Impact of crowders on the morphology of bacterial chromosomes

Abstract

Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical cell. We observe spontaneous emergence of complementary helicity of the confined polymer and crowders. This feature is reproduced within a simplified effective model of the chromosome. This latter model further establishes the occurrence of longitudinal and transverse spatial segregation transitions between the chromosome and crowders upon increasing crowder size.

Balance of osmotic pressures determines the nuclear-to-cytoplasmic volume ratio of the cell

“… 67 , such crowders compress the chromatin, which is consistent with the case for which the dominant intranuclear pressure originates from compression of chromatin—and not the osmotic pressure of its counterions. Importantly, compression of DNA by crowders was demonstrated in molecular dynamics simulations ( 85 ).…”

Elucidation of Spatial Positioning of Ribosomes around Chromosome in Escherichia coli Cytoplasm via a Data-Informed Polymer-Based Model

“…The peaks on both ends of the linear density showcase the higher propensity of ribosomes to populate the ends of the cell. The analysis together suggests that the ribosome is just not an inert, noninteracting crowder, as had been traditionally posited in previous investigations; 14,44,45 rather, a fine balance between attractive and repulsive interactions between a ribosome and chromosome provides a quantitatively more accurate description of chromosome−ribosome spatial positioning. As will be elaborated in the upcoming sections, the requirement of the presence of both attractive and repulsive interactions between DNA and ribosomes is also suggestive of the non-negligible presence of ribosomes inside the chromosome mesh, in contrast to the long-held perspective of complete exclusion of ribosomes by DNA.…”

“…In a majority of the precedent modeling attempts of ribosomes and chromosome for an E. coli cell, ,,, ribosomes have been traditionally treated as inert crowders, devoid of any specific attractive interaction with the chromosome. Majorly driven by the qualitative hypothesis , that nucleoid and ribosomes mutually exclude each other in E.…”

“…The remaining 20% of ribosomes are nontranslating, exist as monomers, and are evenly distributed between the 30S and 50S subunits. 14,31,56 In a majority of the precedent modeling attempts of ribosomes and chromosome for an E. coli cell, 14,20,44,45 ribosomes have been traditionally treated as inert crowders, devoid of any specific attractive interaction with the chromosome. Majorly driven by the qualitative hypothesis 20,29 that nucleoid and ribosomes mutually exclude each other in E. coli cytoplasm, DNA−ribosome interactions had previously been modeled via purely excluded volume interaction (which are essentially soft repulsive interactions between DNA and ribosomes).…”

“…This exclusion is likely due to repulsion by the densely packed nucleoid, with the expelled ribosomes acting as macromolecular crowders for the chromosome, ,, creating an environment in which the cytoplasm is a poor solvent for the chromosome . Previous studies on the spatial positioning of ribosomes have traditionally treated them as inert crowders, assuming that ribosome–DNA interactions are solely driven by nonspecific excluded volume effects. ,− This has led to the long-held notion that the chromosome and ribosomes are spatially anticorrelated and segregated from each other to a high degree. However, recent findings from linear density profiles of the chromosome and ribosomes across the cytoplasm have demonstrated substantial densities of bound ribosomes (polysomes) as well as free ribosomes within the nucleoid-containing region of bacterial cells.…”