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Structural analysis of the role of the two conserved motifs of the ECF41 family sigma factor in the autoregulation of its own promoter in Azospirillum brasilense Sp245
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  • Ekta Pathak,
  • AshutoshPrakash Dubey,
  • Vijay Shankar Singh,
  • Rajeev Mishra,
  • Anil Kumar Tripathi
Ekta Pathak
Banaras Hindu University Faculty of Science

Corresponding Author:ektavpathak@gmail.com

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AshutoshPrakash Dubey
Banaras Hindu University Faculty of Science
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Vijay Shankar Singh
Banaras Hindu University Faculty of Science
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Rajeev Mishra
Banaras Hindu University Faculty of Science
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Anil Kumar Tripathi
Banaras Hindu University Faculty of Science
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Abstract

In Azospirillum brasilense, an extra-cytoplasmic function sigma factor (RpoE10) shows the characteristic 119 amino acid long C-terminal extension found in ECF41-type sigma factors, which possesses three conserved motifs (WLPEP, DGGGR, and NPDKV), one in the linker region between the sigma 2 and sigma 4, and the other two in the SnoaL_2 domain of the C-terminal extension. Here, we have described the role of the two conserved motifs in the SnoaL_2 domain of RpoE10 in the inhibition and activation of its activity, respectively. Truncation of the distal part of the C-terminal sequence of the RpoE10 (including NPDKV but excluding the DGGGR motif) results in its promoter’s activation suggesting autoregulation. Further truncation of the C-terminal sequence up to its proximal part, including NPDKV and DGGGR motif, abolished promoter activation. Replacement of NPDKV motif with NAAAV in RpoE10 increased its ability to activate its promoter, whereas replacement of DGGGR motif led to reduced promoter activation. We have explored the dynamic modulation of sigma2 – sigma4 domains and the relevant molecular interactions mediated by the two conserved motifs of the SnoaL2 domain using molecular dynamics simulation. The analysis enabled us to explain that the NPDKV motif located distally in the C-terminus negatively impacts transcriptional activation. In contrast, the DGGGR motif found proximally of the C-terminal extension is required to activate RpoE1
16 Sep 2021Submitted to PROTEINS: Structure, Function, and Bioinformatics
16 Sep 2021Submission Checks Completed
16 Sep 2021Assigned to Editor
18 Sep 2021Reviewer(s) Assigned
10 Nov 2021Review(s) Completed, Editorial Evaluation Pending
16 Nov 2021Editorial Decision: Revise Major
21 Apr 20221st Revision Received
22 Apr 2022Submission Checks Completed
22 Apr 2022Assigned to Editor
22 Apr 2022Reviewer(s) Assigned
05 May 2022Review(s) Completed, Editorial Evaluation Pending
10 May 2022Editorial Decision: Accept