We have previously shown that cytoplasmic male sterility in sunflower is associated with the insertion into the mitochondrial DNA of a novel open reading frame (ORF) located 3' to the atpA gene. Here, we show that in mitochondria from the sterile line, this novel ORF (ORF522) is cotranscribed with atpA. We have identified the product of the ORF522 as being a 15 kDa protein previously observed in sterile plant mitochondria by in organello translation. Both Western blot analysis and in organello translation assays show reduced levels of the 15 kDa polypeptide upon restoration of fertility. Interestingly, this reduction is tissue specific since it is only observed in the male florets from restored hybrid plants. These results suggest that the 15 kDa novel polypeptide is probably responsible for the CMS phenotype. Northern blot analysis using RNA from both seedlings and male florets shows a flower-specific reduction in the level of the ORF522 transcript in the restored hybrid line. The reduction is not due to a reduced transcription rate as demonstrated by 'run-on' experiments using mitochondria isolated from male florets. This suggests that the product of the nuclear restorer gene acts at the post-transcriptional level to destabilize the novel mitochondrial transcript in a tissue-specific manner and restore male fertility.