Geometrical ordering of DNA in bacteria

Abstract

The bacterium Caulobacter crescentus shows a remarkable spatial ordering of its chromosome that leads to a strong linear correlation between the position of genes on the chromosomal map and their spatial position in the cellular volume. In a recent study we have shown that a robust and universal geometrical ordering mechanism can explain this correlation. We demonstrated that self-avoidance of DNA, specific positioning of one or few DNA loci (such as origin or terminus) together with the action of DNA compaction proteins (that organize the chromosome into topological domains) are sufficient to get a linear arrangement of the chromosome along the cell axis. This configuration, however, only represents the population average. Individual cells can have DNA arrangements that deviate significantly from the mean configuration and that break left-right symmetry. Symmetry breaking is stronger for longer chromosomes. 

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Figures and Tables

Figure 1 Average subcellular position of genes as function of their position on the chromosome in C. crescentus and E. coli as obtained from numerical simulations of compacted DNA . (A and B) show the position of genes along the cell axis as function of their position on the chromosomal map for an average chromosome configuration as obtained from our theoretical model in which compacted DNA is represented by a chain of blobs. The position on the chromosome is parameterized by the contour length s (measured in units of DNA length L). The configurations shown in (A) are for different blob diameters but in all cases 2,000 blobs are used to represent the chromosome (of length 4.02 Mbp) of a C. crescentus swarmer cell. The implemented cell volume has height H = 2 µm and cross section 0.5 µm × 0.5 µm. The fixed positions of ori and ter (at z_ori = 0.1H and z_ter = 0.9H) have been adjusted to minimize the differences between the experimental data of reference 1 (dots) and the predictions of the model. (B) shows a symmetry-breaking chromosomal configuration (blue line) in an individual E. coli cell (with volume 1 µm × 1 µm × 1 µm). The red line represents the average symmetry-breaking configuration (averaged over 50,000 chromosomal arrangements). Bars indicate the standard deviation from the mean configuration. In the configurations shown ori is at the cell pole and ter is positioned in midcell (z_ori = 0.1H and z_ter = 0.5H). The chromosome has a length of 11,310 blobs. Asymmetric chromosomal arrangements occur also for different ori and ter positions. (C) shows the averaged order parameter ξ for cells with volume H × H × H and chromosome length L. The chromosomal arrangements are more asymmetric for longer chromosomes (or smaller cells). The data shown are for z_ori = 0 and z_ter = H.

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