Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
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DOI：
10.1073/pnas.1811971115
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发表时间：
2018-10-23
影响因子：
11.1
通讯作者：
Lewis, Nathan E.
中科院分区：
文献类型：
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作者：
Brunk, Elizabeth;Chang, Roger L.;Lewis, Nathan E.
了解蛋白质翻译后修饰（PTMs）的复杂相互作用是代谢工程、合成生物学和生物医学科学的一个主要挑战。在这里，我们提出了一个集成多重自动基因组编辑（MAGE），基因组尺度代谢建模和原子分子动力学的工作流程，以研究PTMs对代谢酶和微生物适应性的影响。该工作流程包含了跨科学学科的互补方法;提供了在营养变化过程中PTMs如何影响细胞适应性的分子见解；并展示了如何在不同的生物尺度上探索ptm的机制细节。为了证明这一概念，我们对大肠杆菌代谢网络中酶的ptm进行了全球分析。基于我们的工作流程结果，我们对三种蛋白质中的PTMs进行了更详细的机制分析：烯醇化酶、丝氨酸羟甲基转移酶和转醛缩酶。该工作流程的应用确定了特定PTMs在观察到的实验现象中的作用，并演示了单个PTMs如何调节酶、途径，并最终调节细胞表型。
Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coll. Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.