Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement

Abstract

We measured the distance between fluorescent-labeled DNA loci of various interloci contour lengths in Caulobacter crescentus swarmer cells to determine the in vivo configuration of the chromosome. For DNA segments less than about 300 kb, the mean interloci distances, 〈r〉, scale as n 0.22 , where n is the contour length, and cell-to-cell distribution of the interloci distance r is a universal function of r/n 0.22 with broad cell-to-cell variability. For DNA segments greater than about 300 kb, the mean interloci distances scale as n, in agreement with previous observations. The 0.22 value of the scaling exponent for short DNA segments is consistent with theoretical predictions for a branched DNA polymer structure. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated interloci distance distributions predict that confinement leads to "freezing" of the supercoiled configuration. Lateral positions of labeled loci at comparable positions along the length of the cell are strongly correlated when the longitudinal locus positions differ by <0.16 μm. We conclude that the chromosome structure is supercoiled locally and elongated at large length scales and that substantial cell-to-cell variability in the interloci distances indicates that in vivo crowding prevents the chromosome from reaching an equilibrium arrangement. We suggest that the force causing rapid transport of loci remote from the parS centromere to the distal cell pole may arise from the release at the polar region of potential energy within the supercoiled DNA.chromosome organization | DNA segregation | polymer conformation | computational modeling | bacterial genome B acterial chromosomes are vastly longer than their cells, and in vivo chromosomal organization is only partially understood (1). The in vivo DNA is negatively supercoiled, it forms plectoneme structures with random-sized branches (2, 3), and the nucleoid is compacted by nucleoid-associated proteins (4). Fluorescent-labeled bacterial chromosomal loci exhibit random motion within a confined domain (5-8). In the Caulobacter swarmer cell, the chromosomal parS site, 8 kb away from the origin of replication initiation (Cori), is anchored at the flagellated pole (9), and the rest of the chromosome is organized such that the average position of loci along the length of the cell is proportional to their distance on the chromosome from parS (10). Fluorescent-labeled chromosomal loci positions in Escherichia coli cells also show a linear ordering along the cell length (11,12).Physical insights into equilibrium and dynamic polymer behavior can be inferred from the relationship between observable structural quantities and the length of the polymer (13,14). For example, the random-walk nature of polymer molecules frequently leads to the mean interloci distance 〈r〉 obeying a scaling relationship 〈r〉 ∼ n ν , where n is the contour length between segments and ν is a scaling...

The bacterial nucleoid: nature, dynamics and sister segregation

“…In E.coli , this presumably represents incorporation of sister material into the already-developed dual sister nucleoid units. In C. crescentus , it is proposed that localization of sister origins to opposite poles is followed by progressive replication and compaction of material towards the poles to give the final outcome [53]. …”

“…A specific polymer model for E.coli sister segregation envisions an initial event involving entropic exclusion of compacted origin domains, perhaps aided by an “entropic spring” of adjacent disordered regions, followed by organization-mediated accumulation of material into distal (terminus-adjacent) regions [59]. A different polymer model has been suggested to explain Caulobacter segregation events subsequent to bipolar origin localization [53]. All such models always assume a cell-like cylindrical volume; thus, radial confinement is implicitly present as a central component of segregation.…”

“…(C) Type I and Type II configuration patterns for three types of bacteria. C. crescentus remains in Type I throughout (discussion in [53]). B. subtilis cells are multi-nucleate and oscillate between Type I and Type II patterns [54].…”

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

“…Studies in E. coli and Salmonella have shown that RNA polymerase is capable of actively creating and remodeling dynamic supercoiled topological domains (6,33). Similarly, recent experimental work in Caulobacter reveals that highly transcribed genes appear to demarcate topological domains in the chromosome (7), and in vivo measurements of interloci distances in Caulobacter resemble those theoretically predicted for a branched supercoiled conformation with densely packed plectonemes (65). In all three of these organisms, topological domains are measured to possess average sizes of~10 kilobases (7,33) and the importance of transcription in regulating the size of these topological domains is suggested by the high conservation of genomic interspacing of highly expressed genes in the chromosomes of phylogenetically distant bacteria (33).…”

Dynamic spatial organization of multi-protein complexes controlling microbial polar organization, chromosome replication, and cytokinesis

“…There were multiple disciplines represented on the project team, so that the reports covered progress in a range of areas, including development of multi-protein polar complexes (7-9, 11, 25, 26, 45), organization and assembly of the cell division machinery (16-19, 24, 44), advances in imaging technology (2-6, 19, 33), the organization of cell regulation (10-13, 27, 31, 34, 35, 39, 40), chromosome organization (14,20,21,37,38,41), and computational biology (1). There were also five reviews (15,(28)(29)(30)36) …”