Distance matters: the impact of gene proximity in bacterial gene regulation

TL;DR

This paper demonstrates through analytical and numerical methods that the spatial distance between a transcription factor gene and its target gene significantly influences the speed and reliability of bacterial gene regulation, highlighting the importance of gene colocalization.

Contribution

It provides a general theoretical framework linking gene proximity to regulation efficiency, emphasizing the role of local concentration differences and rapid binding site search.

Findings

Distance affects regulation speed and reliability

Local concentration differences are crucial

Gene colocalization enhances regulation efficiency

Abstract

Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.