Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Int J Mol Sci. 2021 Nov 2;22(21):11907. doi: 10.3390/ijms222111907.
Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. As a classical model system for symbiotic nitrogen fixation, rhizobium-legume systems have been studied elaborately for decades. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of USDA110 with its transcriptome and proteome data to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of USDA110 by computational approaches. Based on the comparison of interactomes between USDA110 and other rhizobia, we inferred that the slow growth of USDA110 may be due to the requirement of more protein modifications, and we further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.
共生固氮是氮生物地球化学循环的重要组成部分，也是生物圈的主要氮源。作为共生固氮的经典模式系统，根瘤菌-豆科植物系统已经被深入研究了几十年。关于根瘤菌和宿主植物之间的通讯和协调的分子机制的细节变得越来越清晰。为了获得更系统的认识，人们越来越需要新的研究来整合多组学信息。在这里，我们提出了一个综合的计算框架，该框架整合了 USDA110 的重建蛋白质互作组及其转录组和蛋白质组数据，以研究参与共生系统的复杂蛋白质-蛋白质相互作用（PPI）网络。我们通过计算方法重建了 USDA110 的互作组。基于 USDA110 和其他根瘤菌之间的互作组比较，我们推断 USDA110 的生长缓慢可能是由于需要更多的蛋白质修饰，我们进一步鉴定了 36 个保守的功能 PPI 模块。与转录组和蛋白质组数据集成后，获得了自由生活细胞和共生固氮（SNF）类菌体的互作组。基于 SNF 互作组，确定了共生固氮的核心亚 PPI 网络，并鉴定了九个新的功能模块和十一个在共生中起关键作用的关键蛋白枢纽。重建的 USDA110 互作组可以作为研究根瘤菌和豆科植物 SNF 系统机制的有价值的参考。
