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Characterisation of a transitionally occupied state of domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis
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  • Dávid Tužinčin,
  • Petr Padrta,
  • Kateřina Bendová,
  • Libor Krásný,
  • Lukas Zidek,
  • Pavel Kadeřávek
Dávid Tužinčin
National Centre for Biomolecular Research

Corresponding Author:[email protected]

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Petr Padrta
Stredoevropsky technologicky institut
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Kateřina Bendová
National Centre for Biomolecular Research
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Libor Krásný
Akademie ved Ceske republiky
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Lukas Zidek
National Centre for Biomolecular Research
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Pavel Kadeřávek
Stredoevropsky technologicky institut
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Abstract

σ factors are essential parts of bacterial RNA polymerase (RNAP) as they allow to recognize promotor sequences and initiate transcription. Domain 1.1 of vegetative σ factors occupies the primary channel of RNAP and also prevents binding of the σ factor to promoter DNA alone. Here, we show that domain 1.1 of Bacillus subtilis σ A exists in two structurally distinct variants in dynamic equilibrium. The major conformation at room temperature is represented by a previously reported well-folded structure solved by nuclear magnetic resonance (NMR), but 4% of the protein molecules are present in a less thermodynamically favorable state. We show that this population increases with temperature and may represent as much as 20% at 43.5C. We characterized the minor state of the domain 1.1 using specialized methods of NMR. We found that, in contrast to the major state, the detected minor state is partially unfolded. Its propensity to form secondary structure elements is especially decreased for the first and third α helices, while the second α helix and β strand close to the C-terminus are more stable. In summary, this study reveals conformational dynamics of domain 1.1 and provides a basis for studies of its interaction with RNAP and effects on transcription regulation.
27 Jul 2022Submitted to PROTEINS: Structure, Function, and Bioinformatics
28 Jul 2022Submission Checks Completed
28 Jul 2022Assigned to Editor
03 Oct 2022Reviewer(s) Assigned
27 Oct 2022Review(s) Completed, Editorial Evaluation Pending
27 Oct 2022Editorial Decision: Revise Major
23 Dec 20221st Revision Received
26 Dec 2022Submission Checks Completed
26 Dec 2022Assigned to Editor
26 Dec 2022Review(s) Completed, Editorial Evaluation Pending
26 Dec 2022Reviewer(s) Assigned
02 Jan 2023Editorial Decision: Revise Major
17 Mar 20232nd Revision Received
20 Mar 2023Submission Checks Completed
20 Mar 2023Assigned to Editor
20 Mar 2023Review(s) Completed, Editorial Evaluation Pending
20 Mar 2023Reviewer(s) Assigned
06 Apr 2023Editorial Decision: Revise Minor
08 May 20233rd Revision Received
08 May 2023Submission Checks Completed
08 May 2023Assigned to Editor
08 May 2023Review(s) Completed, Editorial Evaluation Pending
10 May 2023Editorial Decision: Accept