Compaction of bacterial genomic DNA: clarifying the concepts

Abstract

: The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to occupy the whole available volume when constrained to fit in the cell. Still, it has been known for more than half a century that the DNA is localized in a well defined region of the cell, called the nucleoid, which occupies only 15% to 25% of the total volume. Although this problem has focused the attention of many scientists for the past decades, there is still no certainty concerning the mechanism that enables such a dramatic compaction. The goal of this Topical Review is to take stock of our knowledge on this question by listing all possible compaction mechanisms with the proclaimed desire to clarify the physical principles they are based upon and discuss them in the light of experimental results and the results of simulations based on coarse-grained models. In particular, the fundamental differences between ψ-condensation and segregative phase separation and between the condensation by small and long polycations are highlighted. This review suggests that the importance of certain mechanisms, like supercoiling and the architectural properties of DNA-bridging and DNA-bending nucleoid proteins, may have been overestimated, whereas other mechanisms, like segregative phase separation and the self-association of nucleoid proteins, as well as the possible role of the synergy of two or more mechanisms, may conversely deserve more attention.Keywords : bacteria, genomic DNA, nucleoid, compaction, coarse-grained model 2 -IntroductionIllustrations of the hierarchical compaction of genomic DNA in the nuclei of eukaryotic cells can be found in any textbook, from the initial wrapping of DNA around histone proteins to the final X-shaped chromosomes, through the various levels of fiber condensation. While seemingly simpler, the compaction of bacterial genomic DNA is nevertheless more poorly understood. One of the main reasons is that typical cell dimensions and DNA size of prokaryotes are significantly smaller than those of eukaryotes, with cell radii of the order of 1 µm against 10 to 100 µm and DNA size of the order of millions of base pairs against billions of base pairs. As a consequence, optical microscopy experiments are able to show that DNA occupies only a small part of the cell (from 15% to 25%) but fail to provide more detail because of resolution issues [1]. In contrast, electronic microscopy is able to provide information on the ultra-structure of the nucleoid (the region where the DNA is localized) but results depend dramatically on the experimental procedure that is used to prepare the cells [1,2]. Finally, the more recent techniques that consist in labeling specific genes with fluorescent dyes or proteins [3] usually provide information on the dynamics close to the loci of these genes but not on the global organization of the nucleoid. Owing to these difficulties, ev...

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study

“…The size results are shown in Appendix A, Figures 10,11 and 12: these correspond to Figures 4, 5 and 6, and were obtained with a protein size of 2σ. The charge results are shown in Appendix B, Figures 13,14,15: these correspond to Figures 3,4,5. In all cases, the trends are qualitatively identical, and confirm our conclusions above. There are quantitative differences for the size simulations when the volume fraction is high: this is expected as, under those situation, it is the volume fraction, rather than number density, which determines the compression pressure and force.…”

“…Here we present the results corresponding to Figures 3,4 and 5 in the main text, but for charged DNA beads and proteins.…”

A segregative phase separation scenario of the formation of the bacterial nucleoid

“…The models used in this study share several common points with those developed previously to investigate facilitated diffusion, [52][53][54] the interactions of H-NS proteins and DNA, [55][56][57], the formation of the bacterial nucleoid, [4,5,48,[44][45][46][47] as well as questions dealing with spatial confinement and molecular crowding, [58,59] More precisely, genomic DNA is represented by a circular chain of 1440 n = beads of radius a separated at equilibrium by a distance 0 5.0 l = nm, where each bead represents 15 consecutive base pairs. The DNA chain is enclosed in a confining sphere of radius 0 120 R = nm (see Fig.…”

Bacterial chromosome organization. I. Crucial role of release of topological constraints and molecular crowders

“…It is shown in the previous theoretical and experimental studies that the DNA polymer compacts and collapses in the presence of the crowding environment (DNA condensation) [16,32]. In the presence of the charged molecular crowders the effective interactions between DNA-DNA segments increases which leads to the segregative phase separation [16,17,33]. The segregative phase separation may happen if two crowders (e.g., protein, RNAs, etc.)…”