Building a unified framework for understanding bacterial gene regulation and chromosomal architecture

建立理解细菌基因调控和染色体结构的统一框架

• 批准号: 10622670
• 负责人: Lydia Freddolino
• 金额: $ 40.7万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-01 至 2028-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10622670
• 关键词: 3-Dimensional; Architecture; Area; Automobile Driving; Bacteria; Bacterial Antibiotic Resistance; Bacterial Chromosomes; Bacterial Genes; Bacteriophage mu; Behavior; Binding; ChIP-seq; Chromosome Structures; DNA; DNA-Binding Proteins; DNA-Protein Interaction; Dissociation; Epigenetic Process; Escherichia coli; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Growth; Heterochromatin; Impairment; Investigation; Laboratories; Logic; Maps; Measurement; Metabolic; Methods; Modification; Molecular; Nutrient; Organism; Physiological; Play; Post-Translational Protein Processing; Process; Prophages; Proteins; Regulation; Research; Role; Sigma Factor; Structure; Study models; Technology; Therapeutic; Transcriptional Regulation; Virulence; Work; bacterial genetics; cell motility; clinically relevant; crosslink; design; experimental study; genome-wide; global health; innovation; innovative technologies; interest; prevent; protein profiling; rapid technique; response; synthetic biology; targeted treatment; three dimensional structure; tool; transcription factor; transcription regulatory network; virulence gene; 3-Dimensional; Architecture; Area; Automobile Driving; Bacteria; Bacterial Antibiotic Resistance; Bacterial Chromosomes; Bacterial Genes; Bacteriophage mu; Behavior; Binding; ChIP-seq; Chromosome Structures; DNA; DNA-Binding Proteins; DNA-Protein Interaction; Dissociation; Epigenetic Process; Escherichia coli; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Growth; Heterochromatin; Impairment; Investigation; Laboratories; Logic; Maps; Measurement; Metabolic; Methods; Modification; Molecular; Nutrient; Organism; Physiological; Play; Post-Translational Protein Processing; Process; Prophages; Proteins; Regulation; Research; Role; Sigma Factor; Structure; Study models; Technology; Therapeutic; Transcriptional Regulation; Virulence; Work; bacterial genetics; cell motility; clinically relevant; crosslink; design; experimental study; genome-wide; global health; innovation; innovative technologies; interest; prevent; protein profiling; rapid technique; response; synthetic biology; targeted treatment; three dimensional structure; tool; transcription factor; transcription regulatory network; virulence gene

ABSTRACT Transcriptional regulation via protein-DNA interactions plays an important role in the regulatory networks of all known organisms. Bacterial regulatory networks are now an especially fruitful target for detailed investigation: as antibiotic- resistant bacteria continue to emerge as a global health threat, new and innovative approaches to either preventing virulence or impairing bacterial growth are required. As our ability to predict and exploit bacterial behavior for therapeutic purposes hinges on our understanding of the logic behind their regulatory networks, it is of great utility to fully map those networks and the molecular mechanisms underlying them. Several challenges, both old and newly recognized, stand in the way of a comprehensive understanding of regulatory logic even in well-studied models such as Escherichia coli. In additional to classical cis-regulatory logic by transcription factors and sigma factors, recent work by our laboratory and others has revealed contributions due to chromosomal context, large heterochromatin-like regions of repressive occupancy of nucleoid-associated proteins, overall three-dimensional chromosomal structure, and epigenetic modifications of both DNA-binding proteins and the DNA itself that further modulate transcriptional regulation. In addition, for non-model bacteria even the fundamental logic of classical transcriptional regulation is often poorly characterized. Thus, the fundamental regulatory logic behind cellular decisions such as metabolic switches, motility, and induction of virulence is often under-characterized. We have developed several innovative technologies to assist in rapid characterization of bacterial transcriptional regulatory logic, including: IPOD-HR, which allows overall profiling of protein occupancy on bacterial; transposon based methods for rapidly profiling genome-wide effects of genetic context on transcription; and a method based on the transposable phage Mu for crosslinking-free measurement of the 3D structure of the genome. Using these methods alongside classical approaches such as bacterial genetics and ChIP-seq, we are pursuing several avenues of research to investigate bacterial transcriptional regulatory networks. Key areas of interest include: Rapid elucidation of new transcriptional regulatory networks: Leveraging the IPOD-HR technology, which we have shown can be readily applied to new bacterial species, we are mapping the set of cis regulatory interactions driving important environmental responses in several clinically relevant bacterial species. Dynamics and composition of extended protein occupancy domains (EPODs): We have shown that highly protein occupied, heterochromatin like EPODs are present in a broad range of bacterial species, and play key roles in regulating prophages, virulence genes, and metabolic genes. We will continue to investigate the regulatory roles of EPODs, the proteins that comprise them, and the factors dictating their formation/dissociation across a range of bacterial taxa. Interplay of bacterial epigenetic marks with TF binding and EPODs: By interfacing our IPOD-HR and ChIP-seq experiments with tracking of covalent DNA and DNA-binding protein modifications, we will elucidate how these modifications modulate both local and large-scale protein occupancy and transcription in bacteria.

