Evolution and Regulation of Bacterial Proteome Composition

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 了解进化的驱动力和塑造活细胞中蛋白质水平的分子过程。 使用细菌模型系统，我的实验室通过开发定量技术， 测量、操纵和模拟共调节蛋白的表达化学计量以及 不平衡生产对细菌生长、存活和定殖的影响。目前的拨款旨在回答 关于蛋白质化学计量的生理学和调节的几个基本问题。 在生理水平上，我们使用分子和理论方法来确定：1） 每个基因的蛋白质生产率和细胞对非最佳水平的反应，2） 蛋白质生产在突然的环境变化和不平衡生产的后果，和 3)共同发挥作用的蛋白质化学计量的理论基础。这些研究将有助于阐明 构建蛋白质组的新原则，并为疾病中的蛋白质失衡提供了新的思路。 为了理解这种化学计量蛋白质生产背后的基因表达调控原理， 我们使用定量和大规模平行测定来确定1）Rho的序列决定簇， 枯草芽孢杆菌中依赖性转录终止，其RNAP聚合酶的速度超过核糖体 （“失控转录”），2）失控转录的分子基础，3）预测模型， Rho非依赖性转录终止的效率，以及4） 噬菌体mRNA。我们在这些领域的研究将有助于建立一个急需的框架， 从基因组序列预测基因表达，推进细菌基因的基础知识 调控我们预计，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 了解基因组、蛋白质组和适应性之间的相互作用。

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 and the molecular processes that shape protein levels in living cells. Using bacterial model systems, my lab takes a holistic approach by developing quantitative technologies to measure, manipulate, and model the expression stoichiometry of co-regulated proteins and the effect of imbalanced production on bacterial growth, survival, and colonization. This current grant seeks to answer several fundamental questions regarding the physiology and regulation of protein stoichiometry. At the physiological level, we use molecular and theoretical methods to determine 1) the optimality of protein production rates for every gene and the cellular responses to non-optimal levels, 2) the precise ratios of protein production upon sudden environmental changes and the consequences of imbalanced production, and 3) the theoretical basis for the stoichiometry of proteins that function together. These studies will help elucidate new principles for building a proteome and provide a new way of thinking about protein imbalance in disease. To understand the regulatory principles of gene expression behind this stoichiometric protein production, we use quantitative and massively parallel assays to determine 1) the sequence determinant of Rho- dependent transcription termination in Bacillus subtilis, whose RNAP polymerases outpace ribosomes (`runaway transcription'), 2) the molecular basis of runaway transcription, 3) a predictive model for the efficiency of Rho-independent transcription termination, and 4) the landscape of translational control for bacteriophage mRNAs. Our studies in these areas will help establish a critically needed framework for predicting gene expression from genomic sequences and advance fundamental knowledge of bacterial gene regulation. 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 of the interplay between genome, proteome, and fitness.