Computational Molecular Biology 2024, Vol.14, No.5, 191-201 http://bioscipublisher.com/index.php/cmb 191 Feature Review Open Access Protein-Protein Interaction Networks in Rice under Drought Stress: Insights from Proteomics and Bioinformatics Analysis Chunli Wang1, Nant Nyein Zar Ni Naing1,4, Cui Zhang1, JunjieLi 1, QianZhu1,2,3, Dongsun Lee 1,2,3, Lijuan Chen1,2,3 1 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 2 The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 3 College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China 4 Department of Plant Breeding, Physiology and Ecology, Yezin Agricultural University (YAU), Nay Pyi Taw, 15013, Myanmar Corresponding author: chenlijuan@hotmail.com Computational Molecular Biology, 2024, Vol.14, No.5 doi: 10.5376/cmb.2024.14.0022 Received: 27 Jul., 2024 Accepted: 06 Sep., 2024 Published: 20 Sep., 2024 Copyright © 2024 Wang et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang C.L., Ni Niang N.N.Z., Zhang C., Li J.J., Zhu Q., Lee D.S., and Chen L.J., 2024, Protein-protein interaction networks in rice under drought stress: insights from proteomics and bioinformatics analysis, Computational Molecular Biology, 14(5): 191-201 (doi: 10.5376/cmb.2024.14.0022) Abstract This review outlines the physiological and biochemical responses of plants to drought stress, explains the molecular mechanisms, and emphasizes the key role of proteomics in these responses. Drought stress causes dehydration and osmotic changes in plants, leading to cell membrane damage, accumulation of reactive oxygen species (ROS), and metabolic disorders. Plants respond to drought stress through a series of complex physiological and biochemical responses, including regulate of stomatal opening and closing, synthesis protective proteins and metabolites, activate antioxidant systems, and regulate gene expression. Through proteomic and bioinformatic analysis, we systematically synthesis findings that identified key response proteins in rice under drought stress, constructed and analyzed the PPI network, performed functional annotation and pathway enrichment analysis, and demonstrated specific PPI networks involving transcription factors and signaling proteins, interaction networks with osmoprotectants and stress-related proteins, and comparative analysis of PPI networks of different rice varieties under drought stress through case studies. By exploring the response mechanism of rice under drought stress, we propose to develop more effective drought resistance strategies to improve the stability and sustainability of rice production. Keywords Drought stress; Proteomics; Protein-protein interaction networks (PPI Networks); Rice; Bioinformatics analysis 1 Introduction Rice (Oryza sativa L.) is a staple food for more than half of the world's population, making it a critical crop for global food security. Increased rice production plays an extremely important role in ensuring food security and people's living standards. However, rice yields are highly susceptible to environmental stresses, particularly drought, which is one of the most severe limitations on rice productivity (Hamzelou et al., 2020). Drought stress affects approximately 50% of the world's rice production, leading to significant yield losses (Sircar and Parekh, 2018). Understanding the molecular mechanisms underlying drought tolerance in rice is essential for developing drought-resistant rice varieties that can withstand water-deficit conditions. Studying its response to drought stress can provide valuable insights into the adaptive mechanisms and potential targets for genetic improvement (Agrawal et al., 2016). Proteomics is the science of studying the protein composition of cells, tissues or organisms. With the development of science and technology, proteomics methods have changed to high-throughput methods such as tissue microarray (TMA), protein pathway array and mass spectrometry (Chandramouli et al., 2009). However, Protein-Protein Interaction Network Analysis (PPI Network Analysis) is one of the important research components of proteomics. PPI networks are crucial for understanding the complex biological processes that control cellular responses to environmental stresses. PPIs facilitate the coordination of various cellular functions by enabling proteins to interact and form functional complexes. For drought stress, PPI networks can reveal key regulatory proteins and pathways involved in stress response, signal transduction (Paul et al., 2015; Usman et al., 2020). Proteomic approaches, such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS), have advanced our ability to analyze these networks, providing a comprehensive view to
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