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.

项目总结/摘要 蛋白质组是基因组的定量输出，是细胞功能的最终效应子。然而 对蛋白质组构建背后的逻辑知之甚少。我的研究项目的目标是 了解形成蛋白质水平的进化驱动力，以及蛋白质水平的精确调控。 用于达到精确的设定点。我们的切入点是一个强大的定量蛋白质组学方法， 核糖体分析使用细菌模型系统，我们已经表明，许多同源蛋白质具有 在不同物种中定量保守的表达水平，表明对蛋白质表达的强烈限制。 这是我们目前还不了解的。阐明优选蛋白质的机制基础 水平与细胞适应性的关系，我们正在使用理论指导的实验设计来研究 蛋白质的错误调节对E. coli和B.枯草杆菌。此外，我们 建立一个全面的比较蛋白质组学方法，以广泛地确定关键蛋白质， 在整个进化过程中，尽管规则发生了变化，但它们是不变的。这种方法将为以下方面开辟新的途径： 揭示了生物化学系统的控制点，为蛋白质组研究提供了一种新的思路 疾病的不平衡。 我研究计划的第二个分支是了解细胞如何产生蛋白质组， 定量精度正如我们的初步结果所示，这种精确的控制显然对许多人来说很重要。 蛋白质，但我们对这些速率是如何微调的只有初步的了解。我们现在 开发全基因组技术，以询问反馈调节在维持 细菌中的蛋白质组稳态。我们还在研究操纵子中的共调控基因是如何 差异表达以实现精确的蛋白质水平。我们在这方面的做法侧重于发展 定量分析，使我们能够准确地表征分子过程完善的自然 选择.我们预计，我们的机械解剖，加上系统水平的蛋白质组研究， 组成，将使细菌模式生物的第一个系统，我们有一个定量的 从基因组到蛋白质组再到适应性再到适应性。