| The reconstruction of genome-scale metabolic networks is the inexorable trend in post-genome era. It has been known as the product of genome sequencing, high-throughput experimental efforts, -omics, bioinformatics, computer technology, and the most effective, mature method that can describe the metabolic networks in the organism in a mathematic way, even can carry simulation and computation. In this way it bridges the gap between genome-derived biochemical information and metabolic phenotypes. Currently, almost 40 kinds of organism's genome-scale metabolic networks have been finished, and several of them are proved to be useful in the guidance of other technology.Lactobacillus delbrueckii ATCC 11842 is a typical lactate producing organism widely used in the industry, food and medical field. Unlike the genetic engineering and metabolic engineering, genome-scale metabolic networks model provides a systemic view to study the metabolic pathway in it. After carrying simulation, it can find the way to increase the productivity of lactate and reduce cost.In this paper genome annotation and metabolic reaction information are collected from many bioinformatics databases, reviews, biochemical books. The VBA program is used to deal with the high-throughput data, after that manual work is employed for refinement the reconstruction. The conversion of the reconstruction into a mathematical format and the following computation is carried out with the COBRA Toolbox based on MATLAB. The algorithm used in computation is FBA, and the solver software is glpk . Robustness analysis, phenotypic phase plane analysis, gene knockout study are performed to make a better understanding of the organism. The results show that the productivity of lactate is 1.84 mol/mol lactose. The presence of little oxygen has tiny influence on the phenotype, however, excessive oxygen can remarkably change the metabolism such as the sharply decrease in the production rate of lactate and more kinds of products are produced.
|
PDF Full Text Request