TY - JOUR TI - E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation AU - Chen, James AU - Gopalkrishnan, Saumya AU - Chiu, Courtney AU - Chen, Albert Y AU - Campbell, Elizabeth A AU - Gourse, Richard L AU - Ross, Wilma AU - Darst, Seth A A2 - Berger, James M A2 - Storz, Gisela A2 - Wang, Dong VL - 8 PY - 2019 DA - 2019/12/16 SP - e49375 C1 - eLife 2019;8:e49375 DO - 10.7554/eLife.49375 UR - https://doi.org/10.7554/eLife.49375 AB - TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters. KW - cryo-electron microscopy KW - RNA polymerase KW - transcription initiation KW - TraR JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -