Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis.

Eunju Kwon,Shankar Raj Devkota,Dong Young Kim,Deepak Pathak,Pawan Dahal,Maria Sola

doi:10.1371/journal.pone.0221666

Abstract

Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter regions of genes, for the initiation of bacterial transcription. Multiple sigma factors in a bacterium selectively recognize their cognate promoter sequences, thereby inducing the expression of their own regulons. In this paper, we report the crystal structure of the σ4 domain of Bacillus subtilis SigW bound to the -35 promoter element. Purine-specific hydrogen bonds of the -35 promoter element with the recognition helix α9 of the σ4 domain occurs at three nucleotides of the consensus sequence (G-35, A-34, and G’-31 in G-35A-34A-33A-32C-31C-30T-29). The hydrogen bonds of the backbone with the α7 and α8 of the σ4 domain occurs at G’-30. These results elucidate the structural basis of the selective recognition of the promoter by SigW. In addition, comparison of SigW structures complexed with the -35 promoter element or with anti-sigma RsiW reveals that DNA recognition and anti-sigma factor binding of SigW are mutually exclusive.

Highlights

Transcription in bacteria is initiated by sigma factors, which recruit the core RNA polymerase to a cognate promoter [1, 2]
Diffraction data were collected at a resolution of 3.1 Å (Table 1), and the structure was determined by molecular replacement using the structure of a truncated E. coli σE4/-35E
Residues 134–186 of SigW and 11 nucleotide pairs of -35W were traced into the electron density (S1 Fig) and the final structure was refined at R / Rfree values of 24.8 / 29.0% (Table 1). σW4 is comprised of four α-helices (α6–α9) in the crystal structure of the SigW/

Summary

Introduction

Transcription in bacteria is initiated by sigma factors, which recruit the core RNA polymerase to a cognate promoter [1, 2]. Sigma factors selectively recognize promoter elements, -10 and -35 elements, and additional sequences, including extended -10 element and discriminator, which are present upstream of the transcription start site [3, 4]. The -10 element is strand-separated to form a transcription bubble [5, 6], whereas the -35 element is recognized by a helix-turn-helix (HTH) motif in the sigma factor, without strand separation [7, 8]. Group I sigma factors are composed of σ1.1, σ2, σ3, and σ4 domains, which are responsible for the recognition of the discriminator, -10, extended -10, and -35 elements, respectively. The primary sigma factors, which regulate the transcription of housekeeping genes, belong to group I.

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Conclusion