Structure and expression of the rice mitochondrial apocytochrome b gene (cob-1) and pseudogene (cob-2)

Rice mitochondrial DNA contains an intact copy and a pseudogene copy of a apocytochrome b gene (cob-1 and cob-2, respectively). Using primer extension and capping analyses, the transcriptional start site has been mapped; an 11-base motif at the transcription start site closely matches the consensus promoter motifs proposed for maize, wheat and soybean mitochondrial genes. Although both copies are identical in the 5' upstream region and through most of the coding region, only cob-1-specific mRNA is detected on RNA gel-blots. Run-on transcription analysis indicates, however, that both cob-1 and cob-2 mRNAs are synthesized in vivo but less cob-2 is accumulated. At its mapped 3' terminus the cob-1 transcript possesses a sequence that could fold into a double stem-loop structure. The possible roles of a double stem-loop structure in mitochondrial gene expression are discussed.