The absence of TGA codons in the DNA sequence of the Phytophthora megasperma gene for cytochrome c oxidase subunit II

Includes bibliographical references (pages [62]-69)Previous characterization of P. megasperma mitochondrial DNAs revealed two genic inversions between a host-specific and a nonspecific strain. As part of a characterization of oomycete mitochondrial genomes, studies of the nucleotide sequence of the region involving the COI-COII inversion were initiated. The COII genic region was localized, cloned and sequenced. The COII gene encodes a 258 amino acid protein with an approximate molecular weight of 29.6Kd. The data strongly suggests a lack of introns in this gene. The COI protein has been found to be encoded 235bp downstream from COII on the same strand. The translated COII amino acid sequence exhibits a greater than 50$ amino acid homology with other characterized eukaryotic COII proteins, being most homologous with those of plants. The two functionally conserved membrane-spanning helices and the putative copper-binding site, along with other conserved regions, have been identified in the protein. The genic region has an A-T content of 71$. Flanking regions contain 79$ and 90$ A-T contents. As expected for A-T-rich genomes, codon usage tables indicate a strong bias for the use of a third position A/T when choices exist. Of all codons within this gene, 85$ terminate in an A or T. Remarkably, however, all 7 Trp codons are TGG instead of the preferred TGA typical of all but plant mitochondria using a modified genetic code. This would lead to the conclusion that in Phytophthora mitochondrial DNA, TGA is either a stop codon, as it is in plant mitochondria, or an infrequently used trp codon.M.S. (Master of Science