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TitleHuman mitochondrial RNA polymerase structures reveal transcription start site and slippage mechanism.
Journal, issue, pagesMol Cell, Vol. 85, Issue 16, Page 3137-33150.e7, Year 2025
Publish dateAug 21, 2025
AuthorsJiayu Shen / Quinten Goovaerts / Yogeeshwar Ajjugal / Brent De Wijngaert / Kalyan Das / Smita S Patel /
PubMed AbstractTranscription of the human mitochondrial DNA is initiated by POLRMT and initiation factors mitochondrial transcription factor A (TFAM) and mitochondrial transcription factor B2 (TFB2M). We present ...Transcription of the human mitochondrial DNA is initiated by POLRMT and initiation factors mitochondrial transcription factor A (TFAM) and mitochondrial transcription factor B2 (TFB2M). We present cryo-electron microscopy (cryo-EM) structures of three transcription initiation intermediates (pre-catalytic IC3 [pre-IC3], slipped-IC3, and slipped pre-IC4) catalyzing RNA synthesis by normal and slippage pathways with fully resolved transcription bubbles and RNA transcripts starting from the +1 or -1 position. The structural and biochemical studies reveal mechanisms of promoter melting, start site selection, and slippage synthesis. Promoter melting begins at -4 with base-specific interactions of template -4 and -3 guanines with POLRMT and non-template -1 adenine with TFB2M. The NT-stabilizing loop (KLDPRSGGVIKPP) and Y209 of TFB2M and W1026 of POLRMT interact with the non-template strand to guide initiation from the +1 start site. The -1 position is not an alternative start site but supports slippage initiation by base-pairing with a slipped or rebound 2-nt RNA. Cryo-EM resolved additional apo and dimeric complexes whose populations may regulate transcription initiation.
External linksMol Cell / PubMed:40712586 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.5 Å
Structure data

51727

9gzm

EMDB-51727, PDB-9gzm:
Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a 2-mer RNA (pppGpA) and GTP poised for catalysis (pre-IC3)
Method: EM (single particle) / Resolution: 3.4 Å

51728

9gzn

EMDB-51728, PDB-9gzn:
Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFB2M/DNA/RNA) without TFAM; and with a 2-mer RNA (pppGpA) and GTP poised for catalysis (pre-IC3-TFAM)
Method: EM (single particle) / Resolution: 3.5 Å

51729

9gzo

EMDB-51729, PDB-9gzo:
Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFB2M/DNA/RNA) without TFAM; and with a slipped 3-mer RNA, pppGpGpA (slipped IC3-TFAM)
Method: EM (single particle) / Resolution: 3.15 Å

53853

9r95

EMDB-53853, PDB-9r95:
Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA, pppGpGpA (slipped IC3)
Method: EM (single particle) / Resolution: 3.2 Å

53854

9r96

EMDB-53854, PDB-9r96:
Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a slipped 3-mer RNA (pppGpGpA) and GTP poised for catalysis (slipped pre-IC4)
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / POLRMT / TFB2M / TFAM / transcription initiation / polymerase / h-mtRNAP / mtRNAP / RNA polymerase / mitochondrial DNA / mitochondria / slippage / human mitochondrial RNA polymerase / y-mtRNAP / MTF1 / RPO41 / DNA transcription / initiation / mitochondrial / DNA / RNA / RNAP

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