Genomic context influences the activity of maize mitochondrial cox2 promoters

Plant mitochondrial genomes are highly recombinogenic, with a variety of sp ecies specific direct and inverted repeats leading to irt vivo accumulation of multiple DNA forms. In maize, the cox2 gene, which encodes subunit II o f cytochrome c oxidase, lies immediately downstream of a 0.7-kilobase direc t repeat, which is present in two copies in the 570-kilobase master chromos ome. Promoters for cox2 exist upstream of both of these copies, in regions we have termed A and B. Three region B promoters are active for cox2 transc ription in the master chromosome, whereas two region A promoters are active for cox2 transcription after recombination across the direct repeats. We h ave measured the proportion of genomes carrying region A or B upstream of c ox2 in maize seedlings and found a ratio of approximately 1:6. Promoter str ength, based on run-on transcription assays, shows a ratio of 1:4 for regio n A to region B promoters. These data allowed us to predict the relative co ntributions of region A and B to mitochondrial transcript accumulation, bas ed on a simple product of genome-form abundance and promoter strength. When promoter use was determined by using quantitative reverse transcriptase-PC R, however, we found that region A promoters were used at an unexpectedly h igh rate when upstream of cox2 and used less than expected when not upstrea m of cox2. Thus, the use of this set of promoters seems to respond to genom ic context. These results suggest a role for intragenomic and intergenomic recombination in regulating plant mitochondrial gene expression.