Molecular Soil Biology 2025, Vol.16, No.5, 230-240 http://bioscipublisher.com/index.php/msb 231 discovered many functional proteins related to nitrogen fixation. They also revealed the roles of post-translational modification of proteins, subcellular localization and protein-protein interaction networks in regulating efficient nitrogen fixation (Ke et al., 2022; Zhou et al., 2022). This study summarizes the major progress in the field of soybean rhizoma proteomics in recent years, with a focus on the molecular basis of efficient nitrogen fixation, key proteins and their regulatory networks. Meanwhile, this study will also discuss the unique value of proteomics in the complex process of root nodules, introduce in detail the research achievements in root tumor development, energy and nutritional metabolism, signal transduction and environmental adaptation, and analyze the application prospects of different proteomics techniques (such as bottom-up, top-down, spatial proteomics, etc.). At the end of the study, we hope to explore the impact of proteomics on the nitrogen fixation efficiency of soybeans in the future and its application in molecular breeding through prospects. 2 Soybean Nodule Development and Function 2.1 Structural and physiological characteristics of nodules Soybean root nodules are organs specifically responsible for nitrogen fixation and are mainly divided into two parts: one is the central infection area (CIZ), and the other is the vascular bundle (VBs). There are a large number of cells infected by rhizobia in CIZ, which is the main site for nitrogen fixation. VBs is responsible for transporting water, nutrients and fixed nitrogen into the plant body. The morphology and size of root nodules are closely related to the nitrogen fixation efficiency. There are significant differences in the ratios of CIZ and VBs among different soybean varieties, which will affect their nitrogen fixation capacity. The normal development and function of root nodules also require a stable supply of elements such as iron and phosphorus. Iron is often enriched in the infection area and it can enhance the activity of metalloenzymes such as nitrogenase (Chen et al., 2018; Liu et al., 2020; Wang et al., 2020; Nakhforoosh et al., 2024). 2.2 Molecular signaling between soybean roots and rhizobia The symbiotic relationship between soybeans and rhizobia is established through the exchange of molecular signals. Soybean roots secrete some flavonoids, such as daidzein and genistein, which can attract rhizobia and induce rhizobia to produce Nod factors, thereby initiating root hair deformation and the formation of infected filaments (Lyu et al., 2022; Lin et al., 2024; Li et al., 2025). In signal transduction, plants and rhizobia rely on the regulation of various receptor kinases, transcription factors (such as NIN, NF-YA1, NSP1/2), and hormones to complete their interactions (Ren et al., 2025; Zhao et al., 2025). Meanwhile, the light signal and carbon metabolism status can also be transmitted from the aboveground part to the root through proteins such as GmFT2a, thereby affecting the initiation of nodulation and nitrogen fixation capacity (Wang et al., 2021; Li et al., 2022). 2.3 Key pathways regulating nodule initiation, infection, and maturation The process of nodule formation involves several steps: root hair perception, infection filament formation, cortical cell division and organogenesis of root nodules. Nod factor signaling activates the expression of downstream genes through pathways such as CCaMK, NIN, and NSP1/2, promoting the formation of root nodule primorgenes (Wang et al., 2021; Li et al., 2022; Ren et al., 2025; Zhao et al., 2025). Nutritional signals such as iron and phosphorus can also interact with nodular signals. For example, the iron receptor BTSa can regulate the activity of NSP1 through monoubiquitination, ensuring more efficient tumor formation under the condition of sufficient iron (Liu et al., 2020; Ren et al., 2025). Hormones (such as cytokinin and abscisic acid) and some transcription factors (such as GmWRKY17) are also involved in regulating the number and maturity of nodules. During the gradual development of root nodules, the dynamic regulation of energy metabolism, carbon and nitrogen distribution, and mineral nutrition is very important for the maturation and nitrogen fixation efficiency of root nodules (Carter and Tegeder, 2016; Chen et al., 2018; Wang et al., 2020; Yang et al., 2021; Ke et al., 2022; Lyu et al., 2022). 2.4 Overview of nitrogenase activity and energy cost of fixation. Nitrogenase is the most crucial enzyme in root nodules, as it can reduce nitrogen gas to ammonia. Its activity depends on energy supply and the regulation of the microenvironment of the root tumor. The nitrogen fixation
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