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TitleStructural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator.
Journal, issue, pagesNucleic Acids Res, Vol. 50, Issue 10, Page 5974-5987, Year 2022
Publish dateJun 10, 2022
AuthorsJing Shi / Fulin Wang / Fangfang Li / Lu Wang / Ying Xiong / Aijia Wen / Yuanling Jin / Sha Jin / Fei Gao / Zhenzhen Feng / Jiacong Li / Yu Zhang / Zhuo Shang / Shuang Wang / Yu Feng / Wei Lin /
PubMed AbstractRob, which serves as a paradigm of the large AraC/XylS family transcription activators, regulates diverse subsets of genes involved in multidrug resistance and stress response. However, the ...Rob, which serves as a paradigm of the large AraC/XylS family transcription activators, regulates diverse subsets of genes involved in multidrug resistance and stress response. However, the underlying mechanism of how it engages bacterial RNA polymerase and promoter DNA to finely respond to environmental stimuli is still elusive. Here, we present two cryo-EM structures of Rob-dependent transcription activation complex (Rob-TAC) comprising of Escherichia coli RNA polymerase (RNAP), Rob-regulated promoter and Rob in alternative conformations. The structures show that a single Rob engages RNAP by interacting with RNAP αCTD and σ70R4, revealing their generally important regulatory roles. Notably, by occluding σ70R4 from binding to -35 element, Rob specifically binds to the conserved Rob binding box through its consensus HTH motifs, and retains DNA bending by aid of the accessory acidic loop. More strikingly, our ligand docking and biochemical analysis demonstrate that the large Rob C-terminal domain (Rob CTD) shares great structural similarity with the global Gyrl-like domains in effector binding and allosteric regulation, and coordinately promotes formation of competent Rob-TAC. Altogether, our structural and biochemical data highlight the detailed molecular mechanism of Rob-dependent transcription activation, and provide favorable evidences for understanding the physiological roles of the other AraC/XylS-family transcription factors.
External linksNucleic Acids Res / PubMed:35641097 / PubMed Central
MethodsEM (single particle)
Resolution4.0 - 4.57 Å
Structure data

32165

7vwy

EMDB-32165, PDB-7vwy:
Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation
Method: EM (single particle) / Resolution: 4.57 Å

32166

7vwz

EMDB-32166, PDB-7vwz:
Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation
Method: EM (single particle) / Resolution: 4.0 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsTRANSCRIPTION/DNA / bacterial RNA polymerase / TRANSCRIPTION-DNA COMPLEX

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