Shahu, S and Vtyurina, N and Das, M and Meyer, AS and Ganji, M and Abbondanzieri, EA (2024) Bridging DNA contacts allow Dps from E. coli to condense DNA. In: Nucleic Acids Research, 52 (8). pp. 4456-4465.
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Abstract
The DNA-binding protein from starved cells (Dps) plays a crucial role in maintaining bacterial cell viability during periods of stress. Dps is a nucleoid-associated protein that interacts with DNA to create biomolecular condensates in live bacteria. Purified Dps protein can also rapidly form large complexes when combined with DNA in vitro. However, the mechanism that allows these complexes to nucleate on DNA remains unclear. Here, we examine how DNA topology influences the formation of Dps�DNA complexes. We find that DNA supercoils offer the most preferred template for the nucleation of condensed Dps structures. More generally, bridging contacts between different regions of DNA can facilitate the nucleation of condensed Dps structures. In contrast, Dps shows little affinity for stretched linear DNA before it is relaxed. Once DNA is condensed, Dps forms a stable complex that can form inter-strand contacts with nearby DNA, even without free Dps present in solution. Taken together, our results establish the important role played by bridging contacts between DNA strands in nucleating and stabilizing Dps complexes. © The Author(s) 2024.
| Item Type: | Journal Article |
|---|---|
| Publication: | Nucleic Acids Research |
| Publisher: | Oxford University Press |
| Additional Information: | The copyright for this article belongs to author. |
| Keywords: | DNA; DNA binding protein; DNA topoisomerase; DNA topoisomerase (ATP hydrolysing); mitochondrial transcription factor A; bacterial DNA; DNA; DNA binding protein; dps protein, E coli; Escherichia coli protein; outer membrane protein; protein binding, Article; assay; cell viability; cross linking; crystal structure; DNA binding; DNA conformation; Escherichia coli; fluorescence; gene overexpression; in vitro study; in vivo study; Markov chain Monte Carlo method; nonhuman; plasmid; single molecule fluorescence assay; stoichiometry; total internal reflection fluorescence microscopy; chemistry; conformation; DNA supercoiling; genetics; metabolism, Bacterial Outer Membrane Proteins; DNA; DNA, Bacterial; DNA, Superhelical; DNA-Binding Proteins; Escherichia coli; Escherichia coli Proteins; Nucleic Acid Conformation; Protein Binding |
| Department/Centre: | Division of Biological Sciences > Biochemistry |
| Date Deposited: | 31 May 2024 04:29 |
| Last Modified: | 31 May 2024 04:29 |
| URI: | https://eprints.iisc.ac.in/id/eprint/85109 |
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