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Structure paper

TitleStructures and mechanism of transcription initiation by bacterial ECF factors.
Journal, issue, pagesNucleic Acids Res, Vol. 47, Issue 13, Page 7094-7104, Year 2019
Publish dateJul 26, 2019
AuthorsChengli Fang / Lingting Li / Liqiang Shen / Jing Shi / Sheng Wang / Yu Feng / Yu Zhang /
PubMed AbstractBacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure ...Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE-the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.
External linksNucleic Acids Res / PubMed:31131408 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.903 - 4.02 Å
Structure data

9792

6jbq

EMDB-9792, PDB-6jbq:
CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA
Method: EM (single particle) / Resolution: 4.02 Å

PDB-6jcx:
Mycobacterium tuberculosis transcription initiation complex with ECF sigma factor sigma H and 6nt RNA
Method: X-RAY DIFFRACTION / Resolution: 2.903 Å

PDB-6jcy:
Mycobacterium tuberculosis RNA polymerase transcription initiation open complex with a chimeric ECF sigma factor sigH/E
Method: X-RAY DIFFRACTION / Resolution: 3.106 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • Escherichia coli K-12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
  • synthetic construct (others)
  • mycobacterium tuberculosis h37rv (bacteria)
KeywordsTRANSCRIPTION/DNA/RNA / RNA polymerase / Extra-Cytoplasmic Function sigma factors / sigmaE / transcription initiation / TRANSCRIPTION-DNA-RNA complex / TRANSCRIPTION / Mycobacterium tuberculosis / sigma H / open complex / sigma H/E

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