School of Life Sciences, University of Warwick, Warwick, United Kingdom.
Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
Elife. 2023 Feb 17;12:e84379. doi: 10.7554/eLife.84379.
Cycling of co-substrates, whereby a metabolite is converted among alternate forms via different reactions, is ubiquitous in metabolism. Several cycled co-substrates are well known as energy and electron carriers (e.g. ATP and NAD(P)H), but there are also other metabolites that act as cycled co-substrates in different parts of central metabolism. Here, we develop a mathematical framework to analyse the effect of co-substrate cycling on metabolic flux. In the cases of a single reaction and linear pathways, we find that co-substrate cycling imposes an additional flux limit on a reaction, distinct to the limit imposed by the kinetics of the primary enzyme catalysing that reaction. Using analytical methods, we show that this additional limit is a function of the total pool size and turnover rate of the cycled co-substrate. Expanding from this insight and using simulations, we show that regulation of these two parameters can allow regulation of flux dynamics in branched and coupled pathways. To support these theoretical insights, we analysed existing flux measurements and enzyme levels from the central carbon metabolism and identified several reactions that could be limited by the dynamics of co-substrate cycling. We discuss how the limitations imposed by co-substrate cycling provide experimentally testable hypotheses on specific metabolic phenotypes. We conclude that measuring and controlling co-substrate dynamics is crucial for understanding and engineering metabolic fluxes in cells.
循环偶联物，即一种代谢物通过不同的反应转化为不同的形式，在新陈代谢中无处不在。几种循环偶联物是众所周知的能量和电子载体（例如 ATP 和 NAD(P)H），但也有其他代谢物在中心代谢的不同部分充当循环偶联物。在这里，我们开发了一个数学框架来分析偶联物循环对代谢通量的影响。在单个反应和线性途径的情况下，我们发现偶联物循环对该反应施加了额外的通量限制，与该反应的主要酶的动力学所施加的限制不同。使用分析方法，我们表明这种额外的限制是循环偶联物的总池大小和周转率的函数。从这个洞察力扩展，并使用模拟，我们表明，这两个参数的调节可以允许在分支和耦合途径中调节通量动力学。为了支持这些理论见解，我们分析了来自中心碳代谢的现有通量测量值和酶水平，并确定了几个可能受到偶联物循环动力学限制的反应。我们讨论了偶联物循环施加的限制如何为特定代谢表型提供可实验验证的假设。我们的结论是，测量和控制偶联物动力学对于理解和工程细胞中的代谢通量至关重要。
