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Structure paper

TitleStructural visualization of transcription activated by a multidrug-sensing MerR family regulator.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 2702, Year 2021
Publish dateMay 11, 2021
AuthorsYang Yang / Chang Liu / Wei Zhou / Wei Shi / Ming Chen / Baoyue Zhang / David G Schatz / Yangbo Hu / Bin Liu /
PubMed AbstractBacterial 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 ...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.
External linksNat Commun / PubMed:33976201 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.4 - 3.3 Å
Structure data

EMDB-22234, PDB-6xl5:
Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-22235, PDB-6xl6:
Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPo
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-22236, PDB-6xl9:
Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA transcript (EcmrR-RPitc-3nt)
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-22237, PDB-6xla:
Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-3nt
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-22245, PDB-6xlj:
Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 4-nt RNA transcript (EcmrR-RPitc-4nt)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-22246, PDB-6xlk:
Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-4nt
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-22247, PDB-6xll:
Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-22248, PDB-6xlm:
Cryo-EM structure of E.coli RNAP-DNA elongation complex 1 (RDe1) in EcmrR-dependent transcription
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-22249, PDB-6xln:
Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-23291:
Cryo-EM map of EcmrR-RNAP-promoter open complex (EcmrR-RPo) with clear NCR-EcmrR NTD interface density
Method: EM (single particle) / Resolution: 2.9 Å

PDB-6wl5:
Crystal structure of EcmrR C-terminal domain
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-16A:
CETYL-TRIMETHYL-AMMONIUM

ChemComp-GOL:
GLYCEROL

ChemComp-CL:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

ChemComp-1N7:
CHAPSO / detergent*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-118:
TETRAPHENYLANTIMONIUM ION

Source
  • escherichia coli o157:h7 (bacteria)
  • escherichia coli (E. coli)
KeywordsTRANSCRIPTION / Transcriptional factor / TRANSFERASE/DNA / TRANSFERASE-DNA complex / promoter / multidrug recognition / TRANSCRIPTION TRANSFERASE-DNA complex / promoter escape

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