Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization

Zakia Morichaud, Stefano Trapani, Rishi K. Vishwakarma, Laurent Chaloin, Corinne Lionne, Joséphine Lai-Kee-Him, Patrick Bron () and Konstantin Brodolin ()
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Zakia Morichaud: Univ Montpellier, CNRS
Stefano Trapani: Univ Montpellier, CNRS, INSERM
Rishi K. Vishwakarma: Univ Montpellier, CNRS
Laurent Chaloin: Univ Montpellier, CNRS
Corinne Lionne: Univ Montpellier, CNRS, INSERM
Joséphine Lai-Kee-Him: Univ Montpellier, CNRS, INSERM
Patrick Bron: Univ Montpellier, CNRS, INSERM
Konstantin Brodolin: Univ Montpellier, CNRS

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σB factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σB is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation.

Date: 2023
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DOI: 10.1038/s41467-023-36113-y

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