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Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

ABSTRACT: Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.

SUBMITTER: Yang Y

PROVIDER: S-EPMC8113463 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

Yang Yang Y Liu Chang C Zhou Wei W Shi Wei W Chen Ming M Zhang Baoyue B Schatz David G DG Hu Yangbo Y Liu Bin B

Nature communications 20210511 1

Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing M ...[more]

PMID: 33976201

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Project description:The MerR family of transcriptional regulators are dimeric proteins with an N-terminal helix-turn-helix DNA binding domain (DBD), followed by an antiparallel coiled-coil subunit interaction region, and usually by a C-terminal effector binding domain (EBD). This family is distinguished by the high amino acid similarity in the DBD and low similarity in the EBD, consistent with the role of this domain in each protein in sensing effector molecules. Most members of the family are activators, and act at promoters with long spacer regions and respond to the binding of inducers by distorting the promoter DNA to allow open complex formation and transcriptional activation. In MerR proteins the EBD contains a metal binding pocket formed by three cysteines. This Cys center characteristic of MerR regulators is primarily suited for metal binding and mediates activation of metal detoxification systems in bacteria. Over the last decade, it has become clear that the MerR family of regulators is more diverse than originally recognized. The availability of completed bacterial genome sequences has enabled the search for additional types of MerR-like regulators. We here present a novel MerR-like transcription factor lacking an EBD involved in iron uptake regulation (MliR) present in the marine bacterium Bizionia argentinensis (JUB59). An in silico analysis revealed that homologues of the MliR protein are widely distributed among different bacterial species. Deletion of the mliR gene led to decreased cell growth, increased cell adhesion and filamentation. RNA sequencing analysis showed that expression of several iron uptake-related mRNAs were downregulated in mliR-deletion mutant. Through NMR-based metabolomics, ICP-MS, fluorescence microscopy and biochemical analysis we evaluated metabolic and phenotypic changes associated with mliR deletion. This work provides the first evidence of a MerR-family regulator involved in iron uptake and contributes to expanding our current knowledge on iron metabolism.in bacteria.

Project description:UNLABELLED:Bacteria engage in chemical signaling, termed quorum sensing (QS), to mediate intercellular communication, mimicking multicellular organisms. The LuxR family of QS transcription factors regulates gene expression, coordinating population behavior by sensing endogenous acyl homoserine lactones (AHLs). However, some bacteria (such as Escherichia coli) do not produce AHLs. These LuxR orphans sense exogenous AHLs but also regulate transcription in the absence of AHLs. Importantly, this AHL-independent regulatory mechanism is still largely unknown. Here we present several structures of one such orphan LuxR-type protein, SdiA, from enterohemorrhagic E. coli (EHEC), in the presence and absence of AHL. SdiA is actually not in an apo state without AHL but is regulated by a previously unknown endogenous ligand, 1-octanoyl-rac-glycerol (OCL), which is ubiquitously found throughout the tree of life and serves as an energy source, signaling molecule, and substrate for membrane biogenesis. While exogenous AHL renders to SdiA higher stability and DNA binding affinity, OCL may function as a chemical chaperone placeholder that stabilizes SdiA, allowing for basal activity. Structural comparison between SdiA-AHL and SdiA-OCL complexes provides crucial mechanistic insights into the ligand regulation of AHL-dependent and -independent function of LuxR-type proteins. Importantly, in addition to its contribution to basic science, this work has implications for public health, inasmuch as the SdiA signaling system aids the deadly human pathogen EHEC to adapt to a commensal lifestyle in the gastrointestinal (GI) tract of cattle, its main reservoir. These studies open exciting and novel avenues to control shedding of this human pathogen in the environment. IMPORTANCE:Quorum sensing refers to bacterial chemical signaling. The QS acyl homoserine lactone (AHL) signals are recognized by LuxR-type receptors that regulate gene transcription. However, some bacteria have orphan LuxR-type receptors and do not produce AHLs, sensing them from other bacteria. We solved three structures of the E. coli SdiA orphan, in the presence and absence of AHL. SdiA with no AHL is not in an apo state but is regulated by a previously unknown endogenous ligand, 1-octanoyl-rac-glycerol (OCL). OCL is ubiquitously found in prokaryotes and eukaryotes and is a phospholipid precursor for membrane biogenesis and a signaling molecule. While AHL renders to SdiA higher stability and DNA-binding affinity, OCL functions as a chemical chaperone placeholder, stabilizing SdiA and allowing for basal activity. Our studies provide crucial mechanistic insights into the ligand regulation of SdiA activity.

Dataset Information

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

Publications

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

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