Controlled Diversity in Bacterial Stress Response

描述（由申请人提供）：枯草芽孢杆菌是一种医学和工业上重要的土壤生长细菌，以其丰富的应激反应谱而闻名。枯草芽孢杆菌采用了许多巧妙的程序来应对压力，其中包括吸收细胞外DNA、分化成孢子、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遗传应激反应多样化：也就是说，在相同环境条件下的遗传等克隆细胞群体中，一些细胞将开始“选择”应激反应，而其余细胞则激活替代途径。实验室条件的设计是为了防止这种克隆多样性，这是许多实验和工业应用中不希望出现的并发症。然而，两种表型噪声都是虚假的，仅仅因为没有对统一反应的强选择而存在；或者多样化是由细胞控制的，并服务于进化的目的。这项建议是以后一种观点为基础的。越来越多的证据表明，微生物的应激反应多样化可能是对不可预测的环境的适应性反应，我们基于这一假设，并通过我们的初步建模研究。在此，我们提出了一个定向程序来量化枯草芽孢杆菌跨多个应激反应途径的概率决策，并阐明导致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芽孢杆菌细胞在一系列应激条件下参与所有可能的孢子形成、DNA转化能力、枯草杆菌素合成和运动性组合的比例，这些应激条件旨在锻炼控制这些过程的综合网络的每个部分。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。我们计划在平均种群水平、亚种群水平和单细胞水平收集数据，这些数据都与四种应激反应的表达模式有关。该数据集由跨多种模式的协调测量而独特，将通过与数学模型的正式比较进行分析。该研究首次系统地测量、模拟和解释了多种应激反应下的协调多样化，为今后研究微生物多样化的生理意义奠定了基础。

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.