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Structural basis for higher-order DNA binding by a bacterial transcriptional regulator
Frederik Oskar Graversgaard Henriksen1, Lan Bich Van1, Ditlev Egeskov Brodersen1
1Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
Plos Genetics
|June 27, 2025
Summary
The Pseudomonas putida Xre-RES toxin-antitoxin system uses a dynamic 4:2 complex to bind DNA and repress transcription. This complex shifts between non-binding (2:2) and DNA-binding (4:2) forms based on concentration.
Area of Science:
- Bacterial transcriptional regulation
- Molecular mechanisms of gene expression
- Protein-DNA interactions
Background:
- Bacterial transcription factors bind palindromic DNA sequences in promoters.
- Some factors have multiple DNA-binding domains, suggesting higher-order DNA structure interactions.
- The Pseudomonas putida Xre-RES toxin-antitoxin system exhibits unusual 4:2 stoichiometry.
Purpose of the Study:
- To investigate the mechanism of transcriptional autoregulation by the Xre-RES complex.
- To elucidate the structural basis of Xre-RES interaction with DNA.
- To understand the role of stoichiometry in Xre-RES function.
Main Methods:
- Protein-DNA complex formation analysis.
- X-ray crystallography at 2.7 Å resolution.
- Structural prediction of protein-DNA binding.
Main Results:
- The Xre-RES complex specifically binds a palindromic DNA repeat in a 1:1 molar ratio, causing transcriptional repression.
- The crystal structure reveals asymmetric protein-DNA interaction and suggests a secondary binding site.
- Antitoxin dissociation leads to non-repressive Xre monomers and a 2:2 Xre-RES complex.
Conclusions:
- Transcriptional autoregulation by Xre-RES is dynamic and concentration-dependent.
- The complex transitions between non-binding (2:2) and DNA-binding (4:2) forms.
- Stoichiometry and dynamic shifts are crucial for regulating gene expression.
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