DROSOPHILA MITOCHONDRIAL-DNA - CONSERVED SEQUENCES IN THE A+T-RICH REGION AND SUPPORTING EVIDENCE FOR A SECONDARY STRUCTURE MODEL OF THE SMALL RIBOSOMAL-RNA

The sequence of a segment of the Drosophila virilis mitochondrial DNA (mtDNA) molecule that contains the A+T-rich region, the small rRNA gene, the tRNAf-met, tRNAgln, and tRNAile genes, and the portions of the ND2 and tRNAval genes is presented and compared with the corresponding segment of the D. yakuba mtDNA molecule. The A+T-rich regions of D. virilis and D. yakuba contain two correspondingly located sequences of 49 and 276/274 nucleotides that appear to have been conserved during evolution. In each species the replication origin of the mtDNA molecule is calculated to lie within a region that overlaps the larger conserved sequence, and within a region this overlap is found a potential hairpin structure. Substitutions between the larger conserved sequences of the A+T-rich regions, the small mt-rRNA genes, and the ND2 genes are biased in favor of transversions, 71-97% of which are A .dblarw. T changes. There is a 13.8 times higher frequency of nucleotide differences between the 5'' halves than between the 3'' halves of the D. virilis and D. yakuba small mt-rRNA genes. Considerations of the effects of observed substitutions and deletion/insertions on possible nucleotide pairing within the small mt-rRNA genes of D. virilis and D. yakuba strongly support the secondary structure model for the Drosophila small mt-rRNA that we previously proposed.