Nuclear identity specifies transcriptional initiation in plant mitochondria

Alterations in mitochondrial gene expression and abnormal floral phenotypes, such as male sterility, characterize alloplasmic plants having the nucleus from Nicotiana tabacum combined with the cytoplasm from Nicotiana repanda. In all Nicotiana species investigated the mitochondrial atpl gene is co-transcribed with the upstream orf274; however, unique for alloplasmic plants is a marked accumulation of these mitochondrial co-transcripts. In the present work, we show that a major component of the transcript difference is that in the alloplasmic male-sterile plants transcription initiates from novel sites internal to orf274. The sequences surrounding these initiation sites lack the CRTA consensus motif for plant mitochondrial promoters as well as similarity to other known plant mitochondrial promoters. Thus, initiation of transcription is under control of a mitochondrial promoter of a novel non-consensus type. This non-consensus promoter is inactivated when the fertility restoring heritable fragment chromosome from N. repanda is present in the N. tabacum nucleus of the alloplasmic plants. Our data suggest that the fertility-restoring fragment chromosome encodes a factor that represses initiation from this unusual promoter.