Subdiffusion of loci and cytoplasmic particles are different in compressed Escherichia coli cells

Shi Yu,Pietro Cicuta,Bianca Sclavi,Marco Cosentino Lagomarsino,Kevin D Dorfman,Julian Sheats

doi:10.1038/s42003-018-0185-5

Abstract

The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. Although recent work has addressed the role of non-equilibrium sources of activity and crowding, the consequences of mechanical perturbations are relatively less explored. Here we use a microfabricated valve system to track both fluorescently labeled chromosomal loci and cytoplasmic particles in Escherichia coli cells shortly after applying a compressive force, observing the response on time scales that are too sudden to allow for biochemical response from the cell. Cytoplasmic diffusion slows markedly on compression but the exponent governing the growth of the ensemble-averaged mean-squared displacement of cytoplasmic particles is unaffected. In contrast, the corresponding exponent for DNA loci changes significantly. These results suggest that DNA elasticity and nucleoid organization play a more important role in loci subdiffusion than cytoplasmic viscoelasticity under such short time scales.

Highlights

The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell
The mechanism causing the slowing down of cytoplasmic diffusion remains unclear, the effects of compression on E. coli cells are ideal for testing the viscoelastic Rouse model of loci diffusion[11], as measurements made shortly after applying the compressive force directly probe the physical properties of the cell before it has time to respond biochemically
We have trapped E. coli cells under collapsed polydimethylsiloxane (PDMS) valves[23] (Fig. 1a, b) with 200 μm wide control and flow channels[17], allowing us to investigate the dynamics of DNA loci (Fig. 1c) and cytoplasmic particles in the flattened E. coli cells (Fig. 1d) over the relatively short time lags (~100 s) that are relevant for studying loci diffusion[4,6]

Summary

Introduction

The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. Recent atomistic molecular dynamics simulations[7,8] and coarse-grained simulations[9,10] allow access to the dynamics and the heterogeneity of the cytoplasm over very short time scales, e.g., hundreds of nanoseconds, the diffusive behavior of proteins and loci on the experimental time scales of seconds cannot be computed using detailed molecular models To circumvent this limitation, Weber et al.[11] proposed a model combining a Rouse chain and fractional Langevin motion to capture the subdiffusion of a DNA chain in a viscoelastic medium. The mechanism causing the slowing down of cytoplasmic diffusion remains unclear, the effects of compression on E. coli cells are ideal for testing the viscoelastic Rouse model of loci diffusion[11], as measurements made shortly after applying the compressive force directly probe the physical properties of the cell before it has time to respond biochemically. For diffusion in a viscoelastic fluid, particles become subdiffusive (α < 1), where the exponent α is connected to the elastic memory of the fluid[11]

Methods

Results

Conclusion