System Dynamics of the Salmonella Virulence Regulatory Network

沙门氏菌毒力监管网络的系统动力学

• 批准号: 8524180
• 负责人: CHRISTOPHER A VOIGT
• 金额: $ 27.95万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-16 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8524180
• 关键词: Affect; Binding Sites; Biological Models; Bordetella; Burkholderia; Cells; Chlamydia; Code; Codon Nucleotides; Complex; Coupling; DNA; DNA Sequence; DNA biosynthesis; Data; Escherichia coli; Essential Genes; Eukaryotic Cell; Feedback; Flow Cytometry; Functional RNA; Gene Cluster; Gene Expression; Gene Order; Genes; Genetic; Genetic Programming; Genome; Glanders; Gram-Negative Bacteria; Human; Infection; Knowledge; Macromolecular Complexes; Membrane; Methods; Methylation; Modeling; Molecular Chaperones; Molecular Machines; Needles; Noise; Operon; Pathogenicity Island; Plague; Process; Property; Proteins; Pseudomonas; Randomized; Regulation; Relative (related person); Research Design; Ribosomes; Role; Salmonella; Salmonella food poisoning; Scanning; Sexually Transmitted Diseases; Shigella Infections; Signal Transduction; Site; Software Engineering; Syringes; System; Testing; Time; Type III Secretion System Pathway; Typhoid Fever; Variant; Virulence; Yersinia; design; feeding; improved; mathematical model; pathogen; programs; promoter; sensor; stoichiometry; theories; tool; transcription factor

DESCRIPTION (provided by applicant): The central objective of this proposal is to identify the design principles by which gene clusters encoding complex molecular machines are organized and regulated. As a model system, we will study the type III secretion system (T3SS) encoded in Salmonella Pathogenicity Island 1 (SPI-1). The T3SS is a molecular machine that acts a "syringe" to inject proteins into host cells. The T3SS requires the expression of ~18 proteins at the correct ratios to properly assemble and function. Little is known as to how changes in the relative expression levels, the order of expression, and expression noise impact this process. We propose to study SPI-1 by rebuilding it from the bottom-up, using biophysical models and well-characterized genetic parts. This process, known as "refactoring," replaces all of the regulation with synthetic variants and eliminates unknown and poorly characterized regulation. The refactored SPI-1 is controlled by synthetic genetic circuits that implement the dynamics of gene expression. In Aim 1, the refactored system will be used as a platform to determine how gene order and translational coupling impact the robustness of the cluster to perturbations in expression levels. In Aim 2, the impact of different regulatory programs on the proper assembly and function of the T3SS will be determined. Synthetic genetic circuits will be constructed that implement different feed forward and feedback loops that are predicted by mathematical models to affect the noise and dynamics of gene expression. This enables the testing of hypotheses that controlling the temporal order and intrinsic noise of expression is important for the assembly of macromolecular complexes. Together, these studies will identify robust and fragile aspects of common virulence mechanism shared by many human pathogens.

描述（由申请人提供）：本提案的中心目标是确定组织和调节编码复杂分子机器的基因簇的设计原则。作为模型系统，我们将研究沙门氏菌致病岛1（SPI-1）编码的III型分泌系统（T3 SS）。T3 SS是一种分子机器，充当“注射器”将蛋白质注入宿主细胞。T3 SS需要约18种蛋白质以正确的比例表达，以正确组装和发挥功能。关于相对表达水平、表达顺序和表达噪音的变化如何影响这一过程，人们知之甚少。我们建议通过自下而上重建SPI-1，使用生物物理模型和良好表征的遗传部分来研究SPI-1。这个过程被称为“重构”，用合成变体取代所有的调节，并消除未知和特征不佳的调节。重构的SPI-1由实现基因表达动力学的合成遗传电路控制。在目标1中，重构的系统将被用作一个平台，以确定基因顺序和翻译偶联如何影响表达水平扰动的集群鲁棒性。在目标2中，将确定不同调节程序对T3 SS的适当组装和功能的影响。将构建合成遗传电路，实现不同的前馈和反馈回路，这些回路由数学模型预测，以影响基因表达的噪声和动态。这使得能够测试假设，即控制表达的时间顺序和内在噪声对于组装是重要的。 大分子复合物的。总之，这些研究将确定许多人类病原体共有的共同毒力机制的强大和脆弱方面。