Solvent quality and chromosome folding inEscherichia coli

Abstract

<jats:title>Summary</jats:title><jats:p>All cells must fold their genomes, including bacterial cells where the chromosome is compacted into a domain-organized meshwork called nucleoid. Polymer conformation depends highly on the quality of the solvent. Yet, the solvent quality for the DNA polymer inside cells remains unexplored. Here, we developed a method to assess this fundamental physicochemical property in live bacteria. By determining the DNA concentration and apparent average mesh size of the nucleoid, we provide evidence that the cytoplasm is a poor solvent for the chromosome in <jats:italic>Escherichia coli</jats:italic>. Monte Carlo simulations showed that such a poor solvent compacts the chromosome and promotes spontaneous formation of chromosomal domains connected by lower-density DNA regions. Cryo-electron tomography and fluorescence microscopy revealed that the (poly)ribosome density within the nucleoid is spatially heterogenous and correlates negatively with DNA density. These findings have broad implications to our understanding of chromosome folding and intracellular organization.</jats:p>

Physical properties of the cytoplasm modulate the rates of microtubule polymerization and depolymerization

“…Ribosomes alone occupy ∼20% of that volume (Delarue et al, 2018). Biophysical studies revealed that these constituents form a porous, visco-elastic material that allows diffusion of small molecules but impedes movement of larger particles (Luby-Phelps et al, 1986; Moeendarbary et al, 2013; Xiang et al, 2020), and molecular simulations show a high density of macromolecules jostling and colliding from diffusive motion. (Mcguffee and Elcock, 2010; Yu et al, 2016).…”

Genome-in-a-Box: Building a Chromosome from the Bottom Up

“… 13 , 14 , 17 Furthermore, the cytoplasm in bacteria is a poor solvent for DNA, causing the spontaneous compaction and formation of domain-like structures. 10 Lastly, the DNA polymer itself as well as the surrounding cytoplasm were found to exhibit confinement-induced glassy dynamics, both in bacteria 11 and in human cells. 12 , 15 , 16 …”

“…(ii) Distribution of ribosomes (that act as crowders) in E. coli from cryo-electron tomograms. Adapted with permission from ref ( 10 ). Copyright 2020 Xiang et al .…”

“…(iii) Computer simulation that shows that DNA in a poor solvent (bottom) forms heterogeneous structures, while DNA in an ideal solvent (top) is homogeneously distributed throughout the cell (dashed red line). Adapted with permission from ref ( 10 ). Copyright 2020 Xiang et al .…”

“…The past decade, in particular, rapidly expanded our knowledge of how the genetic material is physically organized within the cells of the various kingdoms of life, yielding a string of notable discoveries on the interplay between function, structure, and dynamics of chromosomes. Breakthroughs were, for example, the structural mapping of the genomes using chromosome conformation capture (Hi-C and related) techniques, 3 , 4 the capability of structural maintenance of chromosomes (SMC) protein complexes to extrude loops of DNA as demonstrated using single-molecule fluorescence assays, 5 − 9 how the properties of the cytoplasm, nucleoplasm, and confinement influence the dynamics and structure of chromosomes across species, 10 − 19 or the discovery of the importance of phase separation in various aspects of chromosome organization, 20 − 25 from transcriptional condensates 26 − 33 to heterochromatin formation. 34 − 36 From this brief list, it is already apparent that chromosome organization spans a multitude of scales from single molecules to full chromosomes.…”