ArticleNucleic acids research2022
Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- DDTRN: predicting bacterial transcriptional regulatory networks based on gene sequences using dual descriptor.Briefings in bioinformatics · 2026Article
- Coordinated regulation of trimethylamine catabolism in abundant marine bacteria.Applied and environmental microbiology · 2026Article
- Elucidating the role of mycobacteriophage D29-encoded Gp36 in DNA binding and phage gene expression regulation.Nucleic acids research · 2025Article
- Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.PLoS genetics · 2025Article
- Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in E. coli using a high-throughput approach.Nucleic acids research · 2025Article
- Laboratory evolution inApplied and environmental microbiology · 2025Article
- Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.Briefings in bioinformatics · 2024Article
- Snowprint: a predictive tool for genetic biosensor discovery.Communications biology · 2024Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.
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