The effects of polydisperse crowders on the compaction of theEscherichia colinucleoid

Abstract

DNA binding proteins, supercoiling, macromolecular crowders, and transient DNA attachments to the cell membrane have all been implicated in the organization of the bacterial chromosome. However, it is unclear what role these factors play in compacting the bacterial DNA into a distinct organelle‐like entity, the nucleoid. By analyzing the effects of osmotic shock and mechanical squeezing on Escherichia coli, we show that macromolecular crowders play a dominant role in the compaction of the DNA into the nucleoid. We find that a 30% increase in the crowder concentration from physiological levels leads to a three‐fold decrease in the nucleoid's volume. The compaction is anisotropic, being higher along the long axes of the cell at low crowding levels. At higher crowding levels, the nucleoid becomes spherical, and its compressibility decreases significantly. Furthermore, we find that the compressibility of the nucleoid is not significantly affected by cell growth rates and by prior treatment with rifampicin. The latter results point out that in addition to poly ribosomes, soluble cytoplasmic proteins have a significant contribution in determining the size of the nucleoid. The contribution of poly ribosomes dominates at faster and soluble proteins at slower growth rates.

Impact of crowders on the morphology of bacterial chromosomes

“…In an earlier study [28] we have investigated the impact of changing cell length on the chromosome organization. The current study establishes the impact of crowder size on the relative organization of the chromosome and molecular crowders, a topic of recent experimental interest [45]. The present model is able to simultaneously account both for the compression of the chromosome to a sub-volume of the cell forming a nucleoid-like membrane-less organelle, as well as the induced helicity.…”

Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

“…Cell-surface expansion thus allows cells to control dry-mass density and therefore the level of cytoplasmic macromolecular crowding during growth. Crowding, in turn, impacts processes comprising macromolecular diffusion ( 7 , 8 ), bacterial nucleoid organization ( 9 ), and protein–DNA interactions ( 10 ). Accordingly, it was suggested that biomass growth rate depends on dry-mass density and crowding ( 11 – 13 ).…”

Solvent quality and chromosome folding inEscherichia coli

“…After accounting for the solvent quality of the cytoplasm, the estimated rigidity of the DNA under physiological conditions and the circularity of the chromosome (STAR Methods), we found that the theoretical estimation of the chromosome goes down to ~9 µm 3 , which is only ~10-fold (as opposed to 1,000-fold) larger than its experimentally determined size in cells (Figure 8, inset). The remaining compaction needed is likely achieved by other compacting factors such as DNA supercoiling, NAPs, nucleoid-associated RNAs and macromolecular crowding (Cunha et al, 2001;Dame, 2005;de Vries, 2010;Hammel et al, 2016;Jeon et al, 2017;Jun, 2015;Macvanin et al, 2012;Odijk, 1998;Pelletier et al, 2012;Qian et al, 2017;Shendruk et al, 2015;Wegner et al, 2016;Wu et al, 2019;Yang et al, 2020;Yoshikawa et al, 2010;Zhang et al, 2009;Zimmerman, 1993;Zimmerman and Minton, 1993), though some of these factors may also contribute to the poor solvent quality of the cytoplasm (see below).…”

“…While the direct contribution of these proteins to DNA compaction is not entirely clear (Spurio et al, 1992;Wu et al, 2019), NAPs and SMC protein complexes are known to play important roles in the organization and regulation of chromosome architecture at the level of individual genes and CIDs (Dame et al, 2020). In addition, macromolecular crowding is frequently proposed to drive chromosome compaction through steric effects (Cunha et al, 2001;de Vries, 2010;Jeon et al, 2017;Jun, 2015;Odijk, 1998;Pelletier et al, 2012;Shendruk et al, 2015;Wegner et al, 2016;Wu et al, 2019;Yang et al, 2020;Yoshikawa et al, 2010;Zhang et al, 2009;Zimmerman, 1993;Zimmerman and Minton, 1993). The idea is that cytoplasmic components larger than the DNA mesh size (i.e., crowders) will be excluded from the nucleoid, creating an imbalance in component concentration between the nucleoid region and the rest of the cytoplasm.…”