Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.
Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.
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工程微生物宿主中由于酶混杂而导致的代谢网络破坏分析。
DOI：
10.1016/j.mec.2021.e00170
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发表时间：
2021-06
影响因子：
5.2
通讯作者：
Hassoun S
中科院分区：
文献类型：
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作者：
Porokhin V;Amin SA;Nicks TB;Gopinarayanan VE;Nair NU;Hassoun S
对微生物生理学基础的代谢和调控网络的日益了解使得能够创建用于生物化学、生物医学、农业和环境应用的逐渐更复杂的合成生物系统。然而，尽管尽了最大的努力，混淆表型仍然出现从不可预见的生物部分之间的相互作用，和强大的和模块化的生物系统的设计仍然难以捉摸。这种相互作用在设计合成系统时难以预测，并且在实验测试期间可能表现为需要克服的低效率。将大肠杆菌等生物转化为微生物工厂是通过几种工程策略实现的，单独或组合使用，目的是最大限度地生产选定的目标化合物。一种技术依赖于抑制或过度表达选定的基因;另一种技术涉及将异源酶引入微生物宿主。这些修饰将质量通量导向所需代谢物的集合，但可能产生意想不到的相互作用。在这项工作中，我们开发了一种计算方法，称为代谢中断工作流（MDFlow），用于发现酶混杂产生的相互作用和网络中断-酶作用于结构上与其天然底物相似的广泛分子的能力。我们应用MDFlow两个实验验证的情况下，菌株与必需基因敲除获救的相互作用导致一个或多个其他基因的过度表达。我们展示了酶的混杂如何帮助细胞适应基本代谢功能的破坏。然后，我们应用MDFlow来预测和评估一些假定的混杂反应，可以干扰两个异源途径设计的3-羟基丙酸（3-HP）生产。使用MDFlow，我们可以识别推定的酶混杂性以及随后形成的非预期和不期望的副产物，这些副产物不仅对宿主代谢具有破坏性，而且对高生物合成生产力和产量的预期最终目标也具有破坏性。正如我们所展示的，MDFlow提供了一个创新的工作流程，系统地识别宿主的天然代谢和由于酶混杂而引起的工程修饰之间的不相容性。对细胞宿主的工程修饰导致不期望的副产物。代谢破坏：由于酶混杂而引起的工程宿主的变化。代谢中断工作流程（MDFlow）揭示了代谢中断。MDFlow证实了先前实验验证的混杂相互作用。MDFlow比较了靶向3-HP生产的异源途径引起的破坏。
Increasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation of progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, and environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between biological parts, and the design of robust and modular biological systems remains elusive. Such interactions are difficult to predict when designing synthetic systems and may manifest during experimental testing as inefficiencies that need to be overcome. Transforming organisms such as Escherichia coli into microbial factories is achieved via several engineering strategies, used individually or in combination, with the goal of maximizing the production of chosen target compounds. One technique relies on suppressing or overexpressing selected genes; another involves introducing heterologous enzymes into a microbial host. These modifications steer mass flux towards the set of desired metabolites but may create unexpected interactions. In this work, we develop a computational method, termed Metabolic Disruption Workflow (MDFlow), for discovering interactions and network disruptions arising from enzyme promiscuity – the ability of enzymes to act on a wide range of molecules that are structurally similar to their native substrates. We apply MDFlow to two experimentally verified cases where strains with essential genes knocked out are rescued by interactions resulting from overexpression of one or more other genes. We demonstrate how enzyme promiscuity may aid cells in adapting to disruptions of essential metabolic functions. We then apply MDFlow to predict and evaluate a number of putative promiscuous reactions that can interfere with two heterologous pathways designed for 3-hydroxypropionic acid (3-HP) production. Using MDFlow, we can identify putative enzyme promiscuity and the subsequent formation of unintended and undesirable byproducts that are not only disruptive to the host metabolism but also to the intended end-objective of high biosynthetic productivity and yield. As we demonstrate, MDFlow provides an innovative workflow to systematically identify incompatibilities between the native metabolism of the host and its engineered modifications due to enzyme promiscuity. Engineering modifications to cellular hosts result in undesirable byproducts. Metabolic Disruption: changes in engineered host due to enzyme promiscuity. Metabolic Disruption Workflow (MDFlow) uncovers metabolic disruption. MDFlow corroborates previously experimentally verified promiscuous interactions. MDFlow compares disruption due to heterologous pathways targeting 3-HP production.
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作者：
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通讯作者：
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