Genomic Architecture and the Consequences for Prokaryotic Gene Regulation

描述（由申请人提供）：拟议工作的目标是系统地表征基因组组织对大肠杆菌通过蛋白质转录因子的转录调控高效和有效地调节其基因的能力的影响。细菌能够感知和适应环境的基本机制是通过转录因子对其基因的协调调节。理论上，这些调控分子控制表达的能力可能取决于调控分子与其调控靶点之间的相对染色体距离。由此产生的进化压力可以解释大肠杆菌染色体上转录因子-靶标共定位的异常高度。提出的方法将结合实验和理论方法来定量表征和建模基因组组织对基因调控有效性的影响。通过分子方法与细菌遗传学相结合，大肠杆菌染色体上的调节网络的天然排列将被破坏和重组，并使用最先进的单细胞和单分子技术测量对基因调节的效率、随机性和生物物理学的影响。结果数据可以直接与基因调控的理论模型进行比较，以区分转录因子靶标搜索的竞争理论，更全面地描述驱动染色体组织的基本潜在机制。

DESCRIPTION (provided by applicant): The goal of the proposed work is to systematically characterize the effects of genomic organization on the ability of Escherichia coli to efficiently and effectively regulate its genes through transcriptional regulation by protein transcription factors. The fundamental mechanism through which bacteria are able to sense and adapt to their environment is through the coordinated regulation of their genes by transcription factors. In theory, the ability of these regulatory molecules to control expression may depend on the relative chromosomal distance between regulators and the targets they regulate. The resulting evolutionary pressures may explain the unusually high degree of transcription factor-target co-localization on the E. coli chromosome. The proposed approach will combine experimental and theoretical methods to quantitatively characterize and model the effects of genome organization on the effectiveness of gene regulation. By using molecular methods combined with bacterial genetics, the native arrangement of regulatory networks on the E. coli chromosome will be disrupted and reorganized and the resulting effects on the efficiency, stochasticity, and biophysics of gene regulation will be measured using state of the art single cell and single molecule techniques. The resulting data can then be directly compared to theoretical models of gene regulation to distinguish between competing theories of transcription factor target search, more fully describing the fundamental underlying mechanisms driving chromosomal organization. PUBLIC HEALTH RELEVANCE: A variety of human diseases, including birth defects, cancer, and epigenetic diseases are the result of improper gene regulation. The understanding gained through these proposed studies serve as a starting point for addressing the corresponding questions regarding gene regulation in eukaryotes, where gene regulation is far less well understood, and more complex spatial organization concerns only exacerbate the difficulties of gene regulation. By developing a more complete understanding of the mechanisms underlying gene regulation in both prokaryotes and higher organisms, we will be in a better position to exploit and manipulate these mechanisms in the treatment and prevention of genetic and microbial diseases, as well as to engineer gene pathways in order to accomplish goals that will influence public health and well-being.