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.
Highlights
The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones
The prevailing “recruitment” model of bacterial transcription activation specifies that TFs enrich RNA Polymerase (RNAP) at specific genomic loci by making direct interactions with both RNAP and promoter DNA, thereby creating additional linkage between them[3]
In line with their function, canonical bacterial TFs are typically equipped with a DNA-binding domain (DBD), which reads specific sequence in the form of double-stranded DNA, and small surface patches, which interact with the RNAP-α subunit or domain R4 of σ factors (σ4)[4,5]
Summary
The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. The prevailing “recruitment” model of bacterial transcription activation specifies that TFs enrich RNAP at specific genomic loci by making direct interactions with both RNAP and promoter DNA, thereby creating additional linkage between them[3]. In line with their function, canonical bacterial TFs are typically equipped with a DNA-binding domain (DBD), which reads specific sequence in the form of double-stranded DNA (dsDNA), and small surface patches, which interact with the RNAP-α subunit or domain R4 of σ factors (σ4)[4,5]. Due to the lack of RNAP in those crystal structures, it is unknown how MerR-TFs manage to reconcile with RNAP to bind and reshape promoter
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