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# 1 Schematic illustration of the bacterial cell cycle. Replication begins at the 12' position (ori) on the circular chromosome. Replication forks grow bidirectionally and meet at the opposite clock position (ter). During the bacterial cell cycle, replication and segregation progress hand-inhand, coupled with the growth of the cell

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Note: The most important aspect of physics is included in our "Jun and Wright, Entropy as the driver of chromosome segregation. Nat Rev Microbiol 8:600-607" and its supplementary information. --- This chapter presents polymer physics that is relevant for an understanding of bacterial chromosome segregation. I first show that polymers have a natur...

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... Entropic repulsion between two daughter strands within prokaryote cells can be sufficient for segregation: Excluded volume interactions between the chain segments determine whether they will remain mixed or spontaneously seperate within the nucleoid [2][3][4][5][6][7][8][9]. Thus under high confinement conditions, entropy can drive two daughter strands to recede to opposite poles of the cell in preparation for cytokinesis. ...
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Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
... Crowding particles cause effective interactions between the polymer segments of the same chain and between the two chains in confinement, as studied in the present paper. From a theoretical perspective, overlapped segments of long polymer chains experience entropic repulsion scaling with the number of overlapping polymer blobs [37]. In a dense polymer melt the entanglements of the chains also slow down the polymer dynamics [38] [39]. ...
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During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behaviour of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions $\phi$ of crowders. We also examine the entropic de-mixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analysed. In particular, on systematic variation of the fraction of crowding molecules a $(1-\phi)$-scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number is predicted. Our results help to rationalise the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localised cellular compartments inside eukaryotic cells.
... These models do not, however, exclude a contribution of electrostatic effects; ions which were strongly bound in chromosomes would not be extracted in the conditions used here, and a subtle interplay is seen between the effects of crowding and electrostatic forces when a polyelectrolyte polymer bearing counterions, a model for a polynucleosome chain, collapses in crowded conditions [21,69]. The results described here, together with the evidence that macromolecular crowding is a crucial factor in structuring the interphase genome [64], bacterial chromosomes [20,70], and possibly polytene chromosomes [71] and the liquid crystalline chromosomes of dinoflagellates [72], are consistent with the hypothesis that a crowded environment is an essential characteristic of all genomes. This model has particularly interesting implications for meiotic chromosomes, because pairing of homologous DNAs [73,74] and recA-promoted exchange of DNA strands [75] are stimulated in crowded conditions. ...
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In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.
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How confinement or a physical constraint modifies polymer chains is not only a classical problem in polymer physics but also relevant in a variety of contexts such as single-molecule manipulations, nanofabrication in narrow pores, and modelling of chromosome organization. Here, we review recent progress in our understanding of polymers in a confined (and crowded) space. To this end, we highlight converging views of these systems from computational, experimental, and theoretical approaches, and then clarify what remains to be clarified. In particular, we focus on exploring how cylindrical confinement reshapes individual chains and induces segregation forces between them – by pointing to the relationships between intra-chain organization and chain segregation. In the presence of crowders, chain molecules can be entropically phase-separated into a condensed state. We include a kernel of discussions on the nature of chain compaction by crowders, especially in a confined space. Finally, we discuss the relevance of confined polymers for the nucleoid, an intracellular space in which the bacterial chromosome is tightly packed, in part by cytoplasmic crowders.