA molecule ofDrosophila yakuba: Nucleotide sequence, gene organization, and genetic code

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Summary

The sequence of the 16,019 nucleotide-pair mitochondrial DNA (mtDNA) molecule ofDrosophila yakuba is presented. This molecule contains the genes for two rRNAs, 22 tRNAs, six identified proteins [cytochrome b, cytochrome c oxidase subunits I, II, and III (COI-III), and ATPase subunits 6 and 8] and seven presumptive proteins (URF1-6 and URF4L). Replication originates within a region of 1077 nucleotides that is 92.8% A+T and lacks any open reading frame larger than 123 nucleotides. An equivalent to the sequence found in all mammalian mtDNAs that is associated with initiation of second-strand DNA synthesis is not present inD. yakuba mtDNA. Introns are absent fromD. yakuba mitochondrial genes and there are few (0–31) intergenic nucleotides. The genes found inD. yakuba and mammalian mtDNAs are the same, but there are differences in their arrangement and in the relative proportions of the complementary strands of the molecule that serve as templates for transcription. Although theD. yakuba small and large mitochondrial rRNA genes are exceptionally low in G and C and are shorter than any other metazoan rRNA genes reported, they can be folded into secondary structures remarkably similar to the secondary structures proposed for mammalian mitochondrial rRNAs.D. yakuba mitochondrial tRNA genes, like their mammalian counterparts, are more variable in sequence than nonorganelle tRNAs. In mitochrondrial protein genes ATG, ATT, ATA, and in one case (COI) ATAA appear to be used as translation initiation codons. The only termination codon found in these genes is TAA. In theD. yakuba mitochondrial genetic code, AGA, ATA, and TGA specify serine, isoleucine, and tryptophan, respectively. Fifty-nine types of sense codon are used in theD. yakuba mitochondrial protein genes, but 93.8% of all codons end in A or T. Codon-anticodon interactions may include both G-A and C-A pairing in the wobble position. Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in theD. yakuba mtDNA molecule where these nucleotides are compatible with function.