Controlled Diversity in Bacterial Stress Response

描述(申请人提供)：枯草芽孢杆菌，一种重要的医学和工业土壤生长细菌，以其丰富的应激反应谱而闻名。枯草杆菌利用许多巧妙的程序来应对压力，其中包括它摄取细胞外DNA、分化为孢子、合成降解酶和变得能动的能力。长期以来，人们观察到枯草芽孢杆菌表现出表观应激反应的多样性：即在相同环境条件下，在遗传上相同克隆的细胞群体中，一些细胞会进行选择的应激反应，而其余的细胞则激活其他途径。实验室条件的设计是为了防止这种克隆多样性，这在许多实验和工业应用中是一种不受欢迎的复杂情况。然而，要么是表型噪声是虚假的，仅仅是因为没有对统一反应的强烈选择；要么是多样化由细胞控制并服务于进化目的。这项建议是基于后一种观点。我们的假设基于越来越多的证据，即微生物的应激反应多样化可以是对不可预测的环境的适应性反应，并通过我们的初步模拟研究。在这里，我们提出了一个有指导的计划，以量化在枯草杆菌中跨多个胁迫反应途径的概率决策，并阐明引起切换和多样化的网络特征。更具体地说，我们建议系统地测量枯草杆菌细胞对控制这些过程的整合网络的每一部分在一系列胁迫条件下对孢子形成、DNA转化能力、枯草杆菌蛋白合成和运动性的所有可能组合的贡献率。因为我们的实验设计需要一系列的压力源，而不是单一的压力源，这些数据也将开始量化电路中的环境记忆。我们计划收集平均种群水平、亚种群水平和单个细胞水平的数据，所有这些数据都与四种应激反应的表达模式有关。该数据集将通过与数学模型的正式比较进行分析，这些数据集通过跨多个模态的协调测量而变得独特。这项研究是第一次系统地测量、模拟和解释多种应激反应中的协调多样化，并将为未来关于微生物多样化的生理意义的研究奠定基础。

DESCRIPTION (provided by applicant): Bacillus subtilis, a medically and industrially important soil growing bacterium, is well known for its rich stress response spectrum. Among the many ingenious programs employed by B. subtilis to cope with stress are its ability to take up extracellular DNA, differentiate into spores, synthesize degradative enzymes, and become motile. It has long been observed that B. subtilis exhibits epigenetic stress response diversification: that is, in a genetically isoclonal population of cells under identical environmental conditions, some cells will embark on the 'selected' stress response, while the remainder activate alternative pathways. Laboratory conditions are designed to militate against this clonal diversity, an undesirable complication in many experiments and industrial applications. However, either phenotypic noise is spurious, existing only because there is no strong selection for a uniform response; or diversification is controlled by the cell and serves an evolutionary purpose. This proposal is based on this latter view. We base this hypothesis on a growing body of evidence that stress response diversification in microbes can be an adaptive response to an unpredictable environment, and by our preliminary modeling studies. Here we propose a directed program to quantify the probabilistic decision-making across multiple stress response pathways in B. subtilis, and to elucidate the network features giving rise to switching and diversification. More specifically, we propose to systematically measure the fraction of B. subtilis cells committing to all possible combinations of spore formation, competence for DNA transformation, subtilisin synthesis, and motility, in response to a series of stress conditions designed to exercise each part of the integrated network controlling these processes. Because our experimental design calls for a series of stressors, rather than single stressors, these data will also begin to quantify environmental memory in the circuitry. We plan to collect data at an average population level, a subpopulation level, and a single cell level, all pertaining to the expression patterns of the four stress responses. This data set, made unique by the coordinated measurements across multiple modalities, will be analyzed through formal comparison to a mathematical model. This study is the first effort to systematically measure, model, and explain coordinated diversification across multiple stress responses, and will form the foundation for future studies on the physiological significance of diversification in microbes.