Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.
PLoS Comput Biol. 2012;8(4):e1002491. doi: 10.1371/journal.pcbi.1002491. Epub 2012 Apr 26.
Cellular networks multitask by exhibiting distinct, context-dependent dynamics. However, network states (parameters) that generate a particular dynamic are often sub-optimal for others, defining a source of "tension" between them. Though multitasking is pervasive, it is not clear where tension arises, what consequences it has, and how it is resolved. We developed a generic computational framework to examine the source and consequences of tension between pairs of dynamics exhibited by the well-studied RB-E2F switch regulating cell cycle entry. We found that tension arose from task-dependent shifts in parameters associated with network modules. Although parameter sets common to distinct dynamics did exist, tension reduced both their accessibility and resilience to perturbation, indicating a trade-off between "one-size-fits-all" solutions and robustness. With high tension, robustness can be preserved by dynamic shifting of modules, enabling the network to toggle between tasks, and by increasing network complexity, in this case by gene duplication. We propose that tension is a general constraint on the architecture and operation of multitasking biological networks. To this end, our work provides a framework to quantify the extent of tension between any network dynamics and how it affects network robustness. Such analysis would suggest new ways to interfere with network elements to elucidate the design principles of cellular networks.
细胞网络通过表现出不同的、依赖于上下文的动态来实现多任务处理。然而,产生特定动态的网络状态(参数)对于其他状态通常不是最优的,这定义了它们之间的“张力”的来源。尽管多任务处理很普遍,但尚不清楚张力从何而来、它有什么后果以及它是如何解决的。我们开发了一种通用的计算框架来研究由 RB-E2F 开关调节细胞周期进入的经过充分研究的网络所表现出的两种动力学之间张力的来源和后果。我们发现,张力源于与网络模块相关的参数的任务依赖性变化。尽管确实存在与不同动态共同的参数集,但张力降低了它们的可及性和对扰动的弹性,表明“一刀切”解决方案和鲁棒性之间存在权衡。在高张力的情况下,可以通过模块的动态转移来保持鲁棒性,使网络能够在任务之间切换,并通过增加网络复杂性来实现,在这种情况下可以通过基因复制来实现。我们提出,张力是多任务生物网络的架构和操作的一般约束。为此,我们的工作提供了一种框架来量化任何网络动态之间的张力程度以及它如何影响网络鲁棒性。这种分析将为干扰网络元素以阐明细胞网络的设计原则提供新的思路。