Josić K, López JM, Ott W, Shiau L, Bennett MR. Stochastic delay accelerates signaling in gene networks.
PLoS Comput Biol 2011;
7:e1002264. [PMID:
22102802 PMCID:
PMC3213172 DOI:
10.1371/journal.pcbi.1002264]
[Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/19/2011] [Indexed: 11/22/2022] Open
Abstract
The creation of protein from DNA is a dynamic process consisting of numerous reactions, such as transcription, translation and protein folding. Each of these reactions is further comprised of hundreds or thousands of sub-steps that must be completed before a protein is fully mature. Consequently, the time it takes to create a single protein depends on the number of steps in the reaction chain and the nature of each step. One way to account for these reactions in models of gene regulatory networks is to incorporate dynamical delay. However, the stochastic nature of the reactions necessary to produce protein leads to a waiting time that is randomly distributed. Here, we use queueing theory to examine the effects of such distributed delay on the propagation of information through transcriptionally regulated genetic networks. In an analytically tractable model we find that increasing the randomness in protein production delay can increase signaling speed in transcriptional networks. The effect is confirmed in stochastic simulations, and we demonstrate its impact in several common transcriptional motifs. In particular, we show that in feedforward loops signaling time and magnitude are significantly affected by distributed delay. In addition, delay has previously been shown to cause stable oscillations in circuits with negative feedback. We show that the period and the amplitude of the oscillations monotonically decrease as the variability of the delay time increases.
Delay in gene regulatory networks often arises from the numerous sequential reactions necessary to create fully functional protein from DNA. While the molecular mechanisms behind protein production and maturation are known, it is still unknown to what extent the resulting delay affects signaling in transcriptional networks. In contrast to previous studies that have examined the consequences of fixed delay in gene networks, here we investigate how the variability of the delay time influences the resulting dynamics. The exact distribution of “transcriptional delay” is still unknown, and most likely greatly depends on both intrinsic and extrinsic factors. Nevertheless, we are able to deduce specific effects of distributed delay on transcriptional signaling that are independent of the underlying distribution. We find that the time it takes for a gene encoding a transcription factor to signal its downstream target decreases as the delay variability increases. We use queueing theory to derive a simple relationship describing this result, and use stochastic simulations to confirm it. The consequences of distributed delay for several common transcriptional motifs are also discussed.
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