Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament

Abstract

The stochasticity of chromosome organization was investigated by fluorescently labeling genetic loci in live Escherichia coli cells. In spite of the common assumption that the chromosome is well modeled by an unstructured polymer, measurements of the locus distributions reveal that the E. coli chromosome is precisely organized into a nucleoid filament with a linear order. Loci in the body of the nucleoid show a precision of positioning within the cell of better than 10% of the cell length. The precision of interlocus distance of genomically-proximate loci was better than 4% of the cell length. The measured dependence of the precision of interlocus distance on genomic distance singles out intranucleoid interactions as the mechanism responsible for chromosome organization. From the magnitude of the variance, we infer the existence of an as-yet uncharacterized higher-order DNA organization in bacteria. We demonstrate that both the stochastic and average structure of the nucleoid is captured by a fluctuating elastic filament model. chromosome segregation | chromosome structure | nucleoid structure | polymer physics P rokaryotic chromosomes are organized into a compact DNA-protein complex called the nucleoid (1, 2). The physical structure of chromosomes has functional consequences, for example it affects gene regulation from the simplest prokaryotes (1) to multicellular organisms (3). Nucleoid organization and condensation also appear to play a central role in chromosome segregation: Mutants with defective chromosome segregation are typically accompanied by abnormal nucleoid organization or condensation (2). Although a significant number of such genes have been identified by genetic screens, the mechanism by which these molecular players effect the cellular-scale nucleoid structure is not yet understood (2). Similarly, the mechanism by which prokaryotic chromosomes are segregated is still hotly debated (2, 4, 5). The apparent dispensability of a mitotic-spindle-like mechanism in chromosome segregation in Escherichia coli (2, 4) has led to speculation that nucleoid organization and segregation may be the result of several redundant mechanisms, including polymer physics-embodied by the combined effects of entropy, confinement, and excluded volume-rather than resulting from the action of dedicated cellular machinery alone (2, 6, 7). This paper complements earlier work by focusing on the measurement and theoretical interpretation of two classes of statistical measures of chromosome organization: (i) the distributions of the positions of individual loci within the cell; and (ii) the distributions of displacements between pairs of genetic loci. We argue that the measurement and analysis of these distributions sheds light on the mechanisms of chromosomal positioning that have not been revealed in earlier measurements. The cellular-scale structure of the circular Caulobacter crescentus chromosome has already been shown to be linearly organized between replication cycles, with the origin of replication at one pole and the ter...

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

“…S10 A and B) such that the selectively increased superhelicity of the origin-proximal region and the resultant change in chromosome morphology precede the initiation of replication. Such selectivity suggests a lower superhelical density in the Ter region, consistent with the finding that in the prereplicative state in slow-growing cells the Ter region is extended (55). Concomitantly the increased spatial separation between origin-proximal H-NS target genes and the Ter-proximal location of the hns gene (Fig.…”

Persistent super-diffusive motion of Escherichia coli chromosomal loci

“…Decondensation rapid movements might explain the specificity of the Ter region ( Supplementary Fig. 8), which is reported to be more fluid and localized at the nucleoid periphery 29,30 (this happens far from cell divisions, when the Ter region is instead condensed and tethered 25,28,31 ). In the hypothesis of decondensation, loci that are freed from some chromosomal constraints might perform a faster random motion in the cytoplasm, but their trajectories could be persistent enough to be mistaken for near-ballistic at the observation timescale.…”

Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization

“…Notably, this trend is particularly evident for the Ter macrodomain locus, which becomes less mobile at cell poles and at mid-cell, that is, probably around cell division, when the Ter macrodomain is known to be compacted by MatP and possibly externally tethered 16,18,33 . Conversely, when the Ter macrodomain in its supposed uncompacted state, where it is found all along the cell longitudinal coordinate 8,9 , one can expect increased loci motion. We also reported a small variation of (cell-cycle averaged) apparent diffusion with respect to the growth conditions.…”

“…Some studies of the bacterial chromosome 3 have focussed on the organizational properties valid at particular times, for example, by taking the statistics of the subcellular positioning of loci within a population [8][9][10][11][12][13] . Other studies measure more directly the variation in time of chromosomal organization, which is fundamentally interconnected with chromosome replication and segregation.…”