Structure and activity of Escherichia coli chromosome

大肠杆菌染色体的结构和活性

• 批准号: 7056724
• 负责人: ARKADY B KHODURSKY
• 金额: $ 26.33万
• 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/7056724
• 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（由申请人提供）：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被理解为生化反应的大量分子细节，但基因合成的转录尚无法在还原的生化反应的框架内研究。即使我们有能力研究具有高分子精度的集成活性，我们也会错过控制细胞中基因集合的转录过程的过程的基本宏观特性。最基本和最基本的是转录的过程，这是染色体上基因位置的函数。它的基本性质可以被这样的观念强调，即在此过程的确定性基础上，染色体的结构是有关细胞的重要知识。实际上，结构与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非常成功地提出，理解和验证单个蛋白质和DNA分子的作用机理以及基序。但是，我们对组织高阶大分子（例如染色体）的组织的理解在很大程度上是由于间接技术的低分辨率和直接侵入性的性质的低分辨率。使用完整序列信息设计的整个基因组DNA微阵列使以单个基因分辨率且更高的基因组活性直接读出。我的实验室使用此技术来：i）直接研究和建模大肠杆菌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，基因活性随基因位置的变化包含有关转录过程的有用信息，并且不是完全随机的：可以在转录空间数据序列中使用信号处理，信息理论和统计数据借用的标准分析工具在转录空间数据序列中检测到显着的短 - （〜5 kb）和远距离相关性（〜90KB）。我建议将理论方法与直接实验相结合，以确定：1）内部和外部扰动的影响，这些影响会影响全球染色体状态，对观察到的空间相关性； 2）已知可以控制全局DNA特性的DNA贝贝蛋白的动态分布； 3）细菌染色体的3-D结构。由于这些研究，我希望能够建模染色体活性的机械和结构基础。这项工作将揭示新的原核生物遗传物质及其在细菌生理学中的作用，并将为研究高等生物体染色体的空间相互作用提供框架。