Testable in silico Hypotheses for E.coli Growth

可在计算机中测试大肠杆菌生长的假设

• 批准号: 6727600
• 负责人: BERNHARD O PALSSON
• 金额: $ 60.37万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-04-01 至 2006-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6727600
• 关键词: Escherichia coli; bacterial genetics; computer data analysis; computer simulation; evolution; functional /structural genomics; gene environment interaction; gene expression; gene mutation; high performance liquid chromatography; microarray technology; microorganism growth; microorganism metabolism; model design /development; physical model; polymerase chain reaction; spectrometry

The relation between the genotype and the phenotype of an organism is fundamental to biology. Based on the annotated genome sequence and biochemical information it is possible to reconstruct genome-scale metabolic maps, and in silico methods have been developed to interpret and predict the optimal utilization of the metabolic map under a given growth condition. Using the defined Escherichia coli MG1655 metabolic genotype, experimentally testable hypotheses have been formulated in silico describing the quantitative relation between the uptake rate of a primary carbon source, oxygen uptake rate, and cellular growth. Experiments with E. coli have been performed and experimental data were found to be consistent with the optimal use of the metabolic network to support growth of E. coli under the experimental conditions considered, which were growth on acetate, succinate, and malate. These important results form the basis for the proposed program. It is comprised of three parts, 1) to continue the generation of experimentally testable hypotheses for a broader ranger of carbon sources and to profile the gene expression patterns for these growth conditions, 2) to generate 40 knockout strains and perform both growth experiments and gene expression studies to characterize their metabolic behavior and 3) to perform evolution experiments for wild-type and knockout strains of E. coli that exhibit sub-optimal growth phenotypes. Additionally, gene expression studies will be performed for these evolving strains during and after evolution to identify the molecular events that are elicited during the evolutionary process. Hence the experimental program has the specific aims of determining optimal phase plane behavior for a range of growth conditions, and to determine if metabolic gene expression patterns are consistent with predicted pathway used for both wild-type and knockout strains. If the program is successfully implemented and executed we will have refined and improved our understanding of the metabolic genotype-phenotype relationship for E. coli under the conditions examined, an accomplishment of clear fundamental significance.

生物体的基因型和表型之间的关系是生物学的基础。基于注释的基因组序列和生化信息，可以重建基因组规模的代谢图，并在硅酸盐中开发了用于解释和预测给定生长条件下代谢图的最佳利用。使用定义的大肠杆菌MG1655代谢基因型，已经在硅中提出了可检验的实验测试假设，这些假设描述了原代碳源，氧摄取速率和细胞生长的摄取速率之间的定量关系。已经进行了大肠杆菌的实验，发现实验数据与在所考虑的实验条件下的代谢网络的最佳使用，以支持大肠杆菌的生长，这些实验条件是乙酸，琥珀酸酯和苹果酸盐的生长。这些重要结果构成了拟议计划的基础。它由三个部分组成，1）继续生成更广泛的碳源的实验测试假设，并介绍这些生长条件的基因表达模式，2）以产生40个敲除菌株，并同时进行生长实验和基因表达研究，以表征其代谢性和3），以表征其代理和敲除狂野的表现。表型。此外，将在进化过程中和之后对这些不断发展的菌株进行基因表达研究，以鉴定进化过程中引起的分子事件。因此，实验程序具有确定一系列生长条件的最佳相平面行为的具体目的，并确定代谢基因表达模式是否与用于野生型和敲除菌株所使用的预测途径一致。如果该计划成功实施和执行，我们将在所检查的条件下完善并改善对大肠杆菌代谢基因型 - 表型关系的理解，这是实现明确的基本意义。