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Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18923-18927. doi: 10.1073/pnas.1910827116. Epub 2019 Sep 4.

Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase.

Author information

1
Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY 10065.
2
Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065.
3
Department of Bacteriology, University of Wisconsin, Madison, WI 53706.
4
Pharmaceutical Sciences Division, University of Wisconsin, Madison, WI 53706.
5
Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706.
6
Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065; darst@rockefeller.edu.

Abstract

In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ-factors are negatively regulated by anti-σ-factors. In Escherichia coli, Salmonella enterica, and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σS-regulon by promoting the association of σS with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σS-RNAP in an open promoter complex with a σS-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σSS 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP β'-subunit that we call the β'-clamp-toe (β'CT). Deletion of the β'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β'CT interaction. We conclude that Crl activates σS-dependent transcription in part through stabilizing σS-RNAP by tethering σS 2 and the β'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators.

KEYWORDS:

Crl; RNA polymerase; RpoS; bacterial stress response; cryo-electron microscopy

PMID:
31484766
DOI:
10.1073/pnas.1910827116

Conflict of interest statement

The authors declare no conflict of interest.

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