Reconstruction And Simulation Analysis Of Genome-scale Metabolic Network For Leptolyngbya Sp. JSC-1

Based on the research of systems biology and bioinformatics methods,we can build a biology genome-scale metabolic network of the organism to research biological metabolic characteristics and phenotypic characteristics from the global perspective.This method has important reference value for guiding the biological metabolic engineering experiment and industrial applications. Leptolyngbya sp.JSC-1 is a kind of filamentous cyanobacteria,gram-negative bacteria.JSC-1 can grow in high levels of Fe (?40?), and can accumulate extracellular iron (ferrihydrite) and intracellular iron(ferric phosphates),and can tolerate extreme circumstance such as high temperature,water shortage, oxidative stress, UV, etc.It has complementary chromatic adaptation, and is apparently able to fix nitrogen,can synthesize chlorophyll a and nine carotenoids,and secrete organic acids. The Leptolyngbya sp.JSC-1 genome-scale metabolic network enables us to have a preliminary understanding of the algal growth mechanism and has important significance to explore the physiological and biochemical characteristics.It is a theoretical role to guide the gene and metabolic engineering.In this paper ,we successfully reconstruct the first Leptolyngbya sp.JSC-1 genome-scale metabolic network model in the world. In model building works there are four stages included as follows:1. Extracting the whole genome data and building the primary network of Leptolyngbya sp.JSC-1 with the database, then we can get the primary network;2. Manually refining the primary network, including pretreating the metabolic reaction, determining the reaction direction, distributing the cell compartment and complement of metabolic reactions , balancing the charge and mass of each reaction, constructing the biomass equations, etc ;3. Evaluation and correction the model,we can get the simulation result calculated by FBA and then compare with the real experiment result.Then correcting the model continually in order to improve the accuracy . The final model includes 1387 reactions, 1241 metabolites, 1113 genes and 91 metabolic pathways;4. Simulation and analyzing the JSC-1 metabolic network model based on the principle of the FBA optimization method .Using the MATLAB platform and COBRA toolbox,we can starting the simulation work,which mainly contains: flux balance analysis, flux variability analysis, predicting the biomass Precursor and the cofactors compounds, metabolic flux analysis,robustness analysis, phenotypic phase plane analysis, reactions and genes essentiality analysis. In the systems level we can have a preliminary understanding of growth and metabolism characteristics in Leptolyngbya sp.JSC-1.It also lays the theoretical foundation for genetic and metabolic engineering.