Polymer architecture orchestrates the segregation and spatial organization of replicating<i>E. coli</i>chromosomes in slow growth

Mitra, Debarshi; Pande, Shreerang; Chatterji, A. C.

doi:10.1039/d2sm00734g

Cited by 12 publications

(15 citation statements)

References 74 publications

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“…The role of specific protein cofactors and specific geometries observed as part of bacterial chromosomal segregation can be explained using models whereby protein binding enables physical cross-linking, thereby generating topological constraints that are layered upon the entropically driven segregative transitions. 106 In a similar vein, segregative transitions of rod-like molecules, captured by Onsager's model for liquid−liquid-crystalline phase separation, 97 has had a profound impact on our understanding of membrane phase behavior. 107 The preceding discussion makes the point that the physics of entropically driven phase separation, which only considers the density transitions of hard molecules, can explain many of the basic foundations of spatial organization in cells.…”

Section: Phase Separation In One-component Systems With Repulsive And...mentioning

confidence: 99%

Phase Transitions of Associative Biomacromolecules

et al. 2023

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Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.

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Section: Phase Separation In One-component Systems With Repulsive And...mentioning

confidence: 99%

Phase Transitions of Associative Biomacromolecules

et al. 2023

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“…We observe that for our model, the two oriCs remain localised at cell quarters, consistent with previous studies. 21,40,53 Moreover we also observe that the mother and the daughter chromosomes are properly segregated into different cell halves along the long axis (Figure S8). Such an orientation helps chromosome segregation during cell division which we obtain from our model without any external imposition.…”

Section: Resultsmentioning

confidence: 61%

Development of a Data-driven Integrative Model of Bacterial Chromosome

Wasim

Bera

Mondal

2023

Preprint

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The chromosome of archetypal bacteria E. coli is known for a complex topology with 4.6 X 106base pairs (bp) long sequence of nucleotide packed within a micrometer-sized celllular confinement. The inherent organization underlying this chromosome eludes general consensus due to the lack of a high-resolution picture of its conformation. Here we present our development of an integrative model of E. coli at a 500 bp resolution (https://github.com/JMLab-tifrh/ecoli_finer), which optimally combines a set of multi-resolution genome-wide experimentally measured data within a framework of polymer based architecture. In particular the model is informed with intra-genome contact probability map at 5000 bp resolution derived via Hi-C experiment and RNA-sequencing data at 500 bp resolution. Via dynamical simulations, this data-driven polymer based model generates appropriate conformational ensemble commensurate with chromosome architectures that E. coli adopts. As a key hallmark, the model chromosome spontaneously self-organizes into a set of non-overlapping macrodomains and suitably locates plectonemic loops near the cell membrane. As novel extensions, it predicts a contact probability map simulated at a higher resolution than precedent experiments and can demonstrate segregation of chromosomes in a partially replicating cell. Finally, the modular nature of the model helps us to devise control simulations to quantify the individual role of key features in hierarchical organization of the bacterial chromosome.

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“…More relevant for elucidating the mechanism of bacterial chromosome segregation is examining the effects of ring polymer topology as well as the effects of loop formation through cross-linking, as in the phenomenon of proteins bridging chromosomal DNA segments. 22 Above all, our simulation studies will continue to be guided by ongoing in vitro DNA experiments employing nanofluidic devices.…”

Section: Discussionmentioning

confidence: 99%

“…Numerous computer simulation studies have examined the effects of entropic repulsion for two polymers in such geometries. 1–23 Most of these studies have examined the segregation behaviour of flexible linear polymers, 1–6,8,9,11,13,16,17 though some have also investigated the behaviour of ring polymers 7,10,12,14,15,18 and more complex topologies. 22,23 In addition, the effects of bending rigidity, 11,16 a difference in the contour lengths, 21 macromolecular crowding, 12,15,18 and electrostatics 19,20 on the segregation dynamics and thermodynamics have been examined in detail.…”

Section: Introductionmentioning

confidence: 99%

“…1–23 Most of these studies have examined the segregation behaviour of flexible linear polymers, 1–6,8,9,11,13,16,17 though some have also investigated the behaviour of ring polymers 7,10,12,14,15,18 and more complex topologies. 22,23 In addition, the effects of bending rigidity, 11,16 a difference in the contour lengths, 21 macromolecular crowding, 12,15,18 and electrostatics 19,20 on the segregation dynamics and thermodynamics have been examined in detail. Information gleaned from these studies may be useful in helping advance nanofluidic technology used in applications such as DNA sorting, 24 DNA denaturation mapping, 25,26 and genome mapping.…”

Section: Introductionmentioning

confidence: 99%

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