Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling
复制标题
DOI：
10.1128/msystems.00516-19
复制
发表时间：
2020-01-01
期刊：
影响因子：
6.4
通讯作者：
Lam, Hon-Ming
中科院分区：
文献类型：
--
作者：
Contador, Carolina A.;Lo, Siu-Kit;Lam, Hon-Ming
根瘤菌是能够与多种宿主植物建立共生关系的土壤细菌。具体来说，费氏中华根瘤菌是一种土壤细菌，在包括大豆在内的多种豆类植物中形成固氮根瘤。菌株S. fredii CCBAU 45436是S. fredii是在中国黄淮海平原盐碱土上结瘤的大豆。在这里，我们提出了一个手动策划的共生形式的费氏中华根瘤菌CCBAU 45436的代谢模型。共生反应被定义来描述特定的大豆-微生物共生体协会。当使用标准化基因组尺度代谢模型测试套件进行评估时，重建的性能和质量得分为70%。该模型被用来评估在电脑单基因敲除，以确定控制固氮过程的基因。541个基因中有141个（26%）被发现影响共生过程，其中121个基因被预测为必需的，20个基因被预测为具有部分影响。CCBAU 45436的转录组学图谱用于评估接种微共生体的栽培大豆与野生大豆中的固氮能力。该模型量化了该菌株在这两种寄主中的固氮活性，并预测了栽培大豆中较高的固氮能力。我们的研究结果与已发表的数据相一致，表明栽培大豆中酰脲和总氮含量高于野生大豆。本工作首次对S. fredii作为一个有用的工具，探索可持续农业和生态系统的微共生体的潜在利益的一个例子。重要性氮是最限制植物生长的常量营养素，根瘤菌是重要的农业细菌，因为它们可以固定大气中的氮，并通过与宿主植物建立共生关系，使其可用于豆科植物。本文从基因组水平研究了费氏中华根瘤菌的固氮过程。利用基因组注释和文献资料建立了代谢模型，重建了共生形式的S。弗雷迪。通过模拟基因敲除来鉴定控制固氮过程的基因。此外，S. fredii CCBAU 45436与栽培大豆和野生大豆共生。预测表明，S。fredii与栽培大豆，与已发表的实验证据一致。本文的重建将有助于理解和提高S. fredii，将有利于农业，减少对化肥施用的依赖。
Rhizobia are soil bacteria able to establish symbiosis with diverse host plants. Specifically, Sinorhizobium fredii is a soil bacterium that forms nitrogen-fixing root nodules in diverse legumes, including soybean. The strain S. fredii CCBAU45436 is a dominant sublineage of S. fredii that nodulates soybeans in alkaline-saline soils in the Huang-Huai-Hai Plain region of China. Here, we present a manually curated metabolic model of the symbiotic form of Sinorhizobium fredii CCBAU45436. A symbiosis reaction was defined to describe the specific soybean-microsymbiont association. The performance and quality of the reconstruction had a 70% score when assessed using a standardized genome-scale metabolic model test suite. The model was used to evaluate in silico single-gene knockouts to determine the genes controlling the nitrogen fixation process. One hundred forty-one of 541 genes (26%) were found to influence the symbiotic process, wherein 121 genes were predicted as essential and 20 others as having a partial effect. Transcriptomic profiles of CCBAU45436 were used to evaluate the nitrogen fixation capacity in cultivated versus in wild soybean inoculated with the microsymbiont. The model quantified the nitrogen fixation activities of the strain in these two hosts and predicted a higher nitrogen fixation capacity in cultivated soybean. Our results are consistent with published data demonstrating larger amounts of ureides and total nitrogen in cultivated soybean than in wild soybean. This work presents the first metabolic network reconstruction of S. fredii as an example of a useful tool for exploring the potential benefits of microsymbionts to sustainable agriculture and the ecosystem.IMPORTANCE Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont Sinorhizobium fredii at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of S. fredii. Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of S. fredii CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of S. fredii with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of S. fredii and will be beneficial for agriculture by reducing the reliance on fertilizer applications.