DNA segregation in Escherichia coli cells with 5-bromodeoxyuridine-substituted nucleoids

WITHDRAWN: Symmetries and Asymmetries Associated with Non-Random Segregation of Sister DNA Strands in Escherichia coli

The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.semcdb.2013.05.010. The duplicate article has therefore been withdrawn.

Symmetries and asymmetries associated with non-random segregation of sister DNA strands in Escherichia coli

The successful inheritance of genetic information across generations is a complex process requiring replication of the genome and its faithful segregation into two daughter cells. At each replication cycle there is a risk that new DNA strands incorporate genetic changes caused by miscopying of parental information. By contrast the parental strands retain the original information. This raises the intriguing possibility that specific cell lineages might inherit "immortal" parental DNA strands via non-random segregation. If so, this requires an understanding of the mechanisms of non-random segregation. Here, we review several aspects of asymmetry in the very symmetrical cell, Escherichia coli, in the interest of exploring the potential basis for non-random segregation of leading- and lagging-strand replicated chromosome arms. These considerations lead us to propose a model for DNA replication that integrates chromosome segregation and genomic localisation with non-random strand segregation.

Hypothesis: chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation

To explain how daughter chromosomes are separated into discrete nucleoids and why chromosomes are partitioned with pole preferences, I propose that differential gene expression occurs during DNA replication in Escherichia coli. This differential gene expression means that the daughter chromosomes have different patterns of gene expression and that cell division is not a simple process of binary fission. Differential gene expression arises from autocatalytic gene expression and creates a separate proteolipid domain around each developing chromosome via the coupled transcription-translation-insertion of proteins into membranes (transertion). As these domains are immiscible, daughter chromosomes are simultaneously replicated and separated into discrete nucleoids. I also propose that the partitioning relationship between chromosome age and cell age arises because the poles of cells have a proteolipid composition that favours transertion from one nucleoid rather than from the other. This hypothesis forms part of an ensemble of related hypotheses which attempt to explain cell division, differentiation and wall growth in bacteria in terms of the physical properties and interactions of the principal constituents of cells.

Relationships between chromosome segregation, cell shape and temperature in Escherichia coli

The partitioning of chromosomes into daughter cells during the division of Escherichia coli is non-random. As a result, the chromosome containing the older template DNA strand has a higher probability of segregating toward the old cell pole than toward the new cell pole. The numerical value of this probability is a function of the incubation temperature. It is shown here that a recent model for explaining the physiological basis for non-random chromosome segregation also explains the temperature dependence of the segregation process.

Analysis of a model for minichromosome segregation in Escherichia coli

The present article contains a theoretical, quantitative analysis of the implications of the Helmstetter-Leonard model (1987, J. molec. Biol. 197, 195-204.) for the segregation of chromosomal DNA in Escherichia coli, on the expected copy-number distribution of minichromosomes in a culture in steady-state exponential growth. According to the model, two determinants are involved in the mechanism of chromosome segregation: a partition system that assures the equal allotment of chromosomes between daughter cells at cell division, and a locus within the minimal oriC region that specifies the attachment site of the chromosomes to the cell envelope at initiation of replication. There are many parameters that must be taken into account in such a study, and since some of them are probabilistic in nature, a strictly analytical approach is not feasible and we had to resort to computer simulation. A wide range of parameter values was tested, in all combinations. The minichromosome copy-number distributions obtained all had a prominent mode equal to the number of oriC binding sites and their main features were determined essentially by that and very little by any of the other parameters of the model. In order to avoid the unrealistic situation in which this one feature completely dominates the results, the original model was modified so that each individual minichromosome is no longer required to replicate during every cell generation, by introducing a limit to the number of unsuccessful attempts to locate a suitable binding site. The copy-number distributions predicted by this version of the model are quantitatively and qualitatively very different and depend on all the components of the model. The simulation results are sufficiently well-behaved to allow consideration as to whether a particular empirical minichromosome copy-number distribution--when such data become available--could in fact be governed by the proposed model; it may even be possible to get a rough estimate for the different parameters involved.

