Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways.
Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways.
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DOI：
10.1371/journal.pbio.0060146
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发表时间：
2008-06-17
期刊：
影响因子：
9.8
通讯作者：
Li H
中科院分区：
文献类型：
--
作者：
Chin CS;Chubukov V;Jolly ER;DeRisi J;Li H
遗传网络对环境波动的响应的动态特征代表了基本的功能规范，因此可能会限制网络结构和动力学参数的可能选择。为了探索动力学和网络设计之间的联系，我们分析了在许多代谢途径中常见的一般调控结构。这种结构的特征在于双重控制机制，具有终产物反馈抑制和由中间代谢物介导的转录调节。作为一个案例研究，我们测量了高时间分辨率的诱导配置文件中的酶在亮氨酸生物合成途径中的亮氨酸耗竭，使用自动化系统监测蛋白质表达水平在单细胞。已知该途径中的所有基因都受相同的转录因子共同调控，但我们观察到关键控制点-中间代谢物α-异丙基苹果酸（αIPM）上游和下游酶的动态反应截然不同，αIPM将代谢活性与转录调控结合起来。基于遗传扰动的分析表明，观察到的动态是由于亮氨酸分支特异性转录因子Leu 3的差异调节，并且下游酶受到严格控制，仅在αIPM可用时才高度表达。这些观察使我们能够建立一个简化的数学模型，解释所观察到的动态，并可以正确地预测路径对新扰动的响应。我们的模型还表明，瞬态动力学和稳态可以分别调整，下游酶的高诱导水平是快速亮氨酸恢复所必需的。从这项工作中产生的原则可能可以揭示基因调控如何进化以优化具有类似结构的其他代谢途径的性能。单细胞生物必须不断调整其基因表达程序，以在不断变化的环境中生存。不同分子之间的相互作用形成调节网络来介导这些变化。虽然网络连接通常是已知的，但通过查看其结构的静态图片来弄清楚网络如何动态响应是一个重大挑战。在更精细的时间尺度上测量响应可以揭示网络功能与结构之间的联系。我们在这项工作中研究的系统结构酵母中的亮氨酸生物合成途径与其他代谢途径共享：代谢中间体与转录因子结合以激活途径基因，创造了一个复杂的反馈结构，将代谢与基因表达联系起来。我们测量了高时间分辨率的蛋白质丰度的基因在这条途径中响应亮氨酸耗竭，并研究了基因表达动力学的各种遗传扰动的影响。我们的测量和理论建模表明，只有紧邻中间体下游的基因受到代谢物的高度调节，这是从亮氨酸耗尽中快速恢复所必需的特征。由于我们研究的结构是常见的，我们相信我们的工作可能会导致在其他代谢途径中的基因表达动态的一般原则。一个定量的，高时间分辨率的基因诱导代谢途径的研究揭示了一个复杂的监管架构和系统的动态响应之间的联系，指出这些途径的设计可能的原则。
The dynamic features of a genetic network's response to environmental fluctuations represent essential functional specifications and thus may constrain the possible choices of network architecture and kinetic parameters. To explore the connection between dynamics and network design, we have analyzed a general regulatory architecture that is commonly found in many metabolic pathways. Such architecture is characterized by a dual control mechanism, with end product feedback inhibition and transcriptional regulation mediated by an intermediate metabolite. As a case study, we measured with high temporal resolution the induction profiles of the enzymes in the leucine biosynthetic pathway in response to leucine depletion, using an automated system for monitoring protein expression levels in single cells. All the genes in the pathway are known to be coregulated by the same transcription factors, but we observed drastically different dynamic responses for enzymes upstream and immediately downstream of the key control point—the intermediate metabolite α-isopropylmalate (αIPM), which couples metabolic activity to transcriptional regulation. Analysis based on genetic perturbations suggests that the observed dynamics are due to differential regulation by the leucine branch-specific transcription factor Leu3, and that the downstream enzymes are strictly controlled and highly expressed only when αIPM is available. These observations allow us to build a simplified mathematical model that accounts for the observed dynamics and can correctly predict the pathway's response to new perturbations. Our model also suggests that transient dynamics and steady state can be separately tuned and that the high induction levels of the downstream enzymes are necessary for fast leucine recovery. It is likely that principles emerging from this work can reveal how gene regulation has evolved to optimize performance in other metabolic pathways with similar architecture. Single-cell organisms must constantly adjust their gene expression programs to survive in a changing environment. Interactions between different molecules form a regulatory network to mediate these changes. While the network connections are often known, figuring out how the network responds dynamically by looking at a static picture of its structure presents a significant challenge. Measuring the response at a finer time scales could reveal the link between the network's function and its structure. The architecture of the system we studied in this work—the leucine biosynthesis pathway in yeast—is shared by other metabolic pathways: a metabolic intermediate binds to a transcription factor to activate the pathway genes, creating an intricate feedback structure that links metabolism with gene expression. We measured protein abundance at high temporal resolution for genes in this pathway in response to leucine depletion and studied the effects of various genetic perturbations on gene expression dynamics. Our measurements and theoretical modeling show that only the genes immediately downstream from the intermediate are highly regulated by the metabolite, a feature that is essential to fast recovery from leucine depletion. Since the architecture we studied is common, we believe that our work may lead to general principles governing the dynamics of gene expression in other metabolic pathways. A quantitative, high-temporal resolution study of gene induction in a metabolic pathway reveals an intricate connection between the regulatory architecture and the dynamic response of the system, pointing to possible principles underlying the design of these pathways.
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影响因子：
5.3
作者：
FRIDEN, P;SCHIMMEL, P
通讯作者：
SCHIMMEL, P
影响因子：
5
作者：
Hans, MA;Heinzle, E;Wittmann, C
通讯作者：
Wittmann, C
DOI：
10.1083/jcb.75.2.422
发表时间：
1977-11
期刊：
The Journal of cell biology
影响因子：
--
作者：
Hartwell LH;Unger MW
通讯作者：
Unger MW
影响因子：
56.9
作者：
KIRKPATRICK, S;GELATT, CD;VECCHI, MP
通讯作者：
VECCHI, MP
影响因子：
3.2
作者：
Alberghina, L;Smeraldi, C;Porro, D
通讯作者：
Porro, D