The σ Subunit-Remodeling Factors: An Emerging Paradigms of Transcription Regulation

Abstract

Transcription initiation is a key checkpoint and highly regulated step of gene expression. The sigma (σ) subunit of RNA polymerase (RNAP) controls all transcription initiation steps, from recognition of the -10/-35 promoter elements, upon formation of the closed promoter complex (RPc), to stabilization of the open promoter complex (RPo) and stimulation of the primary steps in RNA synthesis. The canonical mechanism to regulate σ activity upon transcription initiation relies on activators that recognize specific DNA motifs and recruit RNAP to promoters. This mini-review describes an emerging group of transcriptional regulators that form a complex with σ or/and RNAP prior to promoter binding, remodel the σ subunit conformation, and thus modify RNAP activity. Such strategy is widely used by bacteriophages to appropriate the host RNAP. Recent findings on RNAP-binding protein A (RbpA) from Mycobacterium tuberculosis and Crl from Escherichia coli suggest that activator-driven changes in σ conformation can be a widespread regulatory mechanism in bacteria.

Keywords: RNAP-binding transcriptional regulators; RbpA; Tuberculosis; promoter specificity; sigma subunit conformational dynamics.

FIGURE 1

The RNAP-binding σ-regulators and their interaction with RNAP. (A) Scheme of the main steps in transcription initiation. The steps regulated by RNAP-binding transcription factors (RPB-TFs) and DNA-binding transcription factors (DB-TFs) are indicated. (B) Basal promoter architecture (first described in E. coli) and interaction of its key elements with σ-domains. (C) Domain organization of the principal σ subunits and RbpA. NCR – non-conserved region, NTT – N-terminal tail, RCD – RbpA core domain, BL – basic linker, SID – σ-interacting domain. Alignment of the σ subunits from E. coli (Eco), M. tuberculosis (Mtb), C. crescentus (Ccr), C. trachomatis (Ctr), and T. thermophilus (Tth). Amino acid residues implicated in contacts with activators (bottom) are shown in color. (D) Schematic presentation of the RNAP holoenzyme structure with the binding sites for the activators and repressors targeting domains σ2 and σ4, respectively.

FIGURE 2

Regulation of the σ subunit conformational states by RbpA and Gp39. (A) Model representing the mechanism of RbpA–driven transcription activation in Mycobacteria sp. At the bottom, the histograms show the smFRET efficiencies (E_PR) distributions for the double–labeled σ^B subunit in the RNAP holoenzyme without (left) and with RbpA (right) (data from Vishwakarma et al., 2018). (B) Model representing the mechanism of gp39-driven transcription repression in T. thermophilus. (C) Structure of the MtbRNAP-σ^A RPo in complex with RbpA [Protein Data Bank (PDB) code: 6EDT]. (D) Structure of the Tht RNAP-σ^A RPo in complex with gp39 [Protein Data Bank (PDB) code: 3WOD]. The dimension lines show distances between Cα atoms of homologous residues in domain σ2 (Mtb T356, Tht N248) and domain σ4 (Mtb G497, Tht G391).