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.
Bibliographical noteFunding Information:
We thank S. Wu for help with cryo-EM data collection at Yale Titan Krios cryo-EM facility; D. Matthies and Z. Yu for help with grid preparation and cryo-EM data collection at HHMI Janelia Research Campus cryo-EM facility; the staff of Wuhan Institute of Virology Core Facility and Technical Support for help with radioactive tests and anti-RpoA serum preparation; the staff of the Advanced Photon Source beamlines 24-ID-C for technical assistance with X-ray crystallography data collection; R. Breaker for computational resources. This work was performed in part in Dr. Thomas Steitz’s laboratory at Yale University. We particularly thank Dr. Steitz for his advice, mentoring, and support during the early phases of this work. This work was supported by the start-up funding granted to Y.Y. from Iowa State University, the start-up funding granted to B.L. from the Hormel Institute, University of Minnesota, the National Natural Science Foundation of China (31870133) and the Youth Innovation Promotion Association CAS (Y201750) (Y.H.), the Richard K. Gershon and the Francis Trudeau Trainee Research Fellowship from Yale University School of Medicine (C.L.) and NVIDIA GPU Grant Program (Y.Y. and C.L.).
© 2021, The Author(s).
PubMed: MeSH publication types
- Journal Article
- Research Support, Non-U.S. Gov't