Molecular Soil Biology 2025, Vol.16, No.5, 230-240 http://bioscipublisher.com/index.php/msb 234 revealed that some key transcription factors (such as GmCRE1, GmNIN) and signaling pathways can regulate protein expression and affect the development of root nodules and the differentiation of nitrogen-fixation regions (Ke et al., 2022; Sun et al., 2023). Figure 2 Post-translational modifications (PTMs) of proteins of the Calvin–Benson cycle (CBC) and photorespiration (Adopted from Balparda et al., 2023) 5 Case Study: Comparative Proteomics of Efficient vs. Inefficient Nodules 5.1 Selection of soybean genotypes or rhizobial strains with contrasting fixation efficiency Comparative proteomics studies usually select soybean varieties with significant differences in nitrogen fixation efficiency, such as Peking and Williams 82, or use rhizobium strains with different effects, such as Bradyrhizobium elkanii USDA76. To analyze the molecular basis of nitrogen fixation efficiency (Cooper et al., 2017). In addition, some studies have obtained materials with different nitrogen fixation capabilities in phosphorus-deficient environments through genetic modification or gene editing for comparative experiments (Wang et al., 2020; Xing et al., 2022; Sun et al., 2024). 5.2 Experimental design: nodule sampling, proteomic workflow, validation Experimental design usually involves collecting root nodules from different materials under the same conditions and then using high-resolution LC-MS /MS and other methods for protein identification and quantification. Common quantitative methods include label-free, iTRAQ and TMT (Cooper et al., 2017). Researchers will analyze the functions of differential proteins using bioinformatics, and also verify the expression and role of some key proteins through qRT-PCR, Western blotting or transgenic (Wang et al., 2020; Yang et al., 2021; Xing et al., 2022; Yang et al., 2022).
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