Involvement of cell shape in the replication and segregation of chromosomes in Escherichia coli

Chromosome replication appears to initiate in E. coli when the dnaA boxes in oriC become filled with DnaA protein, which could simultaneously mediate both the unwinding of the origin for the start of polymerization and the attachment of oriC to the cell envelope (Bramhill and Kornberg, 1988; Løbner-Olesen et al., 1989; Pierucci et al., 1989). The attachment takes place somewhere within the cell half in which the oriC resides. The boundaries of this attachment/replication zone, which cannot include the polar cap, could be demarcated by the polar and centrally located periseptal annuli (Rothfield, this Forum). Since attachment and polymerization are two aspects of the same process, the attachment probably takes place via the polymerizing strand. Once polymerization begins, the oriC with the older template strand moves away from the younger one, by mechanisms unknown, to eventually take up residence in the equivalent domain of the complementary sister cell. Thus, the template strand that stays within its domain corresponds to the strand that was attached during the previous round of replication, and the template that moves away is the one that was not attached. The driving force for this translocation is not specified by our model, but a number of plausible alternatives have been proposed by others (reviewed in Leonard and Helmstetter, 1990). Throughout the ensuing replication and cell division, the chromosomes are located (or can move freely) within the attachment/replication zone of the developing daughter cell (lateral cylinder and septum). At some time during the course of this process, but before the next initiation event, the replication origins must be released from the attachment sites so that the entire process can be repeated. Thus, the probabilistic non-random chromosome segregation is due to the asymmetry of the attachment/replication zone in the cell, whereas the partitioning system itself must possess a mechanism to discriminate between template strands of different ages. This apparent mechanistic relationship between chromosome replication, chromosome partitioning and the maintenance of cell shape may provide an interesting framework for future experiments.

Chromosome and cell wall segregation in Streptococcus faecium ATCC 9790

Segregation was studied by measuring the positions of autoradiographic grain clusters in chains formed from single cells containing on average less than one radiolabeled chromosome strand. The degree to which chromosomal and cell wall material cosegregated was quantified by using the methods of S. Cooper and M. Weinberger, dividing the number of chains labeled at the middle. This analysis indicated that in contrast to chromosomal segregation in Escherichia coli and, in some studies, to that in gram-positive rods, chromosomal segregation in Streptococcus faecium was slightly nonrandom and did not vary with growth rate. Results were not significantly affected by strand exchange. In contrast, labeled cell wall segregated predominantly nonrandomly.

Mechanism for chromosome and minichromosome segregation in Escherichia coli

A mechanism for the segregation of chromosomes and minichromosomes into daughter cells during division of Escherichia coli is presented. It is based on the idea that the cell envelope contains a large number of sites capable of binding to the chromosomal replication origin, oriC, and that a polymerizing DNA strand becomes attached to one of the sites at initiation of a round of replication. The attachment sites are distributed throughout the actively growing cell envelope, i.e. lateral envelope and septum, but not in the existing cell poles. This asymmetric distribution of oriC attachment sites accounts for the experimentally observed non-random chromosome and minichromosome segregation, and for the variation in the degree of non-random segregation with cell strain and growth rate. The multi-site attachment concept also accounts for the unstable maintenance of minichromosomes.

Bacterial DNA segregation: its motors and positional control

A model for DNA segregation in bacteria is proposed which involves not merely growth of the cell membrane and wall, as previously assumed, but also the active movement of one of the two chromosome sister origins by a DNA helicase enzyme and of the chromosome termini and the bulk of the chromosomes by supercoiling tension exerted by DNA gyrase. This provides a unified mechanism for DNA chromosome movement in prosthecate budding bacteria as well as for bacteria that undergo binary fission. The positional control of DNA segregation and the plane of cell division depend, I suggest, on four things: (1) the attachment of the daughter chromosome termini to the cell wall in a position adjacent to the new cell poles at about the time of septation, (2) the displacement of the parental chromosome terminus from this attachment site by the mobile origin, which attaches itself instead to the wall at that point, (3) the movement of the chromosome terminus to a new location in between the daughter origins by the tension of supercoiling, and (4) the determination of the location of the future septum at the position occupied by the chromosome terminus at the time of septal initiation; septum-initiation proteins are postulated to achieve this by binding directly or indirectly to the chromosome terminus. This mechanism automatically ensures ordered DNA segregation in rapidly growing bacteria with more than two sister origins of replication.