Cotton Genomics and Genetics 2025, Vol.16, No.3, 126-136 http://cropscipublisher.com/index.php/cgg 130 cells are not "drained". Of course, not every cotton plant can respond quickly. Some varieties may synthesize slowly, resulting in faster water loss and more susceptible cells to damage. In those varieties that are more responsive, these metabolic regulation mechanisms are particularly important (Kausar and Komatsu, 2022). 5.3 Stress signaling and transcription factors Proteomic studies have also found that salt stress can upregulate some signal-related proteins and transcription factors. Among them, leucine-rich repeat receptor kinases (LRR-RLKs), 14-3-3 proteins and other signaling molecules can recognize the signals of salt stress and then activate a series of defense responses (Ji et al., 2016). Some transcription factors and stress response proteins, such as universal stress proteins (USPs) and dirigent-like proteins, are also activated under salt stress. They can regulate the expression of some genes related to antioxidant, defense, cell wall remodeling and metabolism (Athar et al., 2022). These proteins play an important coordinating role in regulating the adaptation of plants to salt environments and can help maintain the stable operation of the entire response mechanism. 6 Comparative Analysis of Drought vs. Salt Stress Proteomes 6.1 Shared proteomic responses Although drought and salt stress are different, they both cause similar changes in the proteome of plants. For example, plants accumulate small molecules that can regulate osmotic pressure and increase the expression of proteins related to antioxidants. At the same time, plant photosynthesis and energy metabolism will also be adjusted. Under these two stresses, some common signaling pathways will be activated, such as calcium ion (Ca²⁺) signaling, G protein signaling, 14-3-3 protein and phosphorylation cascade. Among them, some proteins, such as calcium-binding EF-hand family proteins, play a role in both stresses and are the "connection points" between them (Luo et al., 2015). There are also some enzymes related to sugar metabolism and energy production that increase in both drought and salt stress, which shows that plants use similar methods to maintain the homeostasis of cells (Ma et al., 2017). 6.2 Stress-specific protein expression Although there are similarities, drought and salt stress also have their own characteristics. Each stress causes some protein changes that only appear under that condition. Generally speaking, drought has a greater impact on plants, so the number of differentially expressed proteins (DEPs) that are exclusive to drought is also greater. For example, STN7 and BSL are phosphorylated signaling proteins that are activated only under drought conditions; while CDPK21, TPR, and CTR1 are unique to salt stress. In addition, some metabolic enzymes and photosynthesis-related proteins (such as transketolase, RubisCO fragments) respond differently in the two stresses, and some are only expressed under drought or salt stress (Rabey et al., 2015; Rabey et al., 2016). 6.3 Insights into stress tolerance mechanisms By comparing protein changes under different stresses, the study found that although many defense and metabolic pathways are activated, the expression strength and specificity of each protein determines the tolerance of the plant. Some protein families develop different functions according to different adversities, which allows plants to adjust their responses more flexibly. Some "tandem" proteins are involved in regulation in both stresses, and they are potential targets for improving the multi-stress resistance of plants (Du et al., 2020). Combining proteomic and transcriptomic data for analysis can better understand these regulatory networks. This will be of great help to future stress-resistant breeding and genetic engineering, and also provide direction for the development of more drought- and salt-tolerant crop varieties. 7 Case Study: Proteomics of Gossypium hirsutum under Field-Imposed Stress Conditions 7.1 Experimental setup and stress treatments Not all experiments are done in the lab. To understand how field crops like cotton respond to drought and salinity in real environments, we need to move the research to a more realistic scenario. So the researchers designed a set of proteomics experiments to observe the response of upland cotton (Gossypium hirsutum) under simulated drought and salt stress conditions. How to simulate drought? They reduced the relative moisture content of one group of soils to 40%-45%, while maintaining the relative moisture content of another group at 70%-75% as a
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