ArticleNucleic acids research2016
Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
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- Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.Nucleic acids research · 2023Article
- Promoter DNA recognition by theFrontiers in molecular biosciences · 2023Article
- Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex.Analytical biochemistry · 2022Article
- Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to NApplied and environmental microbiology · 2022Article
- Surveying the Genetic Design Space for Transcription Factor-Based Metabolite Biosensors: Synthetic Gamma-Aminobutyric Acid and Propionate Biosensors inFrontiers in bioengineering and biotechnology · 2022Article
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- NIGT1 family proteins exhibit dual mode DNA recognition to regulate nutrient response-associated genes in Arabidopsis.PLoS genetics · 2020Article
- (S)-4-Amino-5-phenoxypentanoate designed as a potential selective agonist of the bacterial transcription factor GabR.Protein science : a publication of the Protein Society · 2020Article
- TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.Nucleic acids research · 2020Article
- Conformational transitions induced by γ-amino butyrate binding in GabR, a bacterial transcriptional regulator.Scientific reports · 2019Article
- Bacillus anthracis Virulence Regulator AtxA Binds Specifically to theJournal of bacteriology · 2019Article
- DdlR, an essential transcriptional regulator of peptidoglycan biosynthesis in Clostridioides difficile.Molecular microbiology · 2019Article
- A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model BacteriumFrontiers in molecular biosciences · 2019Review
- DNA-binding properties of MafR, a global regulator of Enterococcus faecalis.FEBS letters · 2018Article
- A New Facet of Vitamin BAnnual review of biochemistry · 2017Review
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- Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation.International journal of molecular sciences · 2016Article
- Article
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR-DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR-DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites.
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