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TitleTranscription activation mechanism of a noncanonical DNA damage response pathway by the WYL-activator, DriD.
Journal, issue, pagesSci Adv, Vol. 12, Issue 12, Page eaec6337, Year 2026
Publish dateMar 20, 2026
AuthorsRajiv R Singh / Amani Chinni / Emily Cannistraci / Raul Salinas / Sunny Yadav / Kevin Gozzi / Maria A Schumacher /
PubMed AbstractDNA damage repair mechanisms are vital for cell survival. In the bacterium, , DriD is the master regulator of a unique, noncanonical DNA damage pathway. DriD binding to ssDNA, produced upon DNA ...DNA damage repair mechanisms are vital for cell survival. In the bacterium, , DriD is the master regulator of a unique, noncanonical DNA damage pathway. DriD binding to ssDNA, produced upon DNA damage, stimulates its ability to activate transcription from several promoters involved in DNA damage responses. However, the mechanism by which DriD interfaces with the RNAP holoenzyme to activate transcription from its multiple promoters has been unclear. Here, we describe cryo-EM structures of DriD-ssDNA bound to RNAP-holoenzyme and three DriD-regulated promoters. Each subunit of homodimeric DriD contains an DNA binding -terminal winged helix-turn-helix (wHTH) connected to WYL domains by a linker 3-helix bundle (3HB) module. The structures reveal a mechanism of assembly on promoters whereby DriD's 3HBs bind the RNAP α-CTD and β domains, anchoring the RNAP-holoenzyme to regulated promoters. The 3HBs form autoinhibitory contacts with DNABDs in apo DriD and therefore acts as an ssDNA-driven trigger domain, switching between DNABD-bound apo and RNAP-bound forms upon ssDNA-mediated activation. Thus, the structures reveal a unique transcription activation mechanism, likely conserved among the large family of homodimeric WYL activators.
External linksSci Adv / PubMed:41861017 / PubMed Central
MethodsEM (single particle)
Resolution3.54 - 4.24 Å
Structure data

71610

9pfq

EMDB-71610, PDB-9pfq:
The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex
Method: EM (single particle) / Resolution: 4.24 Å

71615

9pfv

EMDB-71615, PDB-9pfv:
The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
Method: EM (single particle) / Resolution: 3.7 Å

71624

9pga

EMDB-71624, PDB-9pga:
The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex
Method: EM (single particle) / Resolution: 3.98 Å

71632

9pgh

EMDB-71632, PDB-9pgh:
The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
Method: EM (single particle) / Resolution: 3.54 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • caulobacter vibrioides na1000 (bacteria)
KeywordsTRANSCRIPTION/DNA / bapE promoter transcription activation complex / DriD / Caulobacter / TRANSCRIPTION / Non-canonical DNA Repair / TRANSCRIPTION-DNA complex / CCNA_03891-CCNA_01149 promoter Transcription Activation Complex / didA promoter transcription activation complex / CCNA_03891-CCNA_01149 promoter complex / RNA Polymerase

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