Reconstruction Of Genome-Scale Metabolic Network For The Rhodococcus Opacus PD630

With the help of bioinformatics and systems biology,the method of building a biology genome-scale metabolic network is conducive to research the distribution of metabolic pathways and the accumulation of metabolites from the global perspective.It's also of great significance to guide the biology metabolic engineering practice and industrial applications.Rhodococcus Opacus PD630 is a well-known lipid producing bacteria of Rhodococcus.A variety of substrates can be used widely as the carbon source and converted to lipid which can be stored in the body.PD630 has a strong ability of transforming the carbon source that the cell are growing well in the industrial and agricultural wastewater which contains cellulose,hemicellulose and lignin.By absorbing organic material as the carbon source of growing needs can PD630 reduce the contaminativity of industrial and agricultural wastewater,effectively.PD630 can grow in the soil that contaminated by petroleum using the alkanes and aromatic hydrocarbon compounds as the carbon source,which effectively alleviate the pollution.PD630 has a very strong capacity of lipid accumulation.Under a certain condition,the triglycerides(TAG),which highest reach to 70%~80% of the cell dry weight,can be accumulated in the body of PD630.Based on the whole genome sequence information PD630 and the results of annotation,the first PD630 genome-scale metabolic network model in the world is reconstructed in this paper.Three parts are included in model building works as follows:(1)The extraction of whole genome annotation data and the building of primary network.(2)Artificial refining of primary network,including pretreatment of metabolic reaction,determination of the reaction direction,distribution of cell compartment and establishment of relevant evaluation mechanism,complement of metabolic reactions,balancing of charge and mass and construction of the biomass equations,etc.(3)Evaluation and correction of model by comparing the result calculated by FBA and the real experiment.The model is corrected continually in order to improve the accuracy.Finally,the model including 1384 reactions,91 metabolic pathways,1026 metabolites and 1785 genes is obtained,in which there are 121 exchange reactions and 153 transport reactions configurated,and a total of 1127 reactions with gene tagging attched.Based on the MATLAB platform and Cobra toolbox,the PD630 metabolic network model is analyzed.The simulation work mainly contains: robustness analysis,phenotypic phase plane analysis,the production of fatty acid and TAG and other by-products,prediction of cofactors compounds,metabolic flow analysis,simulation of using xylose in metabolic engineering,gene essentiality analysis.