Genome-scale metabolic modelling of lifestyle changes in Rhizobium leguminosarum
Genome-scale metabolic modelling of lifestyle changes in Rhizobium leguminosarum
复制标题
豆根瘤菌生活方式变化的基因组规模代谢模型
DOI：
10.1101/2021.07.28.454262
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Schulte C
中科院分区：
文献类型：
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作者：
Schulte C
根瘤菌-豆科植物共生体的生物固氮对于可持续农业实践具有重要意义。为了与植物宿主建立互惠关系，根瘤菌从土壤中的自由生活的细菌过渡到植物根内的感染线，并最终分化为固氮类杆菌。我们重建了一个基因组规模的豆科根瘤菌代谢模型，并整合了转录组，蛋白质组，代谢组和基因的必要性数据，研究这些不同的生活方式的营养吸收和代谢通量特征的模型。亮氨酸、多磷酸盐和AICAR的合成被预测在根际中是重要的，而肌醇催化剂在未分化的根瘤细菌中是活跃的，这与实验证据一致。该模型表明，类杆菌利用木糖和乙醇酸除了二羧酸，这可以解释先前描述的基因表达模式。组氨酸被预测积极合成类菌体，与转录组和蛋白质组数据的几个根瘤菌物种。这些结果为针对根瘤菌-豆科植物共生不同阶段的代谢过程进行有针对性的实验研究提供了基础。重要的是根瘤菌是土壤细菌，能诱导植物根部结瘤并分化为固氮类细菌。详细了解这种复杂的共生关系对于推进正在进行的努力至关重要，这些努力是为了可持续农业而设计与谷类作物的新型共生关系。在这里，我们重建和验证的基因组规模的代谢模型豆科根瘤菌bv.viciae3841。通过将该模型与不同共生形成阶段的实验数据相结合，阐明了根际细菌、根瘤内未分化细菌和固氮类杆菌的代谢特征。我们的模型预测了这三种不同生活方式的代谢通量模式，从而为解释基因组规模的实验数据集和确定未来实验研究的目标提供了一个框架。
Biological nitrogen fixation in rhizobium-legume symbioses is of major importance for sustainable agricultural practices. To establish a mutualistic relationship with their plant host, rhizobia transition from free-living bacteria in soil to growth down infection threads inside plant roots and finally differentiate into nitrogen-fixing bacteroids. We reconstructed a genome-scale metabolic model for Rhizobium leguminosarum and integrated the model with transcriptome, proteome, metabolome, and gene essentiality data to investigate nutrient uptake and metabolic fluxes characteristic of these different lifestyles. Synthesis of leucine, polyphosphate, and AICAR is predicted to be important in the rhizosphere, whilemyo-inositol catabolism is active in undifferentiated nodule bacteria in agreement with experimental evidence. The model indicates that bacteroids utilize xylose and glycolate in addition to dicarboxylates, which could explain previously described gene expression patterns. Histidine is predicted to be actively synthesized in bacteroids, consistent with transcriptome and proteome data for several rhizobial species. These results provide the basis for targeted experimental investigation of metabolic processes specific to the different stages of the rhizobium-legume symbioses.IMPORTANCERhizobia are soil bacteria that induce nodule formation on plant roots and differentiate into nitrogen-fixing bacteroids. A detailed understanding of this complex symbiosis is essential for advancing ongoing efforts to engineer novel symbioses with cereal crops for sustainable agriculture. Here, we reconstruct and validate a genome-scale metabolic model for Rhizobium leguminosarum bv.viciae3841. By integrating the model with various experimental data sets specific to different stages of symbiosis formation, we elucidate the metabolic characteristics of rhizosphere bacteria, undifferentiated bacteria inside root nodules, and nitrogen-fixing bacteroids. Our model predicts metabolic flux patterns for these three distinct lifestyles, thus providing a framework for the interpretation of genome-scale experimental data sets and identifying targets for future experimental studies.