Confinement and crowding control the morphology and dynamics of a model bacterial chromosome

Abstract

Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such a model chromosome spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like subvolume of the cell. With increasing cell length, the longitudinal size of the chromosome increases in a non-linear fashion to finally saturate, its morphology gradually opening up while displaying a changing number of helical turns. For shorter cells, the chromosome extension varies non-monotonically with cell size, which we show is associated with a radial to longitudinal spatial reordering of the crowders. Confinement and crowders constrain chain dynamics leading to anomalous diffusion. While the scaling exponent for the mean squared displacement of center of mass grows and saturates with cell length, that of individual loci displays broad distribution with a sharp maximum.

arXiv comment12 pages, 12 figures

References in corpus (4)

• The effective temperature
• Compression and stretching of a self-avoiding chain in cylindrical nanopores
• Elongation/Compaction of Giant DNA Caused by Depletion Interaction with a Flexible Polymer
• Spontaneous helicity of a polymer with side-loops confined to a cylinder

Cited by in corpus (3)

• Cross-linker mediated compaction and local morphologies in a model chromosome
• Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement
• DNA-polymer architecture orchestrates the segregation and spatio-temporal organization of E. coli chromosomes during replication in slow growth