Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome

Abstract

Despite recent progress in visualization experiments, the mechanism underlying chromosome segregation in bacteria still remains elusive. Here we address a basic physical issue associated with bacterial chromosome segregation, namely the spatial organization of highly confined, self-avoiding polymers (of nontrivial topology) in a rod-shaped cell-like geometry. Through computer simulations, we present evidence that, under strong confinement conditions, topologically distinct domains of a polymer complex effectively repel each other to maximize their conformational entropy, suggesting that duplicated circular chromosomes could partition spontaneously. This mechanism not only is able to account for the spatial separation per se but also captures the major features of the spatiotemporal organization of the duplicating chromosomes observed in Escherichia coli and Caulobacter crescentus.bacterial chromosome segregation ͉ Caulobacter crescentus ͉ Escherichia coli ͉ polymer physics B acteria are arguably the simplest living organisms that are able to reproduce independently. The key step in cellular reproduction consists of the duplication of the genetic material and its subsequent distribution over the offspring. Successful as they are from an evolutionary perspective, bacteria are indeed considered to be highly efficient and accurate in these processes.What then is the mechanism underlying bacterial chromosome segregation? Perhaps the most influential model so far was proposed by Jacob et al. in 1963 (1) in their seminal paper on the replicon model of Escherichia coli; if replicating chromosomes are attached to the elongating cell-wall membrane, they can be segregated passively by insertion of membrane material between the attachment points. Although the hypothesis by Jacob et al.(1) is intuitive and elegant, it has been undermined by a series of recent visualization experiments. In Bacillus subtilis (2) and Caulobacter crescentus (3), for example, the measured rate of movement of the replication origin ranges from 0.1 to 0.3 m͞min, almost 10 times larger than the cell elongation rate. In E. coli, on the other hand, the movement rate of DNA segments is still a matter of debate [see, for example, Elmore et al. (4)]. Nevertheless, all three species, including E. coli, show striking dynamics and directed longitudinal movements of chromosome loci during replication; although details vary from organism to organism, typically the duplicated replication origins (ori) move toward opposite poles in the cell, and the terminus (ter) moves toward the cell center (3, 5-7).A number of alternative models have been proposed recently to explain the driving force for DNA segregation in bacteria [for recent reviews, see Woldringh (8), Errington et al. (9), and Gitai et al. (10) and references therein]. A consensus view that seems to emerge from this more recent literature, at least in case of C. crescentus, favors the existence of putative ''eukaryotic-like'' mechanisms (11-13), which would actively push͞pull the duplicating bacterial c...

Independent Segregation of the Two Arms of theEscherichia coli oriRegion Requires neither RNA Synthesis nor MreB Dynamics

“…Blocking of replication in one replichore does not prevent segregation of loci on the other. It seems plausible that spontaneous chromosome segregation by entropic disentanglement of the chromosomal polymer (1,27,28) may provide the essence of the segregation mechanism. Therefore, the key to efficient and faithful segregation is likely to reside in chromosome organization itself and the processes that drive this organization, as well as independent replication by spatially separated replisomes tracking along the DNA and the subsequent decatenation by TopoIV.…”

“…Finally, thermodynamic considerations of the properties of a highly confined, self-avoiding polymer (representing a DNA molecule) in a rod-shaped cell-like geometry (representing a bacterial cell) have indicated that duplicated circular chromosomes could segregate spontaneously without any additional force in physiologically relevant timescales (1,27,28). Therefore, entropy alone may be sufficient to produce the observed segregation of replicated chromosomes, while plasmids use active partition systems because their small size in a "sea" of chromosomal DNA would not lead to effective spontaneous segregation.…”

Caulobacter requires a dedicated mechanism to initiate chromosome segregation

“…In vivo fluorescence microscopy showed that the speed of segregation of individual loci is too fast to be accounted for by attachment of sister chromosomes to a growing cell envelope (1,3,4), as had been proposed (5). These observations led to the suggestion that rapid segregation may be the consequence of nondedicated mechanisms, such as force exerted by the DNA or RNA polymerases (6,7) or entropic exclusion of sister chromosomes (8), all of which predict that the order of segregation will follow the order of replication. Alternatively, segregation may be driven by a dedicated mechanism acting on a centromeric sequence (9,10), in which case the first sequence to segregate would be the centromere regardless of when it is replicated.…”

“…The ability to uncouple segregation from replication by moving parS away from Cori allowed us to determine whether nondedicated mechanisms are sufficient to effect chromosome segregation in Caulobacter, as has been suggested (8). The strain shown in Fig.…”

“…However, although the absence of parAI in V. cholerae alters chromosome segregation, growth is not affected (19,20). Indeed, despite widespread conservation of the parS sequence, except for V. cholerae chromosome II and Caulobacter crescentus (henceforth, Caulobacter), the absence of parABS elements only mildly impairs growth (18,21), suggesting the presence of redundant chromosome segregation mechanisms (8,(22)(23)(24).…”