PDF(Pubmed)
Abstract：
Sinorhizobium fredii CCBAU45436 is an excellent rhizobium that plays an important role in agricultural production. However, there still needs more comprehensive understanding of the metabolic system of S. fredii CCBAU45436, which hinders its application in agriculture. Therefore, based on the first-generation metabolic model iCC541 we developed a new genome-scale metabolic model iAQY970, which contains 970 genes, 1,052 reactions, 942 metabolites and is scored 89% in the MEMOTE test. Cell growth phenotype predicted by iAQY970 is 81.7% consistent with the experimental data. The results of mapping the proteome data under free-living and symbiosis conditions to the model showed that the biomass production rate in the logarithmic phase was faster than that in the stable phase, and the nitrogen fixation efficiency of rhizobia parasitized in cultivated soybean was higher than that in wild-type soybean, which was consistent with the actual situation. In the symbiotic condition, there are 184 genes that would affect growth, of which 94 are essential; In the free-living condition, there are 143 genes that influence growth, of which 78 are essential. Among them, 86 of the 94 essential genes in the symbiotic condition were consistent with the prediction of iCC541, and 44 essential genes were confirmed by literature information; meanwhile, 30 genes were identified by DEG and 33 genes were identified by Geptop. In addition, we extracted four key nitrogen fixation modules from the model and predicted that sulfite reductase (EC 1.8.7.1) and nitrogenase (EC 1.18.6.1) as the target enzymes to enhance nitrogen fixation by MOMA, which provided a potential focus for strain optimization. Through the comprehensive metabolic model, we can better understand the metabolic capabilities of S. fredii CCBAU45436 and make full use of it in the future.
摘要：
弗氏根瘤菌CCBAU45436是一种优良的根瘤菌，在农业生产中发挥着重要作用。然而,目前仍需要更全面的了解血吸虫CCBAU45436的代谢系统，这阻碍了其在农业中的应用。因此,基于第一代代谢模型iCC541，我们开发了一个新的基因组尺度代谢模型iAQY970，其中包含970个基因，1052个反应,942个代谢物,并且在MEMOTE测试中得分89%。iAQY970预测的细胞生长表型与实验数据一致为81.7%。将自由生活和共生条件下的蛋白质组数据映射到模型中的结果表明，对数期的生物量生产率快于稳定期，栽培大豆寄生根瘤菌的固氮效率高于野生型大豆，这与实际情况是一致的。在共生条件下，有184个基因会影响生长，其中94个是必不可少的；在自由生活条件下，有143个影响生长的基因，其中78是必不可少的。其中,在共生条件下的94个必需基因中,86个与iCC541的预测一致,44个必需基因得到文献信息的证实;同时,通过DEG鉴定了30个基因，通过Geptop鉴定了33个基因。此外,我们从模型中提取了四个关键的固氮模块，并预测亚硫酸盐还原酶（EC1.8.7.1）和固氮酶（EC1.18.6.1）作为增强MOMA固氮的靶酶，这为应变优化提供了潜在的焦点。通过综合代谢模型,我们可以更好地了解血吸虫CCBAU45436的代谢能力，并在未来充分利用它。