抽象的 通过蛋白质-DNA相互作用的转录调节在所有已知的调节网络中起重要作用 有机体。细菌调节网络现在是详细研究的特别富有成果的目标：作为抗生素 - 耐药细菌继续作为全球健康威胁，新的和创新的方法来防止 需要毒力或细菌生长。作为我们预测和利用细菌行为的能力 治疗目的取决于我们对其监管网络背后逻辑的理解，这是非常有用的 充分绘制这些网络以及它们的分子机制。 古老和新认可的几个挑战都妨碍了人们对 即使在诸如大肠杆菌之类的良好模型中，调节逻辑也是如此。除了经典的顺式调节逻辑外 转录因素和西格玛因素，我们的实验室和其他人最近的工作揭示了由于 染色体环境，大杂色素样区域的抑制性占用率与核苷相关蛋白的抑制作用， 总体三维染色体结构，以及DNA结合蛋白的表观遗传学修饰和 DNA本身，进一步调节转录调节。另外，对于非模型细菌，即使是基本的细菌 经典转录调节的逻辑通常表征不佳。因此，背后的基本监管逻辑 诸如代谢开关，运动和毒力诱导之类的细胞决策通常被低估了。 我们已经开发了几种创新技术，以帮助快速表征细菌转录。 调节逻辑，包括：iPod-hr，iPod-HR允许在细菌上进行蛋白质占用率的总体分析；基于转座子 快速分析遗传环境对转录的全基因组影响的方法；以及一种基于 用于基因组3D结构的无交联测量的可替代噬菌体MU。使用这些方法 除了细菌遗传学和CHIP-SEQ等古典方法外，我们正在追求几种研究途径 研究细菌转录调节网络。关键领域包括： 快速阐明新的转录监管网络：利用iPod-HR技术，我们 已经显示的可以很容易地应用于新的细菌物种，我们正在绘制驱动的顺式调节相互作用集 几种临床相关的细菌物种中的重要环境反应。 扩展蛋白占用结构域（EPODS）的动力学和组成：我们已经表明了高度蛋白质 被占据的异染色质像Epods存在于广泛的细菌物种中，并在调节中起关键作用 预言，毒力基因和代谢基因。我们将继续研究Epods的调节作用， 构成它们的蛋白质以及决定其在一系列细菌分类群中形成/解离的因素。 细菌表观遗传标记与TF结合和Epods的相互作用：通过将iPod-HR和ChIP-Seq接口 通过跟踪共价DNA和DNA结合蛋白修饰的实验，我们将阐明如何 修饰调节细菌中的局部和大规模蛋白质占用率和转录。