Testable in silico Hypotheses for E.coli Growth

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，并且已经开发了计算机模拟方法来解释和预测在给定生长条件下代谢图的最佳利用。使用定义的大肠杆菌MG 1655代谢基因型，实验测试的假设已制定在硅片描述的主要碳源的摄取速率，氧摄取速率和细胞生长之间的定量关系。实验用E.大肠杆菌的实验数据被发现是一致的最佳使用的代谢网络，以支持大肠杆菌的生长。大肠杆菌在所考虑的实验条件下，其在乙酸盐、琥珀酸盐和苹果酸盐上生长。这些重要结果构成了拟议方案的基础。本研究包括三个部分：1）继续对更广泛的碳源范围产生实验可验证的假设，并对这些生长条件下的基因表达模式进行分析; 2）产生40株基因敲除菌株，并进行生长实验和基因表达研究，以表征其代谢行为;大肠杆菌，表现出次优的生长表型。此外，将在进化过程中和进化后对这些进化菌株进行基因表达研究，以鉴定进化过程中引发的分子事件。因此，实验程序的具体目标是确定一系列生长条件下的最佳相平面行为，并确定代谢基因表达模式是否与野生型和敲除菌株所用的预测途径一致。如果该计划成功实施和执行，我们将完善和提高我们的理解代谢基因型-表型关系的大肠杆菌。大肠杆菌的条件下检查，一个明确的基本意义的成就。

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.