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Designed architectural proteins that tune DNA looping in bacteria
David H Tse1, Nicole A Becker1, Robert T Young2
1Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA.
Nucleic Acids Research
|September 3, 2021
Summary
Artificial proteins can control DNA shape. Transcription Activator-like Effector (TALE) proteins stiffen DNA to inhibit loops, while TALE-high mobility group B (HMGB) fusions bend DNA to promote looping, demonstrating precise DNA geometry sculpting.
Area of Science:
- Molecular Biology
- Biophysics
- Synthetic Biology
Background:
- Architectural proteins influence DNA structure and function by altering its shape.
- DNA bending and kinking are crucial for regulating gene expression and relieving torsional strain.
- Transcription Activator-like Effector (TALE) proteins and high mobility group B (HMGB) domains are known DNA-binding proteins with distinct structural effects.
Purpose of the Study:
- To design and test artificial architectural proteins based on TALE proteins to modulate DNA geometry.
- To investigate the hypothesis that TALE proteins stiffen DNA, inhibiting loop formation.
- To determine if fusing TALE proteins with HMGB domains creates DNA-bending proteins that facilitate looping.
Main Methods:
- Design and construction of artificial TALE and TALE-HMGB fusion proteins.
- Experimental validation using Escherichia coli Lac repressor gene regulatory loops in vivo.
- Analysis using thermodynamic DNA looping models and molecular modeling.
Main Results:
- TALE protein binding was found to stiffen DNA, inhibiting DNA looping.
- Fusion of TALE proteins with the Nhp6A (an HMGB domain) enhanced DNA looping by bending DNA without inducing twisting.
- Results support the hypothesis that engineered proteins can sculpt DNA geometry with functional outcomes.
Conclusions:
- Artificial architectural proteins, including TALE and TALE-HMGB fusions, can precisely control DNA shape and stability.
- Engineered DNA-binding proteins offer a powerful tool for manipulating DNA looping and gene regulation.
- These findings have implications for understanding and engineering DNA loop stability in biological systems.
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