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Nature communications
01 22, 2021;12 (1): 528.

Structural basis of ribosomal RNA transcription regulation.

Yeonoh Shin, M Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy, Katsuhiko S Murakami
Author Information
  1. Yeonoh Shin: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA. ORCID
  2. M Zuhaib Qayyum: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA.
  3. Danil Pupov: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia. ORCID
  4. Daria Esyunina: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
  5. Andrey Kulbachinskiy: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia. ORCID
  6. Katsuhiko S Murakami: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA. kum14@psu.edu. ORCID
PMID: 33483500 DOI: 10.1038/s41467-020-20776-y

Abstract

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) σ 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 σ from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.

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Grants

  1. R01 GM087350/NIGMS NIH HHS
  2. R35 GM131860/NIGMS NIH HHS

MeSH Term

Cryoelectron Microscopy
DNA, Bacterial
DNA-Directed RNA Polymerases
Escherichia coli
Escherichia coli Proteins
Gene Expression Regulation, Bacterial
Guanosine Tetraphosphate
Holoenzymes
Promoter Regions, Genetic
Protein Conformation
RNA, Bacterial
RNA, Ribosomal
Sigma Factor
Transcription Initiation Site
Transcription, Genetic

Chemicals

DNA, Bacterial
Escherichia coli Proteins
Holoenzymes
RNA, Bacterial
RNA, Ribosomal
Sigma Factor
dksA protein, E coli
Guanosine Tetraphosphate
RNA polymerase sigma 70
DNA-Directed RNA Polymerases
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
Article has an altmetric score of 68

Word Cloud

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