Reconstruction Of Azorhizobium Caulinodans Genome-scale Metabolic Model And Its Analyses

Rhizobia is a soil bacterium that can establish symbiosis relationships with a variety of legume plants.Azorhizobium caulinodans ORS571 is the only rhizobia with double nitrogen fixation ability to date.It can form nodules on the stem and root of Sesbania rostrata.Here,through the reconstruction,validation and analysis of the metabolic network model of A.caulinodans ORS571,it provides new insights in understanding metabolic basis of symbiotic nitrogen fixation ability from a systematic view.In this research,the genome-scale metabolic model of A.caulinodans ORS571 was reconstructed.In addition,the model was carefully curated by references to the published rhizobia model,biochemical databases and literature.The final A.caulinodans ORS571 model named i CX764 contains 941 reactions,793 metabolites and 764 annotated genes.Two physiological states,free growth(FL)and symbiotic nitrogen fixation(SNF)were determined by changing the objective function of the model and the simplest substrate input set respectively to simulate the environmental conditions.Simulation of the utilization of 103 carbon sources showd a 96.12% consistency with the experimental observations,including 19 true positives,80 true negatives,0 false positives,and 4 false negatives.The model was further used to simulate gene knockout phenotype,essential reaction prediction,and integrate transcriptome data to simulate the metabolic flow redistribution of the two physiological states of free-growing and symbiotic nitrogen-fixing models.A huge metabolic re-programming was successfully captured by i CX764,which indicated nitrogen fixation was a distinctive state for rhizobia.In summary,the comprehensive analysis showed that i CX764 had a good predictive performance and can be used as an effective tool for further interpreting omics data of rhizobia.From a metabolic perspective,it provides a useful theoretical supplement for further exploration and understanding of the evolution of nitrogen-fixing characteristics of rhizobia.