Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V

In Saccharomyces cerevisiae, subunit V of the inner mitochondrial membrane protein complex cytochrome c oxidase is encoded by two nonidentical genes, COX5a and COX5b. Both genes are present as single copies in S. cerevisiae and in several other Saccharomyces species. Nucleotide sequencing studies with the S. cerevisiae COX5 genes reveal that they encode proteins of 153 and 151 amino acids, respectively. Overall, the coding sequences of COX5a and COX5b have nucleotide and protein homologies of 67 and 66%, respectively. They are saturated for nucleotide substitutions that result in a synonomous codon, indicating a long divergence time between these two genes. Nucleotide sequences flanking the COX5a and COX5b coding regions exhibit no significant homology. The COX5a protein, pre-subunit Va, contains a 20-amino-acid leader peptide, whereas the COX5b protein, pre-subunit Vb, contains a 17-amino-acid leader peptide. These two leader peptides exhibit only 45% homology in the primary sequence, but have similar predicted secondary structures. By analyzing the RNA transcripts from both genes we have found that COX5a is a contiguous gene but that COX5b contains an intron. Surprisingly, the COX5b intron interrupts the AUG codon that initiates translation of the pre-subunit Vb polypeptide and contains a 5' donor splice sequence that differs from that normally found in yeast introns.