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TitleStructural insights into transcription regulation of the global OmpR/PhoB family regulator PhoP from Mycobacterium tuberculosis.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 1573, Year 2025
Publish dateFeb 13, 2025
AuthorsJing Shi / Zhenzhen Feng / Qian Song / Aijia Wen / Tianyu Liu / Liqiao Xu / Zonghang Ye / Simin Xu / Fei Gao / Liuxiang Xiao / Jiapeng Zhu / Kalyan Das / Guoping Zhao / Jie Li / Yu Feng / Wei Lin /
PubMed AbstractAs a global transcription activator or repressor, the representative OmpR/PhoB family response regulator PhoP plays a crucial role in regulating bacterial pathogenicity and stress adaptation. ...As a global transcription activator or repressor, the representative OmpR/PhoB family response regulator PhoP plays a crucial role in regulating bacterial pathogenicity and stress adaptation. However, the molecular mechanisms underlying the transcriptional regulation that define its differential functions remain largely unclear. In the present study, we determine three cryo-EM structures of Mycobacterium tuberculosis (Mtb) PhoP-dependent transcription activation complexes (PhoP-TACs) and build one preliminary cryo-EM structure model of Mtb PhoP-dependent transcription repression complex (PhoP-TRC). In PhoP-TACs, tandem PhoP dimers cooperatively recognize various types of promoters through conserved PhoP-PHO box interactions, which displace the canonical interactions between the -35 element and σR4 of RNA polymerase (RNAP), unraveling complex transcription activation mechanisms of PhoP. In PhoP-TRC, one PhoP dimer binds and significantly distorts the upstream PHO box of the promoter cross-talked with the global nitrogen regulator GlnR through the PhoP-PHO box, PhoP-GlnR and αCTD-DNA interactions. This unique binding of PhoP creates steric hindrances that prevent additional GlnR binding, positioning PhoP within a unique 'competitive occluding model', as supported by prior biochemical observations. Collectively, these findings reveal the dual molecular mechanisms of PhoP-dependent transcription regulation, and offer valuable insights for further exploration of the enormous PhoP-like OmpR/PhoB family response regulators.
External linksNat Commun / PubMed:39948061 / PubMed Central
MethodsEM (single particle)
Resolution3.31 - 3.7 Å
Structure data

61492

9ji2

EMDB-61492, PDB-9ji2:
Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with unphosphated PhoP
Method: EM (single particle) / Resolution: 3.38 Å

62293

9ket

EMDB-62293, PDB-9ket:
Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with two PhoP molecules(composite map)
Method: EM (single particle) / Resolution: 3.46 Å

62294

9keu

EMDB-62294, PDB-9keu:
Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with four PhoP molecules (composite map)
Method: EM (single particle) / Resolution: 3.7 Å

62295

9kev

EMDB-62295, PDB-9kev:
Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with six PhoP molecules (composite map)
Method: EM (single particle) / Resolution: 3.31 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • mycobacterium tuberculosis (bacteria)
  • mycobacterium tuberculosis h37rv (bacteria)
KeywordsGENE REGULATION / bacterial RNA polymerase / GENE REGULATION/DNA / GENE REGULATION-DNA COMPLEX

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