ArticleNucleic acids research2025
Structural basis for control of integrative and conjugative element excision and transfer by the oligomeric winged helix-turn-helix protein RdfS.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Winged helix-turn-helix (wHTH) proteins are diverse DNA-binding proteins that often oligomerize on DNA and participate in DNA recombination and transcriptional regulation. wHTH recombination directionality factors (RDFs) associated with tyrosine recombinases, stimulate excision of prophage and integrative and conjugative elements (ICEs). RdfS is required for excision and conjugation of the Mesorhizobium japonicum R7A ICE, ICEMlSymR7A, which carries genes for nitrogen-fixing symbiosis. We show RdfS binds to DNA regions within the IntS attachment site (attP) and within the rdfS promoter, enabling RdfS to coordinate rdfS/intS expression and stimulate RdfS/IntS-mediated ICEMlSymR7A excision. Several RdfS DNA-binding sites were identified. However, no consensus motif was apparent and no individual nucleotide substitutions in attP prevented RdfS binding. RdfS forms extensive helical filaments in crystals, with subunits contacting via a novel α1-helix absent in other wHTH-RDFs. RdfS oligomerized in solution in the absence of DNA. Molecular dynamics simulations supported a role for the α1-helix in oligomerization and compaction of nucleoprotein complexes. Removal of RdfS-α1 did not eliminate DNA-binding in vitro but reduced oligomerization and abolished RdfS-mediated ICEMlSymR7A excision and conjugative transfer. We propose the novel RdfS-α1 mediated oligomerization enables RdfS to specifically recognize larger DNA regions with low primary sequence conservation through an indirect readout mechanism.
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