Mechanisms of mitochondrial promoter recognition in humans and other mammalian species

Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.

Automated summary

Recognition of mammalian mitochondrial promoters is achieved through the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. This study provides insights into the heterogeneity of mitochondrial transcripts and accurately identifies the transcription start sites (TSS) of mammalian and other vertebrate species. The divergent structure of mammalian promoters reveals new aspects of mtDNA evolution and the precise register of the DNA in the initiation complex. The findings also shed light on the molecular basis of promoter recognition and the role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.