Description of recent theoretical research in the study of self-organization of cytoplasmic matter via cytoskeletal transport

Ideas in theoretical physics of biological systems

Genome processing relies on the intracellular localization and dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the mechanism of assembly for the most widespread partition systems, ParABS, responsible for active DNA segregation remains elusive. We have combined super-resolution, genome-wide, biochemical and modeling approaches to investigate quantitatively the formation of the nucleoprotein complex organized around the centromere-like sequences, parS. We found that the active confinement of nearly all ParB proteins around parS, observed at the single molecule resolution, relies on a network of synergistic interactions involving protein-protein and protein-DNA interactions. Our physico-mathematical modeling of ParB binding pattern revealed that ParB binds stochastically in the vicinity of parS over long distances. Based on our findings, and consistent with previous data, we propose a new model that relies on a nucleation and looping mechanism leading to the formation of a dynamic lattice for the partition complex assembly. We thus provide new bases to model the DNA segregation process. Our original assembly model may also apply to many unrelated proteins that self-assemble in superstructures through nucleation centers.

Genome processing relies on the intracellular localization and dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the mechanism of assembly for the most widespread partition systems, ParABS, responsible for active DNA segregation remains elusive. We have combined super-resolution, genome-wide, biochemical and modeling approaches to investigate quantitatively the formation of the nucleoprotein complex organized around the centromere-like sequences, parS. We found that the active confinement of nearly all ParB proteins around parS, observed at the single molecule resolution, relies on a network of synergistic interactions involving protein-protein and protein-DNA interactions. Our physico-mathematical modeling of ParB binding pattern revealed that ParB binds stochastically in the vicinity of parS over long distances. Based on our findings, and consistent with previous data, we propose a new model that relies on a nucleation and looping mechanism leading to the formation of a dynamic lattice for the partition complex assembly. We thus provide new bases to model the DNA segregation process. Our original assembly model may also apply to many unrelated proteins that self-assemble in superstructures through nucleation centers.

Genome processing relies on the intracellular localization and dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the mechanism of assembly for the most widespread partition systems, ParABS, responsible for active DNA segregation remains elusive. We have combined super-resolution, genome-wide, biochemical and modeling approaches to investigate quantitatively the formation of the nucleoprotein complex organized around the centromere-like sequences, parS. We found that the active confinement of nearly all ParB proteins around parS, observed at the single molecule resolution, relies on a network of synergistic interactions involving protein-protein and protein-DNA interactions. Our physico-mathematical modeling of ParB binding pattern revealed that ParB binds stochastically in the vicinity of parS over long distances. Based on our findings, and consistent with previous data, we propose a new model that relies on a nucleation and looping mechanism leading to the formation of a dynamic lattice for the partition complex assembly. We thus provide new bases to model the DNA segregation process. Our original assembly model may also apply to many unrelated proteins that self-assemble in superstructures through nucleation centers.