Minimal models of the circadian clock in a novel biological system

光合生物对我们的经济和生存至关重要，在全球碳循环中发挥着关键作用，影响着我们星球的气候。最近的进展为我们提供了了解光合生物生长和活动的复杂控制的方法。24小时的生物钟是植物的关键调节器，对蓝藻、真菌和包括人类在内的动物也很重要。英国的研究小组已经证明，生物钟对生物活动的节律性控制促进了拟南芥植物的生长和存活，这可能是因为拟南芥中约15%的基因受生物钟调节。拟南芥生物钟正在成为系统生物学的一个范例。时钟机制是一个具有多个反馈回路的小基因网络，包括5个伪反应调节因子、3个myb相关蛋白、2个F-box蛋白和其他植物特异性蛋白。米勒的团队已经建立了一个简化的拟南芥时钟机制模型，它有三个连锁的反馈回路。这些模型的预测已经被新的实验验证，确定了时钟网络的一个额外部分。这在任何生物体中都是罕见的成就。然而，包括拟南芥时钟的真实复杂性，将大大扩大模型，使它们更难以使用和理解。时钟系统的动力学是复杂的。它可以产生自主的、24小时的基因表达生物节律，但在自然界中，昼夜循环迫使系统重置时钟。在当前的时钟模型中，光信号调节着四个不同的组件。实际上，这些信号来自至少8种感光蛋白，可能还控制着其他成分。这种复杂性阻碍了拟南芥的昼夜节律研究。一个更简单的时钟系统，每一种蛋白质只包含一种，将极大地促进对时钟机制的实验分析。这将为生物钟机制的复杂性所带来的好处提供一个自然的测试，让人们对其他复杂的生物钟（比如人类的生物钟）有一个大致的了解。如果整个生物体是简单的，它就可以更容易地揭示特定的生物钟调节的生化过程的正确时间是如何带来适应性利益的。法国团队开发了这种理想模型。牛皮Ostreococcus tauri是最小的自由生活的真核生物，其昼夜节律系统与拟南芥密切相关。至关重要的是，每种蛋白质类型在Ostreococcus中仅由一个基因代表。Bouget实验室开发了一套独特的实验工具，用于研究这种生物的功能基因组学。他们最近的研究结果表明，与拟南芥中的时钟一样，Ostreococcus时钟保留了相同的机制和基因相互作用，但系统要简单得多。Lefranc小组的建模证实了非常简单的数学模型，这些模型被拟南芥的数据证明是无效的，准确地描述了Ostreococcus时钟。英国和法国团队的世界领先成绩自然是互补的，但除此之外，双方还得到了大量国家和机构投资的支持。我们已经准备好产生重大影响，从这些资源中获得显著的附加价值，并开辟一个新的应用领域。我们将结合英国团队在复杂模型方面的专业知识，以及丰富的拟南芥比较数据和模型，以及法国团队在非线性动力学方面的实验系统和专业知识。实验上，我们将生成生物材料来监测和操纵Ostreococcus体内的所有时钟成分，然后使用这些材料生成高质量的时间序列数据进行建模。我们将使用RNA表达微阵列和启动子阵列识别所有时钟调控转录本和启动子序列。这些结果将形成植物系统生物学的一个案例研究，展示单细胞系统加速理解核心过程的力量。

Photosynthetic organisms are vital to our economy and survival, playing a critical role in the global carbon cycle and affecting the climate of our planet. Recent advances offer us the methods to understand the complex control of growth and activity in photosynthetic organisms. The 24-hour circadian clock is a key regulator in plants, and is also important in cyanobacteria, fungi and animals including humans. The UK teams have shown that rhythmic control of biological activity by the circadian clock increases growth and survival of Arabidopsis thaliana plants, probably because >15% of genes in Arabidopsis are clock-regulated. The Arabidopsis circadian clock is becoming a paradigm for systems biology. The clock mechanism is a small gene network with multiple feedback loops, comprising five pseudo-response regulators, three myb-related proteins, two F-box proteins, and additional plant-specific proteins. Millar's group has modelled a simplified Arabidopsis clock mechanism, with three interlocking feedback loops. Predictions of the models have been validated by new experiments, identifying an additional part of the clock network. This is still a rare achievement in any organism. Including the real complexity of the Arabidopsis clock, however, will greatly enlarge the models, making them more difficult to use and to understand. The dynamics of the clock system are complex. It can generate autonomous, 24-hour biological rhythms of gene expression but in nature the day/night cycle forces the system, resetting the clock. Light signals regulate four different components in the current clock model. In reality, these signals originate from at least eight photoreceptor proteins and probably control additional components. This complexity hampers circadian research in Arabidopsis. A simpler clock system that included only one of each protein type would enormously facilitate the experimental analysis of the clock mechanism. It would provide a natural test for the proposed benefits of complexity in the clock mechanism, giving general insight into other complex clocks for example in humans. If the whole organism were simple, it could reveal much more easily how correct timing of particular clock-regulated biochemical processes led to adaptive benefits. The French team has developed this ideal model. Ostreococcus tauri is the smallest free-living eukaryote, with a circadian system that is closely related to that of Arabidopsis. Crucially, each protein type is represented by only one gene in Ostreococcus. The Bouget lab has developed a unique set of experimental tools for functional genomics in this organism. Their recent results demonstrate that the Ostreococcus clock conserves the same mechanisms and gene interactions as the clock in Arabidopsis, but in a far simpler system. Modelling by the Lefranc group confirms that very simple mathematical models, which were invalidated by data in Arabidopsis, accurately describe the Ostreococcus clock. The world-leading results of the UK and French teams are naturally complementary, but in addition are supported by significant national and institutional investment on both sides. We are poised to make a major impact, gaining significant added value from these resources and opening up a new application area. We will combine the UK team's expertise in complex models, and the wealth of comparative data and models on Arabidopsis, with the French team's experimental system and expertise in nonlinear dynamics. Experimentally, we will generate biological materials to monitor and manipulate all the clock components in Ostreococcus, then use these materials to generate high-quality timeseries data for modelling. We will identify all clock-regulated transcripts and promoter sequences using RNA expression microarrays and promoter arrays. These results will form a case study for Plant Systems Biology, demonstrating the power of a unicellular system to accelerate understanding of core processes.