Many canonical processes in molecular biology rely on the dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the assembly mechanism of ParABS, the nucleoprotein super-complex that actively segregates the bacterial chromosome and many plasmids, remains elusive. We combined super-resolution microscopy, quantitative genome-wide surveys, biochemistry, and mathematical modeling to investigate the assembly of ParB at the centromere-like sequences parS. We found that nearly all ParB molecules are actively confined around parS by a network of synergistic protein-protein and protein-DNA interactions. Interrogation of the empirically determined, high-resolution ParB genomic distribution with modeling suggests that instead of binding only to specific sequences and subsequently spreading, ParB binds stochastically around parS over long distances. We propose a new model for the formation of the ParABS partition complex based on nucleation and caging: ParB forms a dynamic lattice with the DNA around parS. This assembly model and approach to characterizing large-scale, dynamic interactions between macromolecules may be generalizable to many unrelated machineries that self-assemble in superstructures.

Keywords: plasticity, aging, soft matter, polycrystals, colloids Introduction Virtually all real-life crystalline materials have defects. In particular, most metals and ceramics are aggregates of crystalline grains. Grain-boundaries (GBs), the two-dimensional lattice defects that separate the different grains of a crystal, control the mechanical properties of polycrystalline materials. Although GB motion is known to play important roles in plastic (i.e. irreversible) deformation, the microscopic origin of the plasticity of polycrystalline materials is still largely unknown, because of the limitations of available experimental tools to record, during deformation, the dynamics of the process with a nanometer resolution. Objectives To overcome the limitation intrinsic to atomic systems, we use a colloidal analogue of atomic polycrystals. We take advantage of the much larger characteristic length and time scales, much softer elasticity, and the optical transparency of a colloidal polycrystal to obtain unprecedented space- and time-resolved information on the irreversible deformation of a polycrystal under load. Methodology We use a colloidal analog of atomic crystals, where soft colloids play the role of atoms and are organized on a cubic crystalline lattice (lattice parameter ~ 30 nm) in water. The colloidal crystal is doped with a small amount (at most 1% v/v) of nanoparticles (NPs) of typical size a few tens of nm. NPs act as impurities, and as such, they segregate in the grain boundaries (GBs) of the colloidal polycrystal, allowing their visualization by confocal microscopy (figure 1, a-c) and dominating the signal in scattering experiments. In addition, the average grain size of the polycrystal can be tuned by varying the NP volume fraction (figure 1, a-c) and the crystallization rate [1]. The sample is confined between two parallel glass plates of a home-made shear cell and is submitted to a large number (typically 5000) of shear deformation cycles of amplitude a few %. Our protocol is similar to fatigue tests commonly adopted in material science. We follow the irreversible reorganization of the network of GBs by confocal imaging or by time-resolved light scattering, where a low-angle light scattering setup designed to access the characteristic length scale of the GB network is used. Here, the cross-correlation between two scattering patterns taken after n and p shear cycles allows one to quantify the amount of irreversible rearrangements that have occurred between the nth and pth shear cycles. Results and analysis We find that plasticity slowly remodels the network of GBs. Confocal microscopy (figure 1 d) reveals an irreversible reorganization of the GB network induced by the shear cycles. However it cannot measure small GB displacements when probing a large sample area. A more quantitative account of the plasticity process is therefore provided by time-resolved light scattering. We follow the evolution of the amount of irreversible rearrangements with the number of shear cycles imposed to the sample. We find that the dynamics associated with plasticity slows down until a steady state is reached after a large number of shear cycles (figure 2). Remarkably, the cross-over time between the initial aging regime and the steady state decreases with increasing probed length scale. We extract a characteristic length above which the GB dynamics is stationary, which is found to be of the order of the average grain size and to increase with the shear amplitude. Our data suggest a hierarchical organization of the grain boundary dynamics. We speculate that our findings may also be relevant for amorphous solids, as a polycrystal may be regarded as an amorphous assembly of crystalline grains. References [1] N. Ghofraniha, E. Tamborini, J. Oberdisse, L. Cipelletti and L. Ramos, "Grain refinement and partitioning of impurities in the grain boundaries of a colloidal polycrystal", Soft Matter 8, 6214-6219 (2012). (cover article) [2] E. Tamborini, L. Cipelletti and L. Ramos, "Length-scale dependent aging and plasticity of a colloidal polycrystal under cyclic shear", arXiv:1311.1996 [cond-mat.soft]