Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase

De Wijngaert, Brent; Sultana, Shemaila; Dharia, Chhaya; Vanbuel, Hans; Shen, Jiayu; Vasilchuk, Daniel; Martinez, Sergio E.; Kandiah, Eaazhisai; Patel, Smita S.; Das, Kalyan

Cryo-EM structures of transcription pre-initiation complex (PIC) and initiation complex (IC) of yeast mitochondrial RNA polymerase show fully resolved transcription bubbles and explain promoter melting, template alignment, DNA scrunching, transition into elongation, and abortive synthesis. Promoter melting initiates in PIC with MTF1 trapping the −4 to −2 non-template (NT) bases in its NT-groove. Transition to IC is marked by a large-scale movement that aligns the template with RNA at the active site. RNA synthesis scrunches the NT strand into an NT-loop, which interacts with centrally positioned MTF1 C-tail. Steric clashes of the C-tail with RNA:DNA and NT-loop, and dynamic scrunching-unscrunching of DNA explain abortive synthesis and transition into elongation. Capturing the catalytically active IC-state with UTPαS poised for incorporation enables modeling toxicity of antiviral nucleosides/nucleotides.