Gene regulation in phage lambda: A real-time study with single-event resolution

噬菌体 lambda 的基因调控：单事件分辨率的实时研究

• 批准号: 8313930
• 负责人: Ido Golding
• 金额: $ 30.68万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-04 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8313930
• 关键词: Active Biological Transport; Affect; Bacteria; Bacteriophage lambda; Bacteriophages; Biochemical; Biochemistry; Biological; Biological Models; Capsid; Cell Aging; Cell physiology; Cell surface; Cells; Characteristics; Communities; Complex; Comprehension; Cytolysis; Cytoplasm; DNA Damage; Destinations; Detection; Development; Diffusion; Engineering; Epigenetic Process; Escherichia coli; Eukaryota; Event; Fluorescence Microscopy; Gene Expression; Gene Expression Regulation; Genetic; Genetic Transcription; Genome; Goals; Growth; In Vitro; Individual; Infection; Kinetics; Knowledge; Life; Life Cycle Stages; Literature; Location; Lysogeny; Lytic; Lytic Phase; Maintenance; Measurement; Measures; Messenger RNA; Methods; Microscopic; Modeling; Motion; Noise; Organism; Outcome; Pathway interactions; Phenotype; Physiological; Population; Positioning Attribute; Potential Energy; Process; Production; Prokaryotic Cells; Property; Prophages; Reaction; Research Personnel; Resolution; Role; Scientist; Shapes; Signal Transduction; Source; Spatial Distribution; Staging; System; Systems Biology; Theoretical model; Time; Time Study; Transcript; Virulent; Virus; base; biological systems; cell age; cell injury; chemical reaction; developmental genetics; in vivo; insight; lambda repressor; macromolecule; mathematical model; molecular scale; novel; novel strategies; public health relevance; response; self assembly; spatiotemporal; tool

DESCRIPTION (provided by applicant): The system comprised of the bacterium Escherichia coli and its virus, bacteriophage lambda, serves as the basic paradigm for many aspects of gene regulation, ranging in scale from the molecular to the organismic level. Questions asked within the lambda system often yield insights relevant to "higher" eukaryotic systems. The lambda system has been extensively characterized using the traditional tools of genetics and biochemistry, enabling the formation of an elegant and seemingly complete narrative of the observed phenomenology in terms of the microscopic interactions in the cell. However, from the point of view of a quantitative scientist there is an immense gap of understanding between the genetic and biochemical knowledge on the one hand, and the observed population phenotype on the other. This gap manifests itself in the poor predictive powers of mathematical models of the system. To try and bridge the knowledge gap it is required to "deconstruct" the life cycle of bacteriophage lambda by studying the events comprising this life cycle in real-time, in individual living cells, quantifying the intracellular dynamics with sufficient resolution to describe individual events in space and time. In this proposal we suggest to characterize gene regulation during the lambda life cycle, concentrating on the following aims: (1) Characterizing the function of the lysis/lysogeny switch during the maintenance of the lysogenic (dormant) state as well as the induction of the lytic (virulent) pathway following cell damage. (2) Elucidating spatiotemporal aspects affecting the life cycle, for example how the different stages of the lytic pathway genome replication, gene expression, capsid self-assembly and lysis are organized in space and time. (3) Distinguishing precision versus stochasticity in the lambda life cycle, by separating "real" stochasticity one resulting from actual sources of uncontrolled variability from "apparent" stochasticity, resulting from our own inability to detect and measure differences in physiological parameters between individual cells. PUBLIC HEALTH RELEVANCE: Filling the knowledge gap at the single-event level will in turn bring us closer to a quantitative understanding of whole-system (organism) characteristics in terms of the microscopic constituents, in the vain of "systems biology". Achieving this goal in a simple model system such as lambda can then be followed by similar endeavors in higher organisms.

描述（由申请人提供）：由大肠杆菌及其病毒、噬菌体 lambda 组成的系统作为基因调控许多方面的基本范例，范围从分子水平到生物体水平。在 lambda 系统中提出的问题通常会产生与“高等”真核系统相关的见解。 lambda 系统已使用传统的遗传学和生物化学工具进行了广泛的表征，从而能够根据细胞中的微观相互作用对观察到的现象学形成优雅且看似完整的叙述。然而，从定量科学家的角度来看，一方面遗传和生化知识与另一方面观察到的群体表型之间存在巨大的理解差距。这种差距体现在系统数学模型的预测能力较差。为了尝试弥合知识差距，需要通过在单个活细胞中实时研究构成该生命周期的事件来“解构”噬菌体的生命周期，以足够的分辨率量化细胞内动态以描述单个事件空间和时间。在本提案中，我们建议表征 lambda 生命周期中的基因调控，重点关注以下目标：（1）表征在维持溶原（休眠）状态以及诱导裂解过程中裂解/溶原开关的功能。细胞损伤后的裂解（有毒）途径。 （2）阐明影响生命周期的时空方面，例如裂解途径基因组复制、基因表达、衣壳自组装和裂解的不同阶段如何在空间和时间上组织。 (3) 区分 lambda 生命周期中的精度与随机性，通过将不受控制的变异性的实际来源引起的“真实”随机性与“表观”随机性分开，“表观”随机性是由于我们自己无法检测和测量单个细胞之间生理参数的差异而导致的。 公共卫生相关性：填补单事件层面的知识空白将使我们更接近对微观成分的整个系统（有机体）特征的定量理解，而这只是“系统生物学”的徒劳。在简单的模型系统（例如 lambda）中实现这一目标，然后可以在高等生物体中进行类似的努力。