Yang Yi, Hu Xiao-Pan, Ma Bin-Guang
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
Mol Biosyst. 2017 Feb 28;13(3):607-620. doi: 10.1039/c6mb00553e.
Bradyrhizobium diazoefficiens is a rhizobium able to convert atmospheric nitrogen into ammonium by establishing mutualistic symbiosis with soybean. It has been recognized as an important parent strain for microbial agents and is widely applied in agricultural and environmental fields. In order to study the metabolic properties of symbiotic nitrogen fixation and the differences between a free-living cell and a symbiotic bacteroid, a genome-scale metabolic network of B. diazoefficiens USDA110 was constructed and analyzed. The metabolic network, iYY1101, contains 1031 reactions, 661 metabolites, and 1101 genes in total. Metabolic models reflecting free-living and symbiotic states were determined by defining the corresponding objective functions and substrate input sets, and were further constrained by high-throughput transcriptomic and proteomic data. Constraint-based flux analysis was used to compare the metabolic capacities and the effects on the metabolic targets of genes and reactions between the two physiological states. The results showed that a free-living rhizobium possesses a steady state flux distribution for sustaining a complex supply of biomass precursors while a symbiotic bacteroid maintains a relatively condensed one adapted to nitrogen-fixation. Our metabolic models may serve as a promising platform for better understanding the symbiotic nitrogen fixation of this species.
慢生根瘤菌是一种能够通过与大豆建立互利共生关系将大气中的氮转化为铵的根瘤菌。它已被公认为微生物制剂的重要亲本菌株，并广泛应用于农业和环境领域。为了研究共生固氮的代谢特性以及自由生活细胞与共生类菌体之间的差异，构建并分析了慢生根瘤菌USDA110的基因组规模代谢网络。该代谢网络iYY1101总共包含1031个反应、661种代谢物和1101个基因。通过定义相应的目标函数和底物输入集确定了反映自由生活和共生状态的代谢模型，并进一步受到高通量转录组学和蛋白质组学数据的约束。基于约束的通量分析用于比较两种生理状态之间的代谢能力以及对基因和反应的代谢靶点的影响。结果表明，自由生活的根瘤菌具有稳定的通量分布以维持复杂的生物质前体供应，而共生类菌体则维持相对浓缩的通量分布以适应固氮作用。我们的代谢模型可能是一个有前景的平台，有助于更好地理解该物种的共生固氮作用。
