Dynamics of the Bacterial Proteome

 描述（由申请人提供）：该项目的总体目标是使用定量质谱法表征大肠杆菌蛋白质组的组成和动力学，并使用这些数据来建立粗粒度蛋白质组通量模型，该模型描述细菌对营养限制的生理行为。细菌经历各种各样的环境，并且受到营养缺乏和不利的生长环境的影响。细胞蛋白质的合成是细胞生长中能量消耗最大的方面，并且蛋白质的合成响应于环境受到严格控制。我们已经观察到，蛋白质组将其自身划分为以线性方式响应于碳、氨基酸和抗生素应激的限制的部分。作为生长速率的函数的线性响应可以在具有非常少量的参数的粗粒度蛋白质组扇区模型中捕获。该项目的一个主要目标是将该模型扩展到其他限制和压力，包括磷，硫，氧和铁限制，以及渗透和pH压力。我们还进行了脉冲标记实验，即使在非常缓慢的蛋白质合成条件下，也揭示了蛋白质组的显着周转，第二个主要目标是扩展粗粒度模型，以包括蛋白质降解的能量成本。第三个主要目标将是比较蛋白质组的变化在营养变化的增长率变化的动态目前的理论。该项目是一个全面的方法来表征细菌中蛋白质合成和蛋白质组组成的宏观经济学，将作为各种条件下细菌生理学定量模型的基础。了解细菌生理学是了解细菌如何在感染的不利背景下或作为微生物组的一部分在其有益背景下反应的一个重要方面。

 DESCRIPTION (provided by applicant): The overall goal of this project is to characterize the composition and dynamics of the proteome of Escherichia coli using quantitative mass spectrometry, and to use those data to inform a coarse-grained proteome flux model that describes the physiological behavior of the bacterium in response to nutrient limitations. Bacteria experience a wide variety of environments, and are subject to both nutrient deprivation and unfavorable environments for growth. The synthesis of cellular proteins is the most energetically expensive aspect of cellular growth, and the synthesis of proteins in response to the environment is tightly controlled. We have observed that the proteome partitions itself into sectors that respond in concert in a linear way in response to limitations for carbon, amino acids, and antibiotic stress. The linear response as a function of growth rate can be captured in a coarse-grained proteome sector model that has a very small number of parameters. A major goal of this project is to extend this model to other limitations and stresses, including phosphorus, sulfur, oxygen, and iron limitation, and osmotic and pH stress. We have also performed pulse labeling experiments that reveal significant turnover of the proteome even under very slow protein synthesis conditions, and a second major goal is to extend the coarse-grained model to include the energetic cost of protein degradation. A third major goal will be to compare proteome changes during nutrient shifts to current theories for the dynamics of growth rate changes. This project is a comprehensive approach to characterize the macroeconomics of protein synthesis and proteome composition in bacteria that will serve as the basis for quantitative models of bacterial physiology under a wide variety of conditions. Understanding bacterial physiology is an important aspect of understanding how bacteria respond in the adverse context of infections or in their beneficial context as part of the microbiome.