Mechanisms of mitochondrial promoter recognition in humans and other mammalian species

Abstract

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.

35 Years of TFAM Research: Old Protein, New Puzzles

“…This maxim notwithstanding, nucleoids with little or no TFAM staining have been observed in many studies [ 75 , 89 , 93 , 94 , 95 ], thus leaving open the possibility that conditions for TFAM-independent transcription could be available in vivo. The sequential model of mitochondrial transcription ( Figure 6 ) derived from in vitro and structural studies postulates that the first step in transcription initiation is TFAM binding upstream of mitochondrial promoters (region −36 to −17 nucleotides upstream of the TSS) [ 42 , 108 , 109 ].…”

“…The sequential model of mitochondrial transcription initiation posits that the initiating event in the assembly of transcription complexes is TFAM binding upstream of mitochondrial promoters [ 14 , 35 , 38 , 108 ]. Structural studies indicate that TFAM binding to HSP1 promoter DNA alone [ 50 ] is opposite to that found in open transcription complexes at the same promoter [ 42 ].…”

Irisin: A Potentially Fresh Insight into the Molecular Mechanisms Underlying Vascular Aging

“…Irisin treatment markedly increased the mitochondrial number and ATP synthesis in LPS-treated ECs. Additionally, irisin may maintain the integrity of the endothelial barrier by enhancing AMPK/PGC-1α signaling, which in turn causes Nrf and its downstream receptor, Tfam, to be expressed [102,103], thereby enhancing mitochondrial biogenesis [101]. AMPK activation can promote the expression of UCP2, which prevents hyperglycemic ECs from producing superoxide radicals and protects blood vessels.…”

Key Amino Acid Residues of Mitochondrial Transcription Factor A Synergize with Abasic (AP) Site Dynamics To Facilitate AP-Lyase Reactions

“…In addition, mitochondrial transcription factor A (TFAM) has emerged as a new player in mtDNA turnover. − As a key mtDNA-packaging protein, TFAM organizes mtDNA into DNA-protein complexes known as nucleoids . In addition, TFAM is an essential factor in mtDNA transcription activation. , Recently, TFAM has been shown to cleave DNA molecules containing abasic (AP) sites in vitro and in cells, , arguing its role in damaged mtDNA turnover. AP sites are one of the most abundant DNA lesions in mtDNA and nDNA, present at a level of 1 AP lesion/10 5 –10 6 nt …”

“…23 In addition, TFAM is an essential factor in mtDNA transcription activation. 24,25 Recently, TFAM has been shown to cleave DNA molecules containing abasic (AP) sites in vitro and in cells, 20,21 arguing its role in damaged mtDNA turnover. AP sites are one of the most abundant DNA lesions in mtDNA and nDNA, present at a level of 1 AP lesion/10 5 −10 6 nt.…”