Structural basis of ribosomal RNA transcription regulation

Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) sigma (70) holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized alpha subunit carboxyl-terminal domains and scrunches the template DNA with the sigma finger and beta' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of sigma domain 2 that opens a gate for DNA loading and ejects sigma (1.1) from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to sigma (1.1) ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp. Ribosomal RNA (rRNA) expression is regulated at the initiation stage of RNA synthesis. Here, the authors report cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp on the way to open complex formation, identifying key steps in promoter recognition and opening.

Automated summary

The study reveals the cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp during open complex formation, providing insights into the key steps of promoter recognition and opening.