Computational Molecular Biology 2024, Vol.14, No.5, 191-201 http://bioscipublisher.com/index.php/cmb 195 5.2 Construction and analysis of PPI networks under drought stress The construction and analysis of PPI networks under drought stress provide insights into the complex molecular interactions that underpin drought tolerance. Proteomic approaches have enabled the identification of numerous proteins whose abundance is altered in response to drought, thus facilitating the construction of PPI networks. Salekdeh et al. (2002) employed 2D-PAGE and MS methods to detect over 1,000 proteins, with 42 exhibiting significant alterations in abundance in response to drought stress. These proteins can be mapped into PPI networks to understand their interactions and regulatory roles. Besides, bioinformatics tools have been utilized to analyze these networks, thereby elucidating the key pathways and molecular functions involved in drought response (Jangam et al., 2016). 5.3 Functional annotation and pathway enrichment analysis of PPI networks The functional annotation and pathway enrichment analysis of PPI networks facilitate the elucidation of the biological processes and pathways involved in drought stress response. Transcriptome analysis has demonstrated that a considerable number of drought-responsive genes are regulated in a manner that is a specific to the tissue or development stage-express, indicating the presence of a complex regulatory network (Wang et al., 2011). Gene ontology (GO) analysis and pathway enrichment studies have identified several critical pathways, including plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the mitogen-activated protein kinase (MAPK) signaling pathways, which are enriched in drought-responsive proteins (Hao et al., 2022)., The integration of proteomic and bioinformatics data facilitates a comprehensive understanding of the molecular mechanisms that underpin drought tolerance in rice. 6 Case Studies 6.1 Specific PPI networks involving TFs and signaling proteins A number of studies have emphasized the significance of TFs and signaling proteins in the PPI networks of rice in response to drought stress. Wang et al. (2020a) discovered the TFs (OsNAC006) is the positive regulators and can be target for genome editing in rice, knockout of OsNAC006 results in drought sensitivity. Usman et al. (2020) reported that ABA receptors (OsPYL9) also positive regulated the drought tolerance mechanisms. The OsPYL9 is mutagenized through CRISPR/Cas9 system. The OsPYL9 mutants exhibited higher ABA levels, antioxidant activity and accumulated more waxy crystals on the leaf epidermis and showed decreased vascular bundles (Figure 2) under drought conditions, which were markedly superior to those observed in the wild type. Finally, the OsPYL9 mutants show an increase in grain yield under both well watered field and drought conditions. The observed phenotypic about an increase in wax accumulation and change in vascular structure, represent crucial adaptations process for mutant plants to enhance their stress responses. And proteomic analysis revealed that proteins such as GIGANTEA, Adagio-like, and Pseudo-response regulator proteins exhibited higher interaction within the PPI network, thereby indicating their significant roles in circadian rhythm and drought response. Additionally, another study focuses on edited the Grain Size 3 (GS3) gene also for obtaining valuable and stable long-grain rice mutants. The mutants’ plant of PPI networks found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction (Usman et al., 2021). These study demonstrated the successful application of CRISPR/Cas9 technology in enhancing rice drought resistance and yield through targeted gene editing and regulation of specific TFs and signaling proteins involved in the PPI network. Furthermore, OsbHLH148, a bHLH protein, has been observed to interact with OsJAZ proteins within the jasmonate signaling pathway, which plays a pivotal role in the development of drought tolerance. This interaction indicated the presence of a complex regulatory mechanism involving multiple signaling pathways (Seo et al., 2011). 6.2 Interaction networks related to osmoprotectants and stress-related proteins It is evident that osmoprotectants and stress-related proteins play a pivotal role in the drought stress response in rice. One study demonstrated the interaction of the F-box protein OsFBX257 with protein kinases and phosphatases, which modulated root architecture and drought stress tolerance. This protein constituted part of the SCF complex and interacts with 14-3-3 rice proteins, thereby indicating its role in the regulation of
RkJQdWJsaXNoZXIy MjQ4ODYzNA==