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TitleCryo-EM structure of σ RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation.
Journal, issue, pagesJ Biol Chem, Vol. 293, Issue 19, Page 7367-7375, Year 2018
Publish dateMay 11, 2018
AuthorsAnoop Narayanan / Frank S Vago / Kunpeng Li / M Zuhaib Qayyum / Dinesh Yernool / Wen Jiang / Katsuhiko S Murakami /
PubMed AbstractFirst step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP ...First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP holoenzyme to express housekeeping genes. The σ contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the RNAP σ holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σ and promoter DNA just upstream of the -10 element, which was not observed in a previously determined RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σ and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.
External linksJ Biol Chem / PubMed:29581236 / PubMed Central
MethodsEM (single particle)
Resolution4.25 - 5.75 Å
Structure data

7438

6c9y

EMDB-7438, PDB-6c9y:
Cryo-EM structure of E. coli RNAP sigma70 holoenzyme
Method: EM (single particle) / Resolution: 4.25 Å

7439

6ca0

EMDB-7439, PDB-6ca0:
Cryo-EM structure of E. coli RNAP sigma70 open complex
Method: EM (single particle) / Resolution: 5.75 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • Escherichia coli (E. coli)
  • escherichia coli (strain k12) (bacteria)
KeywordsTRANSCRIPTION / Escherichia coli / RNA polymerase / transcription/dna / transcription-dna complex

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