Dynamics of the Bacterial Proteome

 描述(由申请人提供)：本项目的总体目标是使用定量质谱学来表征大肠杆菌蛋白质组的组成和动态，并使用这些数据来提供描述细菌在营养限制下的生理行为的粗粒度蛋白质组通量模型。细菌经历了各种各样的环境，既受到营养缺乏的影响，也受到不利于生长的环境的影响。细胞蛋白质的合成是细胞生长最耗费能量的方面，而蛋白质的合成对环境的反应受到严格的控制。我们已经观察到，蛋白质组将自己分割成几个部分，这些部分以线性的方式对碳、氨基酸和抗生素应激的限制做出一致反应。作为生长速率函数的线性响应可以在具有非常少量参数的粗粒度蛋白质组扇区模型中捕捉到。该项目的一个主要目标是将该模型扩展到其他限制和胁迫，包括磷、硫、氧和铁限制，以及渗透和pH胁迫。我们还进行了脉冲标记实验，表明即使在非常缓慢的蛋白质合成条件下，蛋白质组也会显著周转，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将营养转移过程中的蛋白质组变化与当前生长速度变化动态理论进行比较。这个项目是一种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，这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在感染的不利环境中或在其作为微生物组一部分的有益环境中如何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.