We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}.
In this work, we investigate how does the release of topological constraints help in the organization of the DNA-polymer. Furthermore, we show that the chain compaction induced by the crowded environment in the bacterial cytoplasm contributes to the organization of the DNA-polymer. We model the DNA chain as a flexible bead-spring ring polymer, where each bead represents $1000$ base pairs. The specific positions of the cross-links have been taken from the experimental contact maps of the bacteria {\em C. crescentus} and {\em E. coli}. We introduce different extents of topological constraints in our model by systematically changing the diameter of the monomer bead. It varies from the value where the chain crossing can occur freely to the value where the chain crossing is disallowed. We also study the role of molecular crowders by introducing an effective Lennard Jones attraction between the monomers. Using Monte-Carlo simulations, we show that the release of topological constraints and the crowding environment play a crucial role to obtain a unique organization of the polymer.
Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical cell. We observe spontaneous emergence of complementary helicity of the confined polymer and crowders. This feature is reproduced within a simplified effective model of the chromosome. This latter model further establishes the occurrence of longitudinal and transverse spatial segregation transitions between the chromosome and crowders upon increasing crowder…
Using a bead-spring model of bacterial DNA polymers of {\em C. crescentus} and {\em E. coli} we show that just $33$ and $38$ effective cross-links at special positions along the chain contour of the DNA can lead to the large-scale organization of the DNA polymer, where confinement effects of the cell walls play a key role in the organization. The positions of the $33$ cross-links along the chain contour are chosen from the contact map data of {\em C. crescentus}. We represent $1000$ base pairs as a coarse-grained monomer in our bead-spring flexible ring polymer model of the DNA. Thus a $4017$ …
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such a model chromosome spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like subvolume of the cell. With increasing cell length, the longitudinal size of the chromosome increases in a non-linear fashion to finally saturate, its morphology gradually opening up while displaying a changing number of helica…
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about thousand times larger outside from the cell. Here, by performing numerical simulations with coarse-grained models, we elaborate on the conjecture that the formation of the nucleoid may result from a segregative phase separation mechanis…
Nucleoid clustering drives stepwise expansion and segregation of replicating bacterial chromosomes
SUPA, School of Physics and Astronomy, University of Edinburgh（爱丁堡大学物理与天文学学院）；Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá di Padova（帕多瓦大学物理与天文学系及INFN分部）
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven maximum entropy approach to extract the distribution of single-cell chromosome conformations from experimental normalized Hi-C data. We apply this inference to the model organism Caulobacter crescentus. On small genomic scales of 104-105 basepairs, our model reveals a pattern of local chromosome extensions that correlates with transcriptional and DNA loop extrus…
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various nucleoid-associated proteins, including the ATPase SMC condensin. Although the molecular structure of these ATPases has been mapped in detail, it still remains unclear by which physical mechanisms they collectively generate long-range chromosomal contacts. Here, we develop a computational model that captures the subtle interplay between molecular-scale activity of…
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser e…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic segregation. Here we establish that `internal' loops within a modified-ring polymer architecture enhances entropic repulsion between two overlapping polymers confined in a cylinder. Moreover it also induces entropy-driven spatial organization of polymer segments as seen in-vivo. To that end, we design polymers of different architectures in our simulations, by introduci…
The spatiotemporal organization of bacterial cells is crucial for the active segregation of replicating chromosomes. In several species, including Caulobacter crescentus, the ATPase ParA binds to DNA and forms a gradient along the long cell axis. The ParB partitioning complex on the newly replicated chromosome translocates up this ParA gradient, thereby contributing to chromosome segregation. A DNA-relay mechanism - deriving from the elasticity of the fluctuating chromosome - has been proposed as the driving force for this cargo translocation, but a mechanistic theoretical description remains …
Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria with very compact nucleoids show that such spherical nucleoids are invariably positioned at the center of mononucleoid cells. The present work aims to determine whether such preferential localization results from generic (entropic) interactions between the nucleoid and the cell membrane or instead requires some specific mechanism, like the tethering of DNA at …
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder, we use Monte carlo simulations to show that the segregation dynamics is spontaneously enhanced by the adoption of a certain DNA-polymer architecture as replication progresses. Secondly, the chosen polymer-topology ensures its self-organization along the cell axis while segregation is in progress, such that various chromosomal loci get spatially localized. Th…
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. 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 experiment…
Mechanistic insights into the spatial organization of RNA polymerase proteins and the chromosome in E. coli cells
Leibniz-Institut für Polymerforschung Dresden（德累斯顿莱布尼茨聚合物研究所）；Institute for Theoretical Physics, TU Dresden（德累斯顿工业大学理论物理研究所）；Cluster of Excellence Physics of Life, TU Dresden（德累斯顿工业大学生命物理卓越集群）
ParABS system induces topological modifications to spatio-temporally organize its mother and daughter chromosomes in the replicating C. crescentus cell
Indian Institute of Science Education and Research (IISER-Pune)（印度科学教育研究所（浦那））
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE) and measurements using magnetic tweezer experiments, we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the experimental data quantitatively, and suggests that condensin must un…
