Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa).

IF 3.6 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Journal, genetic engineering & biotechnology Pub Date : 2023-05-29 DOI:10.1186/s43141-023-00515-8
Samadhi S Wimalagunasekara, Janith W J K Weeraman, Shamala Tirimanne, Pasan C Fernando
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Abstract

Background: The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance.

Results: Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs.

Conclusions: These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.

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蛋白质-蛋白质相互作用(PPI)网络分析揭示了水稻根系发育的重要枢纽蛋白和子网络模块。
背景:根系对植物的生长和生存至关重要。因此,对根系进行遗传改良有利于培育耐胁迫和改良的植物品种。这需要鉴定对根系发育有重要贡献的蛋白质。分析蛋白质-蛋白质相互作用(PPI)网络对研究发育表型(如根发育)非常有益,因为表型是几种蛋白质相互作用的结果。可以分析PPI网络来识别模块,并获得控制表型的重要蛋白质的全局理解。水稻根系发育的PPI网络分析以前从未进行过,有可能在提高胁迫耐受性方面产生新的发现。结果:本文从STRING数据库中检索到的全球Oryza sativa PPI网络中提取了根系发育网络模块。预测新的候选蛋白,并从提取的模块中鉴定出枢纽蛋白和子模块。预测的验证产生了75个新的候选蛋白,6个子模块,20个模内枢纽和2个模间枢纽。结论:这些结果显示了PPI网络模块是如何组织根系发育的,并可用于未来生产改良水稻品种的湿室研究。
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