Promiscuity, serendipity, and metabolic innovation

滥交、偶然性和代谢创新

• 批准号: 10355520
• 负责人: SHELLEY D. COPLEY
• 金额: $ 37.29万
• 依托单位: UNIVERSITY OF COLORADO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10355520
• 关键词: Address; Adverse effects; Affect; Antimetabolites; Automobile Driving; Bacteria; Biochemical Genetics; Biochemical Pathway; Bioinformatics; Biological Models; Carbon; Catalysis; Chemicals; Collection; Communicable Diseases; Complex; Dependence; Drug usage; Ecosystem; Environment; Enzymes; Escherichia coli; Evolution; Gene Duplication; Generations; Genes; Genome; Growth; Health; Homoserine; Human; Laboratories; Malignant Neoplasms; Metabolic; Metabolic Pathway; Microbe; Morphologic artifacts; Mutation; Natural Products; Organism; Outcome; Pathway interactions; Pesticides; Pharmaceutical Preparations; Pharmacologic Substance; Phosphotransferases; Physiological; Planet Earth; Play; Process; Pyridoxal Phosphate; Reaction; Recovery; Reproduction; Role; Source; Structure; System; Testing; Work; anthropogenesis; base; enzyme activity; fitness; improved; innovation; insight; life history; metabolomics; new growth; novel; pressure; recruit; resistance mechanism; theories

Bioinformatic and structure/function studies suggest that most extant metabolic pathways were patched together from previously existing promiscuous enzyme activities that, even if inefficient, provided some degree of catalysis. However, we cannot explain why certain pathways arose rather than the thousands of other possibilities. Further, we have little insight into the process by which novel pathways were patched together and flux was improved via mutations. This project will exploit a model system in which the pathway for synthesis of pyridoxal 5- phosphate (PLP) has been disrupted to identify “serendipitous pathways” (SPs) that restore PLP synthesis by patching together promiscuous activities of enzymes that normally serve other functions. The enzymes that catalyze steps in SPs will be characterized. The mechanisms by which mutations increase flux through a SP to a physiologically significant level will be identified. Finally, the dependence of the evolutionary outcome on environmental conditions and genome content will be defined. The feasibility of this project is supported by preliminary results identifying two SPs after evolution of ∆pdxB E. coli in different conditions and evidence that PLP synthesis can be restored after evolution in other conditions, as well. Biochemical, genetic, and metabolomics approaches have revealed the mechanisms by which mutations enabled assembly of one of these SPs. E. coli and other bacteria in which a gene required for PLP synthesis has been deleted will be subjected to laboratory evolution. If growth can be restored, the responsible mutations will be identified. The mechanisms by which these mutations have facilitated recruitment of a promiscuous enzyme to replace the missing enzyme, or, more interestingly, emergence of a SP will be defined using a battery of biochemical, genetic and ‘omics approaches. This project will provide new insights into the assembly of metabolic pathways, how genome content and growth conditions affect the evolution of novel pathways, and how flux through initially inefficient pathways can be elevated due to mutations. These insights will help us understand how bacteria have evolved throughout the history of life on earth, and how they will continue to evolve as humans exert new selective pressures due to introduction of anthropogenic chemicals such as pesticides and pharmaceuticals. Evolution of pathways capable for degradation of anthropogenic compounds is critical to minimize adverse effects on the health of ecosystems and humans. On the other hand, evolution of novel pathways might be an unrecognized mechanism for resistance to antimetabolite drugs used to treat infectious diseases and cancer.

生物信息学和结构/功能研究表明，大多数现存的代谢途径 从以前现有的混杂酶活动中修补在一起，即使 效率低下，提供了一定程度的催化。但是，我们无法解释为什么某些途径 出现而不是成千上万的其他可能性。此外，我们对 通过突变，通过将新途径修补并改善通量的过程。 该项目将利用一个模型系统，在该系统中，合成吡啶还原5--的途径 磷酸盐（PLP）已被破坏以识别恢复PLP的“偶然途径”（SPS） 通过将通常服务于其他酶的酶的混杂活性拼凑在一起合成 功能。将表征催化SPS中的步骤的酶。这些机制 将确定这些突变通过SP提高到物理意义的水平。 最后，进化结果对环境条件和基因组的依赖性 内容将被定义。 该项目的可行性得到了初步结果，以确定两个SP之后 ∆PDXB大肠杆菌在不同条件下的演变，证明可以恢复PLP合成的证据 在其他条件下进化后。生化，遗传和代谢组学方法 已经揭示了突变能够组装这些SP的机制。 大肠杆菌和其他已删除了PLP合成基因的细菌将 受到实验室进化的影响。如果可以恢复增长，负责的突变将是 确定。这些突变准备募集的机制 混杂酶代替丢失的酶，或更有趣的是，SP的出现 将使用一系列生化，遗传和“ OMICS方法”来定义。 该项目将为代谢途径的组装提供新的见解，基因组如何 内容和生长条件会影响新途径的演变，以及最初的通量如何 由于突变，效率低下的途径可以提高。这些见解将帮助我们理解 细菌如何在地球上生命的整个生活史中发展，以及它们将如何继续发展 由于引入人为化学物质，因此人类施加了新的选择压力的进化 例如农药和药物。能够降解的途径的演变 人为化合物对于最大程度地减少对生态系统健康的不利影响至关重要 人类。另一方面，新途径的演变可能是一种未认识的机制 用于抗药性药物用于治疗传染病和癌症的药物。