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

Abstract

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 model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering 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 loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the 'tightness' of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Focus on bacterial mechanics

“…Interestingly, the ParB cluster spreads over thousands of basepairs by forming both bonds between adjacent sites on the DNA and between distant sites along the DNA through DNA looping. In the work by Walter et al [24], this system is studied in terms of a statistical model of ParB binding, interaction, and DNA loop formation, which accurately predicts ParB binding profiles in agreement with previous experimental CHIP-Seq data. While the ParB cluster on DNA contains almost all ParB proteins in the cell, many membraneembedded proteins form multiple distinct clusters.…”

A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids

“…Neither “1D spreading” nor “Spreading & bridging” physical models could describe these data in the conditions tested (Broedersz et al , ). A variant of the latter model has explored the ParB binding pattern in the low spreading strength limit (Walter et al , ). This “Looping & clustering” model also predicts variations in the ParB binding pattern over a simulated 4‐fold range of ParB amount, which is in contrast to the invariant pattern observed experimentally over more than three orders of magnitude (Fig ).…”

Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes

“…It is widely acknowledged that ParB loading on parS is a prerequisite for the conformational changes that prime ParB for nucleation [135][136][137]. The ability of ParBs to build large nucleoprotein complexes may be a result of lateral ParB interactions (1D) and bridging interactions (3D) between ParB molecules located at distant DNA segments [117,134], clustering or building a ParB cage around parS by weak but dynamic interactions between protein dimers and DNA [129,138,139]. The ParB interactions around parS result in significant DNA compaction via loop formation.…”