Effects of restrained degradation on gene expression and regulation

TL;DR

This paper investigates how environmental degradation capacity limits affect gene expression and regulation, revealing significant impacts on mRNA distribution, noise characteristics, and system dynamics.

Contribution

It introduces the $K$ effect as a key factor influencing gene expression variability and regulation, supported by stochastic modeling and analysis.

Findings

The $K$ effect alters mRNA copy-number distribution.

It causes the Fano factor to slightly exceed 1, aligning with experimental observations.

It significantly impacts the mean first passage time and reduces stochastic resonance signal-to-noise ratio.

Abstract

The effects of carrying capacity of environment $K$ for degradation (the $K$ effect for short) on the constitutive gene expression and a simple genetic regulation system, are investigated by employing a stochastic Langevin equation combined with the corresponding Fokker-Planck equation for the two stochastic systems subjected to internal and external noises. This $K$ effect characterizes the limited degradation ability of the environment for RNA or proteins, such as insufficient catabolic enzymes. The $K$ effect could significantly change the distribution of mRNA copy-number in constitutive gene expression, and interestingly, it leads to the Fano factor slightly larger than 1 if only the internal noise exists. Therefore, that the recent experimental measurements suggests the Fano factor deviates from 1 slightly (Science {\bf 346} (2014) 1533), probably originates from the $K$ effect. The $K$ effects on the steady and transient properties of genetic regulation system, have been investigated in detail. It could enhance the mean first passage time significantly especially when the noises are weak and reduce the signal-to-noise ratio in stochastic resonance substantially.