Abstract
In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.
Highlights
The E. coli bacterial chromosome, which consists of a 1.6 mm long negatively supercoiled circular DNA strand (4.6 Mbp), is subject to strong spatial restraints [1], as it needs to fit within the 2 × 1 × 1 μm ellipsoid bacterial cell wall
To compare the two-dimensional projection of 3D diffusion in our simulation results to optical microscope observations on focusing plane [11] directly, the 2D diffusion coefficient and the exponent characterizing the subdiffusion of cytoplasmic particles and loci can be fitted according to the Equation (4) as follows
In this article, using a simple polymer model and a cylindrical confinement, the subdiffusion of both cytoplasmic particles and loci were reproduced by Langevin dynamics simulation
Summary
The E. coli bacterial chromosome, which consists of a 1.6 mm long negatively supercoiled circular DNA strand (4.6 Mbp), is subject to strong spatial restraints [1], as it needs to fit within the 2 × 1 × 1 μm ellipsoid bacterial cell wall. When E. coli bacterial cell is compressed, the motions of cytoplasmic particles have been slowed down for about one order of magnitude [10,11], while the loci subdiffusion remains almost unaffected [11] Perturbation such as weak compression (∼5 psi) does not change the rates of cell elongation, proliferation, DNA replication, and protein synthesis significantly in E. coli cell [12] so that E. coli bacterial cells can still grow and divide under compressive force [13]. While extensive research has been carried out to explore the slowing down of cytoplasmic diffusion resulting from the hydrodynamics and crowding effects [14,25,26], there are fewer studies on how the bacterial chromosome affects the cytoplasmic diffusion In this manuscript, a simple coarse-grained polymer model of bacterial chromosome (“feather-boa model”) [27,28] was adopted to simulate the motions of various loci as well as cytoplasmic particles in confinement. Since the highly dynamic bacterial chromosome structure can contribute to the heterogeneity of the environment in cell, hopefully, this work might shed some light on the further development of analytical models which can accurately capture the mechanical properties of bacterial cell
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