The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription

Abstract

The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure of a B. subtilis transcription activation complex comprising B. subtilis six-subunit (2αββ‘ωε) RNA Polymerase (RNAP) core enzyme, σA, a promoter DNA, and the ligand-bound B. subtilis BmrR, a prototype of MerR-family TFs. The structure reveals that RNAP and BmrR recognize the upstream promoter DNA from opposite faces and induce four significant kinks from the −35 element to the −10 element of the promoter DNA in a cooperative manner, which restores otherwise inactive promoter activity by shortening the length of promoter non-optimal −35/−10 spacer. Our structure supports a DNA-distortion and RNAP-non-contact paradigm of transcriptional activation by MerR TFs.

RNA polymerases from Low G+C Gram Positive Bacteria

“…The holoenzyme structure (core + σ A ) shown in Fig. 1A is based on the complex with multidrug resistance regulator BmrR (9) and shows an open complex (DNA strands separated at the −10 region, red oval, and template strand inserted in the active site within the primary channel). In this structure much of the lineage-specific βln5 insertion (see below) is missing, but the flexible β-flap tip, important in binding essential transcription factor NusA (15), is visible and binds to the σ4 domain that also binds the −35 promoter sequence (red circle, Fig.…”

“…Determination of the structure of B. subtilis holoenzyme and a transcription recycling complex comprising core RNAP with the ATP-dependent remodelling factor HelD revealed ε bound in a pocket formed mainly by the β′ and α1 subunits behind the secondary channel on the downstream side of the enzyme (Fig. 1B; (9)(10)(11). The location of ε overlaps that of the βln10 and -12 inserts of Thermus thermophilus RNAP as well as a region of Archaeal/Eukaryotic Pol II Rpo3/RPB3 associated with enzyme stability, suggesting a similar role for ε in organisms, such as B.…”

“…2). A closed initiation complex, based on the open complex structure of (9) in which the N-terminal σ1.1 domain (44) that competes with nucleic acid binding in the primary channel can be modelled in situ based on equivalent structures from E. coli (24) is shown in Fig. 2A.…”

“…Such structural data on the Gram-positive B. subtilis system has been lagging, but high resolution structures of several important complexes of B. subtilis RNAP (RNAPBS) have been recently published that enable a similar reconciliation of structural and molecular data (9)(10)(11). Despite the considerable similarity between all multi-subunit RNAPs from bacteria, there are important mechanistic differences that can now be examined.…”

Recognition of Streptococcal Promoters by the Pneumococcal SigA Protein

“…In the RNA polymerase holoenzyme, the negatively charged domain 1.1 (a mimicry of DNA negative charge) needs to be displaced from its initial position for the DNA-RNA polymerase complex to become transcriptionally competent. The displacement process takes place more easily at some promoters while behaving more inhibitory or difficult to move out at others, therefore it assists in the promoter selection process ( Paget, 2015 ; Fang et al, 2020 ; Shin et al, 2021 ).…”