Structure and activity of Escherichia coli chromosome

大肠杆菌染色体的结构和活性

• 批准号: 6610855
• 负责人: ARKADY B KHODURSKY
• 金额: $ 32.17万
• 依托单位: UNIVERSITY OF MINNESOTA
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-05-01 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6610855
• 关键词: DNA binding protein; Escherichia coli k12; bacterial genetics; cell component structure /function; chromosomes; conformation; functional /structural genomics; genetic mapping; genetic transcription; microarray technology; microorganism growth; physical model; protein localization

DESCRIPTION (provided by applicant): Information stored in genes is realized through the process of transcription. While transcription of individual genes is understood as a biochemical reaction in a great deal of molecular detail, the transcription of gene ensembles cannot yet be studied in a framework of the reduced biochemical reaction. It is also likely that even if we were equipped to study ensemble activities with high molecular precision, we would miss essential macroscopic properties of the processes that govern transcription of gene ensembles in the cell. The most basic and fundamental is the process of transcription as a function of position of the genes on a chromosome. The fundamental nature of it can be underscored by the notion that at the deterministic basis of this process lays the structure of a chromosome - a critical piece of knowledge about the cell. Indeed, the relationship between structure and function is one of the fundamental principles in molecular biology. The relationship between molecular structure and function has been used very successfully to propose, understand, and verify mechanisms of action of individual protein and DNA molecules as well as their motifs. However, our understanding of organization of the higher order macromolecules, such as chromosomes, has been slow and ineffective largely due to the low-resolution capacity of indirect techniques and invasive nature of the direct ones. Whole genome DNA microarrays designed using complete sequence information made possible direct read-out of genome's activity at a single gene resolution and higher. My laboratory uses this technique to: i) directly study and model the structure of the Escherichia coli K12 (E. coli) chromosome; ii) determine how the structure of the chromosome influences its activity and vice versa. We demonstrated that variations in gene activity as a function of gene position contain useful information about the process of transcription and are not entirely random: significant short- (~ 5 kb) and long-range correlations (~ 90kb) can be detected in transcriptional spatial data series by using standard analytical tools borrowed from signal processing, information theory and statistics. I propose to extend the combined use of theoretical approaches with direct experimentation to determine: 1) the effects of internal and external perturbations, which are known to affect global chromosomal state(s), on the observed spatial correlations; 2) dynamic distribution of DNA biding proteins that are known to control global DNA properties; 3) 3-D structure of the bacterial chromosome. As a result of these studies I expect to be able to model mechanistic and structural basis for the chromosome activity. This work will reveal a new level of organization of prokaryotic genetic material and its role in bacterial physiology, and also will provide a framework for studying spatial interactions in the chromosomes of higher organisms.

描述（申请人提供）：基因中存储的信息是通过转录过程实现的。虽然单个基因的转录在大量分子细节上被理解为生化反应，但基因组的转录尚不能在简化的生化反应的框架中进行研究。即使我们有能力以高分子精度研究整体活动，我们也可能会错过控制细胞中基因整体转录过程的基本宏观特性。最基本和最基本的是作为染色体上基因位置的函数的转录过程。染色体的结构是这一过程的确定性基础，而染色体的结构是关于细胞的重要知识，这一概念可以强调其基本性质。事实上，结构和功能之间的关系是分子生物学的基本原理之一。分子结构和功能之间的关系已被非常成功地用于提出、理解和验证单个蛋白质和 DNA 分子及其基序的作用机制。然而，我们对染色体等高级大分子组织的理解一直缓慢且无效，很大程度上是由于间接技术的低分辨率能力和直接技术的侵入性。使用完整序列信息设计的全基因组 DNA 微阵列使得以单基因分辨率或更高分辨率直接读取基因组活性成为可能。我的实验室使用该技术来： i) 直接研究和模拟大肠杆菌 K12（大肠杆菌）染色体的结构； ii) 确定染色体的结构如何影响其活性，反之亦然。我们证明，基因活性的变化作为基因位置的函数包含有关转录过程的有用信息，并且不完全随机：可以在转录空间中检测到显着的短程相关性（〜5 kb）和长程相关性（〜90kb）使用信号处理、信息论和统计学中借用的标准分析工具生成数据系列。我建议扩展理论方法与直接实验的结合使用，以确定：1）已知会影响全局染色体状态的内部和外部扰动对观察到的空间相关性的影响； 2）已知控制整体DNA特性的DNA结合蛋白的动态分布； 3) 细菌染色体的 3-D 结构。作为这些研究的结果，我希望能够模拟染色体活性的机制和结构基础。这项工作将揭示原核遗传物质的新组织水平及其在细菌生理学中的作用，并且还将为研究高等生物染色体的空间相互作用提供一个框架。