Controlled Diversity in Bacterial Stress Response

细菌应激反应的受控多样性

• 批准号: 7379908
• 负责人: Adam P Arkin
• 金额: $ 36.59万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-03-03 至 2010-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7379908
• 关键词: Adherence; Algorithms; Antibiotics; Bacillus subtilis; Back; Bacteria; Behavior; Biochemical Genetics; Biotin; Calcium Signaling; Cell Count; Cell Density; Cell Wall; Cells; Commit; Competence; Complement; Complication; Condition; Culture Media; DNA; DNA Microarray Chip; DNA Microarray format; Data; Data Analyses; Data Set; Data Sources; Decision Making; Development; Dimerization; Discrimination; Dot Immunoblotting; Drug Formulations; Elements; Environment; Enzymes; Epigenetic Process; Equation; Exercise; Exhibits; Experimental Designs; Experimental Models; Facility Construction Funding Category; Flow Cytometry; Fluorescence; Foundations; Funding; Future; Gene Components; Gene Expression; Gene Expression Profile; Generations; Genes; Genome; Goals; Hand; Kinetics; Laboratories; Lactobacillus; Ligand Binding Domain; Ligands; Literature; Maps; Measurement; Measures; Memory; Methods; Microbe; Microscopy; Modality; Modeling; Molecular; Mutate; Mutation; Noise; Organism; Pathway interactions; Pattern; Personal Satisfaction; Phase; Phenotype; Physiologic pulse; Physiological; Population; Population Density; Population Heterogeneity; Probability; Process; Protocols documentation; Pulse taking; Purpose; Range; Reaction; Reporter; Reproducibility; Reproduction spores; Research; Role; Sampling; Series; Signal Transduction; Soil; Sorting - Cell Movement; Source; Statistically Significant; Stress; Study models; Subtilisin; Subtilisins; Surface; Techniques; Technology; Testing; Time; Validation; Vesnarinone; base; biological adaptation to stress; cell motility; comparative; coping; density; design; environmental stressor; experimental analysis; extracellular; feeding; fitness; follow-up; functional genomics; fusion gene; mathematical model; mutant; network models; programs; promoter; research study; response; satisfaction; simulation; stressor; surface coating; theories; tool

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, differentiateinto 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.

枯草芽孢杆菌是一种重要的医学和工业土壤生长细菌，以其丰富的 应力反应谱。枯草杆菌使用了许多巧妙的程序来应对压力 是它摄取细胞外DNA，分化成孢子，合成降解酶的能力，以及 变得能动。长期以来，人们观察到枯草杆菌表现出表观遗传的应激反应多样化： 也就是说，在遗传上相同克隆的细胞群体中，在相同的环境条件下，一些细胞将 开始“选定的”压力反应，而其余的则激活其他途径。实验室 条件的设计是为了防止这种克隆多样性，这在许多情况下是一种不受欢迎的并发症 实验和工业应用。然而，任何一种表型噪声都是虚假的，存在的唯一原因是 没有强有力的选择来做出统一的反应；或者多样化由细胞控制，并为 进化的目的。这项建议是基于后一种观点。我们把这一假设建立在一个不断增长的身体上 有证据表明，微生物的应激反应多样化可以是对不可预测的 环境，并通过我们的初步建模研究。在这里，我们提出了一个有指导的计划来量化 枯草杆菌多条胁迫反应途径的概率决策，并阐明 网络特征带来了交换和多样化。更具体地说，我们建议有系统地 测量枯草杆菌细胞致力于所有可能的孢子形成组合的比例， 对一系列胁迫的DNA转化、枯草杆菌菌素合成和运动性的反应能力 为执行控制这些过程的综合网络的每个部分而设计的条件。因为我们的 实验设计需要一系列压力源，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。我们计划在平均人口水平上收集数据， 亚群水平和单细胞水平，都与四种胁迫的表达模式有关 回应。该数据集通过跨多个通道的协调测量而变得唯一，将是 通过形式对比分析了一个数学模型。这项研究是第一次系统地 衡量、模拟和解释跨多种压力反应的协调多样化，并将形成 为今后研究微生物多样化的生理意义奠定基础。