DNA supercoiling enhances DNA condensation by ParB proteins

• Published in: Nucleic acids research 2024-11, Vol.52 (21), p.13255-13268
• Main Authors: Martin-Gonzalez, Alejandro, Tišma, Miloš, Analikwu, Brian T, Barth, Anders, Janissen, Richard, Antar, Hammam, Kemps, Gianluca, Gruber, Stephan, Dekker, Cees
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Chromosome Segregation; Chromosomes, Bacterial - chemistry; Chromosomes, Bacterial - metabolism; DNA, Bacterial - metabolism; DNA, Superhelical - chemistry; DNA, Superhelical - metabolism; DNA-Binding Proteins - metabolism; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Molecular and Structural Biology; Single Molecule Imaging
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae936

The ParABS system plays a critical role in bacterial chromosome segregation. The key component of this system, ParB, loads and spreads along DNA to form a local protein-DNA condensate known as a partition complex. As bacterial chromosomes are heavily supercoiled due to the continuous action of RNA polymerases, topoisomerases and nucleoid-associated proteins, it is important to study the impact of DNA supercoiling on the ParB-DNA partition complex formation. Here, we use an in-vitro single-molecule assay to visualize ParB on supercoiled DNA. Unlike most DNA-binding proteins, individual ParB proteins are found to not pin plectonemes on supercoiled DNA, but freely diffuse along supercoiled DNA. We find that DNA supercoiling enhances ParB-DNA condensation, which initiates at lower ParB concentrations than on DNA that is torsionally relaxed. ParB proteins induce a DNA-protein condensate that strikingly absorbs all supercoiling writhe. Our findings provide mechanistic insights that have important implications for our understanding of bacterial chromosome organization and segregation.