Cotton Genomics and Genetics 2025, Vol.16, No.4, 192-201 http://cropscipublisher.com/index.php/cgg 196 5.2 Protein degradation and energy metabolism As the fiber gradually matures, some proteins and enzymes are no longer needed. At this time, they must be degraded, and ubiquitination, a post-translational modification, can do this. The advantage of doing this is that the fiber cells can smoothly transition from the "elongation" state to the "maturity" stage. It can also save energy and use this energy in more important places, such as making cellulose and lignin (Hammarén et al., 2022). Therefore, PTMs not only help clean up old proteins, but also make metabolic activities in cells more organized. This is critical for maintaining normal cell function and supporting cotton fiber maturation. 5.3 PTM regulation of senescence-related processes As fibers gradually mature, some aging-related processes also begin to occur, such as programmed cell death and the slow cessation of metabolic activity. PTMs also play a role at this time. They regulate proteins related to aging signals to ensure that these proteins play a role at the right time. In this way, fiber cells can complete their development step by step and eventually become mature fibers with good structure and stable performance. 6 Application of Omics Data in PTM Studies 6.1 Joint analysis of transcriptome and proteome To understand how cotton fiber develops and matures, it is not enough to look at genes or proteins alone. Analyzing the two together can give us a more comprehensive view. Transcriptome studies gene expression, while proteome looks at changes in proteins. If we compare the gene expression data with the protein modification, we can know which genes may regulate which proteins. This method is more reliable than analyzing one omics alone, and can also discover associations that were not noticed before (Manzoni et al., 2016; Misra et al., 2019; Rajczewski et al., 2022). This joint analysis can also help us understand what kind of post-translational modification will occur to the protein generated after a gene is expressed. This is particularly helpful for understanding how cotton fiber develops step by step. 6.2 PTMs identification technology and database To find out which modifications have occurred on proteins, mass spectrometry (MS) technology is the most commonly used. It can quickly detect the modification of many proteins and can also quantitatively analyze these changes (Rajczewski et al., 2022). Mass spectrometry technology is becoming more and more advanced. Whether it is analyzing the entire protein or just one segment, it can give accurate results. There are also many professional databases that include a lot of PTMs information in cotton or other plants. Researchers can directly refer to these data, which is more reproducible and more convenient for collaboration (Misra et al., 2019; Lu et al., 2023). 6.3 Bioinformatics prediction and network construction It would be slow to analyze these complex data experimentally alone, so bioinformatics tools are particularly useful. These tools can help us predict where modifications may occur in proteins. They can also help us draw a diagram of the relationship between proteins, that is, the regulatory network (Yin, 2023; Sanches et al., 2024). With the help of network analysis and machine learning, researchers can find proteins that play a key role in fiber development more quickly. These predictions can also help us design subsequent experiments, avoid detours, and save time (Vlachavas et al., 2021; O’Connor et al., 2023). 7 Case Studies 7.1 Functional analysis of GhPIN phosphorylation in fiber polarity The study found that phosphorylation, a post-translational modification (PTM), is very important in the development of cotton fibers. For example, GhMPK3-1 adds a phosphate group to the transcription factor GhWRKY16, which is particularly critical to its function. In this way, GhWRKY16 can normally regulate some genes related to fiber initiation and elongation. This shows that whether it is GhWRKY16 or GhPIN, their phosphorylation state may determine how the cell expands. By regulating the activity of these proteins, cotton fibers can establish the correct growth direction (Figure 2) (Wang et al., 2021). 7.2 Acetylation of GhXTHs and its impact on cell wall extensibility Researchers have found that protein post-translational modification (PTM) affects the function of cell wall-related enzymes. Modifications such as acetylation will change the activity and stability of a protein called XTH. XTH is
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