Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae.,Molecular Plant Pathology

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Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae.
Molecular Plant Pathology ( IF 4.8 ) Pub Date : 2020-02-18 , DOI: 10.1111/mpp.12914
Lokanand Koduru ₁ , Hyang Yeon Kim ₂ , Meiyappan Lakshmanan ₁ , Bijayalaxmi Mohanty ₁ , Yi Qing Lee ₃ , Choong Hwan Lee ₂ , Dong-Yup Lee _{1,

3}

Affiliation

Xanthomonas oryzae pv. oryzae (Xoo) is a vascular pathogen that causes leaf blight in rice, leading to severe yield losses. Since the usage of chemical control methods has not been very promising for the future disease management, it is of high importance to systematically gain new insights about Xoo virulence and pathogenesis, and devise effective strategies to combat the rice disease. To do this, we reconstructed a genome‐scale metabolic model of Xoo (iXOO673) and validated the model predictions using culture experiments. Comparison of the metabolic architecture of Xoo and other plant pathogens indicated that the Entner–Doudoroff pathway is a more common feature in these bacteria than previously thought, while suggesting some of the unique virulence mechanisms related to Xoo metabolism. Subsequent constraint‐based flux analysis allowed us to show that Xoo modulates fluxes through gluconeogenesis, glycogen biosynthesis, and degradation pathways, thereby exacerbating the leaf blight in rice exposed to nitrogenous fertilizers, which is remarkably consistent with published experimental literature. Moreover, model‐based interrogation of transcriptomic data revealed the metabolic components under the diffusible signal factor regulon that are crucial for virulence and survival in Xoo. Finally, we identified promising antibacterial targets for the control of leaf blight in rice by using gene essentiality analysis.

中文翻译：

水稻叶枯病病原体米黄单胞菌的基因组规模代谢重建和计算机分析。

米黄单胞菌pv. oryzae (Xoo) 是一种维管束病原体，可引起水稻叶枯病，导致严重的产量损失。由于化学防治方法的使用对于未来的病害管理前景并不乐观，因此系统地获得有关 Xoo 毒力和发病机制的新见解并制定有效的策略来防治水稻病害具有非常重要的意义。为此，我们重建了 Xoo ( i XOO673) 的基因组规模代谢模型，并使用培养实验验证了模型预测。 Xoo 和其他植物病原体的代谢结构的比较表明，Entner-Doudoroff 途径是这些细菌中比以前认为的更常见的特征，同时提示了与 Xoo 代谢相关的一些独特的毒力机制。随后基于约束的通量分析使我们能够表明，Xoo 通过糖异生、糖原生物合成和降解途径调节通量，从而加剧暴露于氮肥的水稻的叶枯病，这与已发表的实验文献非常一致。此外，基于模型的转录组数据询问揭示了可扩散信号因子调节子下的代谢成分，这对于 Xoo 的毒力和生存至关重要。最后，我们通过基因必要性分析确定了控制水稻叶枯病的有希望的抗菌靶标。

更新日期：2020-02-18

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