DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos

Abstract

Spatial ordering of macromolecular components inside cells is important for cellular physiology and replication. In bacteria, ParA/B systems are known to generate various intracellular patterns that underlie the transport and partitioning of low-copy-number cargos such as plasmids. ParA/B systems consist of ParA, an ATPase that dimerizes and binds DNA upon ATP binding, and ParB, a protein that binds the cargo and stimulates ParA ATPase activity. Inside cells, ParA is asymmetrically distributed, forming a propagating wave that is followed by the ParB-rich cargo. These correlated dynamics lead to cargo oscillation or equidistant spacing over the nucleoid depending on whether the cargo is in single or multiple copies. Currently, there is no model that explains how these different spatial patterns arise and relate to each other. Here, we test a simple DNArelay model that has no imposed asymmetry and that only considers the ParA/ParB biochemistry and the known fluctuating and elastic dynamics of chromosomal loci. Stochastic simulations with experimentally derived parameters demonstrate that this model is sufficient to reproduce the signature patterns of ParA/B systems: the propagating ParA gradient correlated with the cargo dynamics, the single-cargo oscillatory motion, and the multicargo equidistant patterning. Stochasticity of ATP hydrolysis breaks the initial symmetry in ParA distribution, resulting in imbalance of elastic force acting on the cargo. Our results may apply beyond ParA/B systems as they reveal how a minimal system of two players, one binding to DNA and the other modulating this binding, can transform directionally random DNA fluctuations into directed motion and intracellular patterning. intracellular patterning | active transport | ParA/B system | partitioning | mathematical model S patial patterns are omnipresent in biology, spanning a wide range of size scales and organizational levels. At the singlecell level, spatial patterns are readily apparent in the formation of protein gradients and the regular arrangement of cytoskeletal structures, macromolecular complexes, and organelles. Intracellular patterning serves important functions, as it provides a means for cells to organize their intracellular space, sense their geometry, and partition their cellular content (1-5). However, the mechanisms that drive intracellular patterning are often poorly understood.In this study, we aimed to understand how spatial patterns driven by bacterial ParA/B systems can arise within a small (micrometer-scale) intracellular space dominated by fluctuations and diffusion. ParA/B systems consist of only two proteins, ParA and ParB, that drive the transport and equipartitioning of lowcopy-number macromolecular complexes, often referred to as cargos. ParA/B systems are widespread among bacteria (6). For example, many low-copy-number plasmids encode a ParA/B system that distributes plasmid copies at regular intervals along the cell length (7-10). This striking plasmid patterning ensures that division at midcell results in ...

Surfing on Protein Waves: Proteophoresis as a Mechanism for Bacterial Genome Partitioning

“…This process entails the oscillation of ParA from pole to pole and the separation of the ParBS partition complex into two complexes with distinct sub-cellular trajectories and long-term localization. Overall, these interactions result in an equidistant, stable positioning of the duplicated DNA molecules along the cell axis.The specific modeling of ParABS systems falls into two categories: either "filament" (pushing/pulling the cargos, similar to eukaryotic spindle apparatus [3]) or reaction-diffusion models [8][9][10][11][12][13][14][15]. Recent superresolution microscopy experiments have been unable to observe filamentous structures of ParA [5,13], disfavoring polymerization-based models [12].…”

“…Reaction-diffusion models have been mainly investigated numerically to describe experimental observations like single or multiple ParBS complex positioning. In most cases, these models require other assumptions -such as DNA elasticity [13,14] -as simple reaction-diffusion mechanisms are not sufficient to predict proper positioning. Other reaction-diffusion models considered the dynamics of the partition complex on the surface of the nucleoid [8][9][10][11].…”

“…Our continuum reaction-diffusion approach goes beyond the previous diffusiophoretic mechanisms [11,12,14,18] by accounting for the finite diffusion of ParA-slow and ParA-fast, as well as the interaction of ParA-slow with the entire volume of ParBS partition complexes. VoluarXiv:1702.07372v2 [q-bio.SC]…”

“…Some of these [11,14] failed to observe a stable equipositioning regime because ParA-slow was not allowed to diffuse (D 2 = 0): thus α diverges, setting the system in the unstable regime. In [14], relative positioning occurs only with multiple cargos as a crowding effect, whereas it is known that positioning can occur even with a single plasmid [22], as predicted by certain modeling studies [12,18].…”

“…Some of these [11,14] failed to observe a stable equipositioning regime because ParA-slow was not allowed to diffuse (D 2 = 0): thus α diverges, setting the system in the unstable regime. In [14], relative positioning occurs only with multiple cargos as a crowding effect, whereas it is known that positioning can occur even with a single plasmid [22], as predicted by certain modeling studies [12,18]. In line with the most recent experimental findings [5], we assume that partition complexes evolve within the nucleoid volume near the axis of the rodshaped bacterial cells, in contrast with the translocation surface mechanism presented in [8][9][10][11] performed on large surfaces coated by ParA, lacking the confinement necessary for equipositioning.…”