Addition And Application In Byproducts Analysis Of Transport Reaction In Metabolic Network Models

With the rapid development of high-throughput analysis and the continualaccumulation of vast amounts of data, the applications of genome-scale metabolicnetwork models are more and more important. However, the reconstructed metabolicnetwork models ID are much less than the sequenced organisms. One of the mainimportant reasons is that there are many time-consuming manual processes needed inmetabolic network reconstruction to improve the network quality.The addition of transport reaction is an important step to utilize metabolic modelfor flux balance analysis. Transport reactions define the input and output of biologicalsystems directly. The addition of transport reactions also requires a lot of manualwork.In this paper, transport reactions and external metabolites of48publishedgenome-scale metabolic network models are extracted and used to build a transportreaction dataset. This dataset is available from the Genome Scale Metabolic NetworkDataset (GSMNDB) website (http://synbio.tju.edu.cn/GSMNDB/Pages/transport.htm).It is a comprehensive and systematic transport reaction platform for users to findproper transport reactions to be added to the network model. Based on this dataset, wedevelop a new method for semi-automatically adding transport reactions.In addition, this paper analyzed the effect of knocking different transportreactions in different growth conditions, particularly at different oxygen availability.Knockout the synthesis pathway of metabolites which have higher priority to thetarget product could improve the yield of target product. For example, we canimprove the production of Lactic acid by knockout the acetate kinase (acetate)、alcohol dehydrogenase (ethanol).