Paper detail

Optimal first-passage time in gene regulatory networks

The inherent probabilistic nature of the biochemical reactions, and low copy number of species can lead to stochasticity in gene expression across identical cells. As a result, after induction of gene expression, the time at which a specific protein count is reached is stochastic as well. Therefore events taking place at a critical protein level will see stochasticity in their timing. First-passage time (FPT), the time at which a stochastic process hits a critical threshold, provides a framework to model such events. Here, we investigate stochasticity in FPT. Particularly, we consider events for which controlling stochasticity is advantageous. As a possible regulatory mechanism, we also investigate effect of auto-regulation, where the transcription rate of gene depends on protein count, on stochasticity of FPT. Specifically, we investigate for an optimal auto-regulation which minimizes stochasticity in FPT, given fixed mean FPT and threshold. For this purpose, we model the gene expression at a single cell level. We find analytic formulas for statistical moments of the FPT in terms of model parameters. Moreover, we examine the gene expression model with auto-regulation. Interestingly, our results show that the stochasticity in FPT, for a fixed mean, is minimized when the transcription rate is independent of protein count. Further, we discuss the results in context of lysis time of an \textit{E. coli} cell infected by a $λ$ phage virus. An optimal lysis time provides evolutionary advantage to the $λ$ phage, suggesting a possible regulation to minimize its stochasticity. Our results indicate that there is no auto-regulation of the protein responsible for lysis. Moreover, congruent to experimental evidences, our analysis predicts that the expression of the lysis protein should have a small burst size.