Spatial organization of bacterial transcription and translation

TL;DR

This study models bacterial cellular organization, revealing mRNA segregation to cell poles and a ribosome circulation driven by mRNA flux, highlighting the impact of spatial arrangement on gene expression.

Contribution

It introduces a minimal reaction-diffusion model capturing spatial segregation and flux of mRNAs and ribosomes, including a novel method for transient interactions.

Findings

~90% of mRNAs are localized at the poles.

Ribosomes circulate driven by mRNA flux.

Transient interactions affect ribosome efficiency.

Abstract

In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes$-$molecular complexes that translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the poles. We study the impact of this spatial organization using a minimal reaction-diffusion model for the cellular transcriptional-translational machinery. Our model predicts that $\sim 90\%$ of mRNAs are segregated to the poles and reveals a "circulation" of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. To address the existence of non-specific, transient interactions between ribosomes and mRNAs, we developed a novel method to efficiently incorporate such transient interactions into reaction-diffusion equations, which allowed us to quantify the biological implications of such non-specific interactions, e.g. for ribosome efficiency.