Structural basis of ribosomal RNA transcription regulation.
Yeonoh ShinM Zuhaib QayyumDanil PupovDaria EsyuninaAndrey KulbachinskiyKatsuhiko S MurakamiPublished in: Nature communications (2021)
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) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.
Keyphrases
- transcription factor
- electron microscopy
- single molecule
- circulating tumor
- dna binding
- nucleic acid
- cell free
- structural basis
- dna methylation
- escherichia coli
- gene expression
- minimally invasive
- high resolution
- climate change
- circulating tumor cells
- oxidative stress
- staphylococcus aureus
- stress induced
- mass spectrometry
- molecular dynamics simulations
- binding protein
- loop mediated isothermal amplification
- protein kinase
- heat shock protein
- sensitive detection
- quantum dots