Mapping combinatorial stress responses in bacteria using chimeric proteins and probabilistic modelling

生命系统适应不断变化的环境，以求生存、生长和繁殖。到目前为止，适应性反应的特征已经以相当一维的方式进行了研究，然而我们知道细胞通过负责细胞生长和生存的关键参与者之间的相互作用网络来运作。这些玩家可以感觉到压力，其中一些会导致新玩家出现在细胞中，其中一些会以不同的方式克服压力。然而，这些不同参与者之间的关系以及他们运作的水平在很大程度上是未知的。特别是，对一组强加条件的单一唯一解决方案是否是可以在牢房中合理运行的全部，这是一个主要的未知因素。了解细胞可接受的边界条件将极大地帮助推进需要细胞特殊性质的工作，例如在许多生物技术和合成生物学环境中。通过研究两种重要但相对具有实验适应性的单细胞细菌，我们将研究当细胞对压力做出反应时，细胞成分发生了什么变化，以及它们的反应模式如何相当于对压力的综合反应。为此，我们将收集细胞活动的几个不同区域的数据，并将使用新的控制蛋白来干扰细胞，以重新引导反应，使其远离特定的施加压力。将进行与数学建模相结合的数据分析，以整合和描述观察到的细胞行为，并帮助解释促进细胞反应的过程作为一个整体是如何工作的。收集数据的目的是直接为细胞反应机制模型的开发和评估提供信息。我们选择在两个不同的细菌生物体中进行相同的实验计划。这一拟议研究项目的比较维度使我们能够探索与细菌发病密切相关的压力反应背后的进化方面。这也有可能为合成生物学的未来分析提供信息，或尝试指导微生物进化。在研究计划结束时，我们希望能够更好地预测细胞如何应对环境的巨大变化，通过了解细胞内的哪些活动是实现对压力的适应的关键。这项工作的结果应该为深入了解细胞可能如何为特定目的向前进化提供见解，并确定可能存在的特定脆弱性，这些脆弱性可能为补救疗法提供新的靶点，例如新的抗生素靶点。

Living systems adapt to changing environments in order to survive and to grow and reproduce. Features of an adaptive response have to date been studied in a fairly one dimensional way, yet we know that the cell operates using networks of interactions between the key players that are responsible for the cells growth and viability. These players can sense stress, some will cause new players to appear in the cell, and some of these will work to overcome the stress in different ways. However the relationships between these different players and the levels at which they operate are largely unknown. In particular whether or not a single unique solution to a set of imposed conditions is all that can reasonably operate in the cell is a major unknown. Knowledge of the boundary conditions acceptable to a cell will greatly help advance work where special properties of a cell are desirable, as for example in many biotechnological and synthetic biology settings. By studying two important but relatively experimentally amenable single cell bacteria we will study what cell components change when the cells respond to stress and how their patterns of response amount to an integrated response to stress. To do so we will collect data across several different areas of cell activity, and will perturb cells using novel control proteins to redirect responses away from particular imposed stresses. Data analysis coupled to mathematical modelling will be conducted in order to integrate and describe the observed cellular behaviour, and to help explain how the processes contributing to the cell's responses work as a whole. The collection of data is targeted directly at informing the development and evaluation of mechanistic models of cell response. We have chosen to conduct the same experimental programme in two different bacterial organisms. This comparative dimension to the proposed research project allows us to explore the evolutionary aspects underlying the response to stresses that are intimately linked to bacterial pathogenesis. This also has the potential to inform future analyses in synthetic biology or attempts to direct microorganismal evolution. At the end of the research program we expect to able to better predict how cells cope with large changes in their environments, through a knowledge of which activities within the cell are key to achieving adaptation to stress. Outcomes of the work should provide insights into how cells might be forward evolved for particular purposes, and identify where particular vulnerabilities might exist that may suggest new targets for remedial therapies such as new antibiotic targets.