Computational Molecular Biology 2024, Vol.14, No.5, 191-201 http://bioscipublisher.com/index.php/cmb 192 understand the proteomic changes under drought conditions (Salekdeh et al., 2002). Nowadays by integrating bioinformatics tools, researchers can analyze PPI networks to identify critical proteins that interactions that contribute to drought tolerance. This review combines findings from proteomics and bioinformatics studies to comprehensively analyze the PPI network of rice under drought stress, summarizes the current knowledge on the effects of drought stress on rice at the proteomic level, clarifies the construction and analysis of the PPI network under drought stress conditions, identifies key proteins and interactions involved in the drought stress response of rice, and discusses the potential application of these findings to breeding programs and biotechnological interventions to enhance drought resistance. Through this review, we hope to bridge the gap between proteomics data and practical applications in rice improvement and provide directions for future research and development in this critical area. 2 Drought Stress Responses in Rice 2.1 Physiological and biochemical responses to drought stress Drought stress significantly impacts the physiological and biochemical processes in rice. One of the primary physiological responses is the reduction of leaf water content, which can lead to stomatal closure to minimize water loss through transpiration. This process, however, also limits CO2 uptake, thereby reducing photosynthesis and growth (Maksup et al., 2014). Additionally, drought stress induces the accumulation of osmo protectants such as proline and soluble sugars, which help maintain cell turgor and protect cellular structures (Hamzelou et al., 2020). In response to drought stress, plants accumulate organic and inorganic solute, achieve osmotic adaptations by accumulating osmoprotectants and increase antioxidant activity for scavenging Reactive Oxygen Species (ROS) to improve drought tolerance. 2.2 Molecular mechanisms responses to drought stress At the molecular level, drought stress triggers a complex network of gene expression changes. Key molecular mechanisms is the upregulated ABA (abscisic acid)-dependent signaling pathway with energy metabolic processes (Sircar and Parekh, 2019; Hsu et al., 2021). Various transcription factors (TFs) such as bHLH (basic helix-loop-helix) and bZIP (basic leucine zipper), MYB (myeloblastosis), are involved in the regulation of ABAdependent signaling pathways and play a major role in the stress response by regulating the expression of many downstream drought-responsive genes (Peleg et al., 2011; Soltanpour et al., 2022). Furthermore, drought stress induces the expression of heat shock proteins (HSPs), late embryogenesis abundant (LEAs), calmodulin-like protein (CML) and other stress-related proteins that help in protein folding, protection, and repair. Proteomic studies have identified actin depolymerizing factor and S-like RNase homologues proteins, that are differentially expressed under drought conditions, suggesting their roles in maintaining cellular structure and function during drought stress (Hong et al., 2016; Pant et al., 2022). 2.3 Importance of proteomics in understanding drought stress responses Proteomics provides a comprehensive approach to understanding the drought stress responses, which offering insights that are not apparent from transcriptomic or genomic studies alone. Proteomic analyses have revealed that drought stress leads to significant changes in the abundance of proteins involved in photosynthesis, carbohydrate metabolism, and protein synthesis and other metabolic pathways (Wu et al., 2016; Hamzelou et al., 2020). Wu et al. (2016) characterized a new ClpD1 protease, indicating a shift in metabolic priorities to cope with stress, which downregulated of photosynthetic proteins and upregulated of stress-related proteins in drought-tolerant rice varieties. Furthermore, the field of proteomics has been instrumental in uncovering previously unknown proteins that respond to drought stress. These proteins play vital roles in cell defense and energy metabolism, making them promising candidates for serving as biomarkers in the development of drought-tolerant crops (Maksup et al., 2014; Agrawal et al., 2016). The integration of proteomic data with transcriptomics and metabolomics can provide a system understanding for the complex regulatory networks involved in drought stress responses (Shu et al., 2011; Yun et al., 2022). By leveraging proteomic technologies, researchers can identify key proteins and pathways that contribute to drought tolerance, thereby facilitating the development of more resilient crop varieties through genetic engineering and breeding programs.
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