Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome

Not scheduled
20m

Speaker

Nils-Ole Walliser (L2C, Univ Montpellier, CNRS, Montpellier, France)

Description

The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking.

Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate parS binding site.

Primary authors

Jean-Charles Walter (L2C, Univ Montpellier, CNRS, Montpellier, France) Nils-Ole Walliser (L2C, Univ Montpellier, CNRS, Montpellier, France) Gabriel David (L2C, Univ Montpellier, CNRS, Montpellier, France) Jérôme Dorignac (L2C, Univ Montpellier, CNRS, Montpellier, France) Frédéric Geniet (L2C, Univ Montpellier, CNRS, Montpellier, France) John Palmeri (L2C, Univ Montpellier, CNRS, Montpellier, France) Andrea Parmeggiani (L2C and DIMNP, Univ Montpellier, CNRS, Montpellier, France) Ned S. Wingreen (Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, USA) Chase P. Broedersz (Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Munich, Germany)

Presentation Materials

Your browser is out of date!

Update your browser to view this website correctly. Update my browser now

×