Evolution and Regulation of Bacterial Proteome Composition

细菌蛋白质组组成的进化与调控

• 批准号: 9894421
• 负责人: Gene-Wei Li
• 金额: $ 5.8万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9894421
• 关键词: Animal Model; Area; Back; Bacteria; Bacterial Infections; Bacterial Model; Biochemical; Biological Assay; Biological Models; Cell physiology; Cells; Coupled; Development; Disease; Dissection; Escherichia coli; Evolution; Experimental Designs; Feedback; Genes; Genome; Goals; Homeostasis; Homologous Protein; Human; Logic; Malignant Neoplasms; Methods; Molecular; Natural Selections; Operon; Output; Physiology; Population; Prevalence; Process; Proliferating; Proteins; Proteome; Proteomics; Regulation; Research; Shapes; System; Techniques; Thinking; arm; base; cell transformation; comparative; design; differential expression; driving force; fitness; genome-wide; insight; microbial community; pathogenic bacteria; programs; ribosome profiling; theories

Project Summary/Abstract The proteome is a quantitative output of a genome and the ultimate effector of cellular functions. Yet remarkably little is known about the logic behind proteome construction. The goal of my research program is to understand the evolutionary driving forces that shape protein levels, as well as the precise regulation that is employed to arrive at the exact set point. Our entry point is a powerful quantitative proteomics method based on ribosome profiling. Using bacterial model systems, we have shown that many homologous proteins have quantitatively conserved expression levels across divergent species, suggesting strong constraints on protein abundance that we do not currently understand. To elucidate the mechanistic basis for the preferred protein levels in relation to cell fitness, we are using theory-guided experimental design to investigate the consequence of protein misregulation on global physiology in E. coli and B. subtilis. Furthermore, we are establishing a comprehensive comparative proteomics approach to broadly identify key proteins whose levels are invariant despite regulatory changes throughout evolution. This approach will open up new avenues for uncovering the control points of biochemical systems, and provide a new way of thinking about proteome imbalance in diseases. The second arm of my research program is to understand how cells produce their proteome with quantitative precision. As indicated by our preliminary results, such precise control is clearly important to many proteins, but we have only a rudimentary understanding of how these rates are finely tuned. We are now developing genome-wide techniques to interrogate the prevalence of feedback regulation in maintaining proteome homeostasis in bacteria. We are also investigating how co-regulated genes in operons are differentially expressed to achieve exact protein levels. Our approach in this area focuses on the development of quantitative assays that allow us to accurately characterize the molecular processes perfected by natural selection. We anticipate that our mechanistic dissection, coupled with systems-level inquiry into proteome composition, will make bacterial model organisms the first system for which we have a quantitative understanding from genome to proteome to fitness and back.

项目摘要/摘要 蛋白质组是基因组的定量输出，也是细胞功能的最终效应子。然而 关于蛋白质组构建背后的逻辑知之甚少。我的研究计划的目标是 了解塑造蛋白质水平的进化驱动力以及确切的调节 被用来到达确切的设定点。我们的切入点是基于强大的定量蛋白质组学方法 在核糖体分析上。使用细菌模型系统，我们表明许多同源蛋白具有 跨不同物种的定量保守表达水平，表明对蛋白质的强烈限制 我们目前不了解的丰富。阐明首选蛋白质的机械基础 与细胞适应性有关的水平，我们使用理论指导的实验设计来研究 大肠杆菌和枯草芽孢杆菌中蛋白质不调节对全球生理学的结果。此外，我们是 建立一种全面的比较蛋白质组学方法，以广泛识别其水平的关键蛋白 尽管监管变化在整个进化中，但还是不变的。这种方法将为 揭示生化系统的控制点，并提供有关蛋白质组的新方法 疾病不平衡。 我的研究计划的第二组是了解细胞如何与 定量精度。正如我们的初步结果所表明的那样，这种精确的控制显然对许多人很重要 蛋白质，但我们只对这些速率进行细调的方式有基本的了解。我们现在 开发全基因组技术以询问反馈调节的普遍性 细菌中的蛋白质组稳态。我们还正在研究操纵子中共同调节的基因 差异表达以达到精确的蛋白质水平。我们在这一领域的方法着重于发展 定量测定，使我们能够准确地表征自然的分子过程 选择。我们预计我们的机械解剖，再加上系统水平的蛋白质组研究 组成，将使细菌模型生物成为我们有定量的第一个系统 从基因组到蛋白质组到健身和背部的理解。