Evolution and Regulation of Bacterial Proteome Composition

细菌蛋白质组组成的进化与调控

• 批准号: 10246335
• 负责人: Gene-Wei Li
• 金额: $ 38.68万
• 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 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10246335
• 关键词: Animal Model; Area; Bacillus subtilis; 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量化产物，是细胞功能的最终效应者。还没有 值得注意的是，人们对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 了解影响蛋白质水平的进化驱动力，以及 被用来达到准确的设定点。我们的切入点是一种强大的定量蛋白质组学方法 核糖体图谱。使用细菌模型系统，我们已经证明了许多同源蛋白具有 在不同物种中数量上保守的表达水平，表明对蛋白质的强烈限制 我们目前还不了解的丰富。阐明首选蛋白质的机制基础 与细胞适合性相关的水平，我们正在使用理论指导的实验设计来研究 蛋白质失调对大肠杆菌和枯草杆菌整体生理的影响。此外，我们正在 建立一种全面的比较蛋白质组学方法来广泛识别其水平的关键蛋白质 是不变的，尽管在整个进化过程中发生了调控变化。这一方法将开辟新的途径， 揭示生化系统的控制点，为蛋白质组研究提供新的思路 疾病的不平衡。 我的研究计划的第二个方面是了解细胞如何通过 定量精确度。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来说很重要 蛋白质，但我们对这些速率是如何微调的只有一个初步的了解。我们现在是 开发全基因组技术以询问维持过程中反馈调节的普遍性 细菌中的蛋白质组态平衡。我们还在研究操纵子中的共同调控基因是如何 差异表达以达到准确的蛋白质水平。我们在这方面的做法侧重于发展 的定量分析，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，加上对蛋白质组的系统水平的研究 组成，将使细菌模式生物成为我们第一个有定量研究的系统 从基因组到蛋白质组再到健康和回归的理解。