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Title TraR allosterically regulates transcription initiation by altering RNA polymerase conformation.
Journal, issue, pagesElife, Vol. 8, Year 2019
Publish dateDec 16, 2019
AuthorsJames Chen / Saumya Gopalkrishnan / Courtney Chiu / Albert Y Chen / Elizabeth A Campbell / Richard L Gourse / Wilma Ross / Seth A Darst /
PubMed AbstractTraR 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 ...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 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 σ region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.
External linksElife / PubMed:31841111 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 4.05 Å
Structure data

0348

6n57

EMDB-0348, PDB-6n57:
Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation I
Method: EM (single particle) / Resolution: 3.7 Å

0349

6n58

EMDB-0349, PDB-6n58:
Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II
Method: EM (single particle) / Resolution: 3.78 Å

20203

6oul

EMDB-20203, PDB-6oul:
Cryo-EM structure of Escherichia coli RNAP polymerase bound to rpsTP2 promoter DNA
Method: EM (single particle) / Resolution: 3.4 Å

20230

6p1k

EMDB-20230: Cryo-EM structure of Escherichia coli RNAP polymerase holoenzyme
PDB-6p1k: Cryo-EM structure of Escherichia coli sigma70 bound RNAP polymerase holoenzyme
Method: EM (single particle) / Resolution: 4.05 Å

EMDB-20231:
Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation III
Method: EM (single particle) / Resolution: 3.91 Å

EMDB-20232:
Cryo-EM structure of Escherichia coli RNAP polymerase bound to DNA promoter rpsTP2 (class 2)
Method: EM (single particle) / Resolution: 3.91 Å

Chemicals

ChemComp-1N7:
CHAPSO / detergent*YM / CHAPS detergent

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsTRANSFERASE / protein-DNA complex / transcription initiation / RNA polyermase / DNA promoter melting / Transcription

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