Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan.
PLoS One. 2012;7(2):e30489. doi: 10.1371/journal.pone.0030489. Epub 2012 Feb 20.
Many organisms have evolved molecular clocks to anticipate daily changes in their environment. The molecular mechanisms by which the circadian clock network produces sustained cycles have extensively been studied and transcriptional-translational feedback loops are common structures to many organisms. Although a simple or single feedback loop is sufficient for sustained oscillations, circadian clocks implement multiple, complicated feedback loops. In general, different types of feedback loops are suggested to affect the robustness and entrainment of circadian rhythms. To reveal the mechanism by which such a complex feedback system evolves, we quantify the robustness and light entrainment of four competing models: the single, semi-dual, dual, and redundant feedback models. To extract the global properties of those models, all plausible kinetic parameter sets that generate circadian oscillations are searched to characterize their oscillatory features. To efficiently perform such analyses, we used the two-phase search (TPS) method as a fast and non-biased search method and quasi-multiparameter sensitivity (QMPS) as a fast and exact measure of robustness to uncertainty of all kinetic parameters.So far the redundant feedback model has been regarded as the most robust oscillator, but our extensive analysis corrects or overcomes this hypothesis. The dual feedback model, which is employed in biology, provides the most robust oscillator to multiple parameter perturbations within a cell and most readily entrains to a wide range of light-dark cycles. The kinetic symmetry between the dual loops and their coupling via a protein complex are found critically responsible for robust and entrainable oscillations. We first demonstrate how the dual feedback architecture with kinetic symmetry evolves out of many competing feedback systems.
许多生物已经进化出分子钟,以预测其环境中日常的变化。生物钟网络产生持续循环的分子机制已经得到了广泛的研究,转录-翻译反馈回路是许多生物的常见结构。尽管简单或单一的反馈回路足以产生持续的振荡,但生物钟会实现多个复杂的反馈回路。一般来说,不同类型的反馈回路被认为会影响生物钟节律的稳定性和适应能力。为了揭示这种复杂反馈系统进化的机制,我们量化了四个竞争模型的稳定性和光适应能力:单、半双、双和冗余反馈模型。为了提取这些模型的全局特性,我们搜索了所有可能产生生物钟振荡的动力学参数集,以描述它们的振荡特征。为了有效地进行这样的分析,我们使用了两阶段搜索(TPS)方法作为一种快速且无偏的搜索方法,以及准多参数灵敏度(QMPS)作为一种快速且精确的测量所有动力学参数不确定性的稳定性的方法。到目前为止,冗余反馈模型一直被认为是最稳健的振荡器,但我们广泛的分析纠正或推翻了这一假设。双反馈模型在生物学中被广泛应用,它为细胞内的多个参数扰动提供了最稳健的振荡器,并最容易适应广泛的明暗循环。我们发现,双环之间的动力学对称性及其通过蛋白质复合物的耦合对稳健和可适应的振荡至关重要。我们首先展示了具有动力学对称性的双反馈架构如何从许多竞争反馈系统中进化而来。