Molecular Plant Breeding 2025, Vol.16, No.2, 105-118 http://genbreedpublisher.com/index.php/mpb 107 3 Transcriptional Regulation under Water Deficit 3.1 Overview of transcriptional regulation in plants Plant transcriptional regulation involves TFs including MYB, bZIP, AP2/ERF, NAC, etc., controlling gene expression. These TFs bind to specific DNA sequences near the genes they regulate, known as cis-regulatory elements, such as promoter regions, thereby regulating the expression of downstream genes. This process is crucial for plants to adapt to various environmental stresses, including water deficit. TFs can activate or repress the transcription of target genes, leading to changes in the levels of mRNA and, consequently, protein production. These changes enable plants to modify their physiological and developmental processes to cope with stress conditions (Yun et al., 2010; Wilkins et al., 2016; Favreau et al., 2023). In addition to TFs themselves, there are complex signaling pathways in plants that sense environmental changes and transmit signals to TFs, thereby initiating or inhibiting the expression of specific genes (Cutler et al., 2010). Moreover, epigenetic regulatory mechanisms also play a vital role in plants' response to environmental stresses. Epigenetic changes such as DNA methylation and histone modification can affect chromatin structure, thus influencing the binding ability of TFs to DNA and regulating gene expression (Kim et al., 2015). 3.2 Key TFs involved in water deficit response Several key TFs have been identified as crucial players in the response of plants to water deficit. For instance, the NAC TF ONAC022 has been shown to improve drought tolerance in rice by modulating an ABA-mediated pathway, leading to increased proline and soluble sugar contents, reduced water loss, and enhanced survival under drought conditions (Hong et al., 2016). Additionally, MYB TFs are involved in regulating drought-inducible genes, contributing to the plant’s ability to withstand water deficit (Smita et al., 2015). Dehydration-responsive element-binding protein (DREB) can bind to specific DNA sequences under drought conditions, thereby initiating the expression of a series of defense genes to enhance plant drought tolerance (Lata and Prasad, 2011). WRKY TFs participate in various physiological processes of plants, including responses to drought, by regulating the expression of downstream target genes. For example, WRKY46 in arabidopsis has been found to enhance plant drought tolerance by activating the expression of antioxidant enzyme genes (Liu et al., 2019). TFs of the AP2/ERF family play a significant role in plant responses to drought stress. They can recognize and bind to drought response elements (DRE) in gene promoters, thus activating the expression of a series of drought-related genes (Yoshida et al., 2014). Other important TFs include bZIP, ERF, etc., which can regulate various stress response genes and pathways (Seeve et al., 2017; Chen et al., 2021). 3.3 Regulatory networks and pathways activated under water deficit The regulatory networks activated under water deficit conditions are complex and involve multiple layers of regulation. Environmental gene regulatory influence networks (EGRINs) have been identified in rice, which coordinate the timing and rate of gene expression in response to water deficit. These networks include interactions between many TFs and their target genes, integrating signals from various stress-responsive pathways (Wilkins et al., 2016). For example, the TCONS_00021861/miR528-3p/YUCCA7 regulatory axis has been identified as a key component of the drought response in rice, where the lncRNA TCONS_00021861 acts as a competing endogenous RNA to regulate the expression of YUCCA7 (Figure 1), leading to increased auxin (IAA) production and enhanced drought tolerance (Chen et al., 2021). The figure in Chen et al. (2021) shows the effects of overexpression TCONS_00021861 and miR528-3p on rice seedling growth indexes and ROS accumulation under drought stress. The dry weight, root length, leaf length, and H2O2 and O2 contents of roots and leaves were observed in different treatment groups by simulating drought stress by PEG. The results showed that overexpression of TCONS_00021861 and miR528-3p significantly affected the growth and ROS accumulation of rice seedlings under drought conditions. Specifically, the LNC and MIR treatment groups showed different response patterns in root and leaf growth, while the LNC+MIR combined treatment further enhanced the drought response. These results suggest that TCONS_00021861 and miR528-3p may affect drought adaptation of rice by regulating ROS accumulation and signaling pathways, revealing important signaling pathways involved in the response to water shortage.
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