Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact

Jung, Youngkyun; Jeon, Chan Hong; Kim, Juin; Jeong, Hawoong; Jun, Suckjoon; Ha, Bae‐Yeun

doi:10.1039/c1sm05706e

Cited by 75 publications

(185 citation statements)

References 39 publications

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“…The equilibrium volume of the in vitro chromosomes isolated in microchannels is several times smaller than the ones isolated in the absence of confinement (Table 1 and SI Appendix, Section II.B). This shape-dependent decrease in total chromosomal volume is consistent with a polymer model of the bacterial chromosome (11,17,44).…”

Section: Discussionsupporting

confidence: 82%

“…In previous work, we suggested how chromosome segregation (demixing) can be driven by physical processes using a confined polymer model (11,17,44). Considering the intriguing quantitative agreement between our measurements and the same model (Figs.…”

Section: Discussionsupporting

confidence: 80%

“…1 and 4), means that entropic forces can readily and dynamically influence the chromosome, from segregation and organization (11,13,17,44) to compaction (3,23), as suggested previously and demonstrated in this work.…”

Section: Discussionsupporting

confidence: 76%

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Physical manipulation of the Escherichia coli chromosome reveals its soft nature

Pelletier

Halvorsen

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In this work, we demonstrate experimentally the fundamentally soft nature of the bacterial chromosome and the entropic forces that can compact it in a crowded intracellular environment. We developed a unique "micropiston" and measured the force-compression behavior of single Escherichia coli chromosomes in confinement. Our data show that forces on the order of 100 pN and free energies on the order of 10 5 k B T are sufficient to compress the chromosome to its in vivo size. For comparison, the pressure required to hold the chromosome at this size is a thousand-fold smaller than the surrounding turgor pressure inside the cell. Furthermore, by manipulation of molecular crowding conditions (entropic forces), we were able to observe in real time fast (approximately 10 s), abrupt, reversible, and repeatable compaction-decompaction cycles of individual chromosomes in confinement. In contrast, we observed much slower dissociation kinetics of a histone-like protein HU from the whole chromosome during its in vivo to in vitro transition. These results for the first time provide quantitative, experimental support for a physical model in which the bacterial chromosome behaves as a loaded entropic spring in vivo.chromosome segregation | depletion forces | polymer physics | mother machine | optical trap

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Section: Discussionsupporting

confidence: 82%

Section: Discussionsupporting

confidence: 80%

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Physical manipulation of the Escherichia coli chromosome reveals its soft nature

Pelletier

Halvorsen

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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185

270

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“…12,13 It is worth emphasizing that the entropic picture is rather generic and largely independent of molecular details. 6 It remains relevant under a variety of physical constraints (e.g., ring chain topology and chain crosslinking). 3,6 A recent study even points out that various DNA binding proteins cooperate with the process of entropic segregation.…”

Section: Introductionmentioning

confidence: 99%

“…6 It remains relevant under a variety of physical constraints (e.g., ring chain topology and chain crosslinking). 3,6 A recent study even points out that various DNA binding proteins cooperate with the process of entropic segregation. 3 However, confined polymers have been much better understood at the single-chain level, whether they are flexible or stiff.…”

Section: Introductionmentioning

confidence: 99%

Intrachain Ordering and Segregation of Polymers under Confinement

et al. 2012

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We study the relationship between intrachain ordering and segregation tendency of two polymers confined in a cylindrical space. We find the chains segregate spontaneously even outside de Gennes' linear-ordering scaling regime, in which each chain is a linear array of blobs. When the chains are weakly compressed against each other, linear ordering is well preserved and the chains remain segregated. On the other hand, for moderate compression, new chain-ordering units emerge at intermediate length scales, within which blobs are randomly packed; yet these units (termed "superblobs") are linearly ordered, and the chains still segregate in the confined space. As the chains continue to be compressed, the linear regime disappears, but the chains can resist mixing effectively, more so in a more asymmetric space. We conclude that the linearly ordered E. coli chromosome is in the segregation regime.

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The Microscopic Structure–Property Relationship of Metal–Organic Polyhedron Nanocomposites

et al. 2019

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Monodispersed hairy nanocomposites with typical 2 nm (isophthalic acid)24Cu24 metal–organic polyhedra (MOP) as a core protected by 24 polymer chains with controlled narrow molecular weight distribution has been probed by imaging and scattering studies for the heterogeneity of polymers in the nanocomposites and the confinement effect the MOPs imposing on anchored polymers. Typical confined‐extending surrounded by one entanglement area is proposed to describe the physical states of the polymer chains. This model dictates the counterintuitive thermal and rheological properties and prohibited solvent exchange properties of the nanocomposites, whilst those polymer chain states are tunable and deterministic based on their component inputs. From the relationship between the structure and behavior of the MOP nanocomposites, a MOP‐composited thermoplastic elastomer was obtained, providing practical solutions to improve mechanical/rheological performances and processabilities of inorganic MOPs.

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Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact

Cited by 75 publications

References 39 publications

Physical manipulation of the Escherichia coli chromosome reveals its soft nature

Physical manipulation of the Escherichia coli chromosome reveals its soft nature

Intrachain Ordering and Segregation of Polymers under Confinement

The Microscopic Structure–Property Relationship of Metal–Organic Polyhedron Nanocomposites

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