Genome-wide Changes in Bacterial Transcription Units as a Function of Oxygen Limitation

该项目的总体目标是开发和实施一种策略，以定义细菌转录单位的高分辨率地图以及这些转录单位在不同生长条件下的变化。该策略包括两个部分：(i)确定模式细菌大肠杆菌在好氧和厌氧生长条件下的启动子和转录单位；（ii）确定关键调控因子的全基因组结合位点。这些目标将通过追求三个具体目标来实现：(i)系统地定义大肠杆菌转录单位；（ii）确定转录单位在不同生长条件下的变化；（iii）利用寡核苷酸微阵列绘制转录调控因子的结合位点。该项目将在两个领域产生科学影响。首先，由于大肠杆菌是研究最广泛的微生物，有关它的知识为微生物细胞和分子生物学的详细机制研究以及系统生物学、合成生物学和复杂生物网络的计算机建模等不断发展的领域提供了框架。通过严谨的实验提供准确的信息，该项目将有助于为大肠杆菌和相关生物的研究奠定坚实的基础。其次，综合实验策略的发展将提供一个范例，以及可以广泛应用于许多细菌的工具和技术。该项目将通过从前沿的角度培养实验微生物科学的研究生和本科生，并通过开发细菌转录的教学模块，产生重大而广泛的影响。

The overall objective of this project is to develop and implement a strategy to define high-resolution maps of bacterial transcription units and changes in these transcription units in different growth conditions. The strategy has two parts: (i) to define the promoters and transcription units of a model bacterium, E. coli, under aerobic and anaerobic growth conditions; and (ii) to determine the genomewide binding sites of key regulators. These goals will be accomplished by pursuing three specific aims: (i) systematically define E. coli transcription units; (ii) determine how transcription units change in different growth conditions; and (iii) map binding sites for transcriptional regulators using oligonucleotide microarrays. The project will have scientific impact in two areas. First, because E. coli is the most widely studied microorganism, knowledge about it provides the framework for detailed mechanistic studies of microbial cell and molecular biology and for the growing fields of systems biology, synthetic biology, and in silico modeling of complex biological networks. By providing accurate information based on rigorous experiments, the project will help build a solid foundation for study of E. coli and related organisms. Second, development of an integrated experimental strategy will provide a paradigm, as well as tools and technology that can be broadly applied to many bacteria. The project will have significant broader impacts by training graduate and undergraduate students in experimental microbial science from a cutting-edge perspective and by developing an instructional module on bacterial transcription.