Molecular Pathogens, 2025, Vol.16, No.5, 226-235 http://microbescipublisher.com/index.php/mp 228 strain and the host. When the roots of leguminous plants such as soybeans sense Nod factors, the Nod factor receptor kinases on the root epidermal membrane bind to these signaling molecules with high affinity, thereby triggering downstream signaling cascades. This Nod factor-receptor recognition mechanism confers specificity to legume-rhizobia interactions (Figure 1) (Bellés-Sancho et al., 2024). Figure 1 a Methodology used to inoculate and process the P. phymatumTn-seq library on soybean seedlings. After 21 days, nodules containing Tn-seq mutants were collected, DNA from the nodules was extracted, and libraries were generated for sequencing using the circularization method. b Soybean plants inoculated with B. diazoefficiens USDA 110T spc4 (positive control), P. phymatum STM815T wild-type (negative control), and seven soybean plants inoculated with P. phymatum Tn-seq library with developed nodules (Tn-seq plants). Scale bar: 2 mm (Adopted from Bellés-Sancho et al., 2024) 3.2 Symbiotic signaling network and key gene regulation After the Nod factor-receptor complex is formed, a series of signaling events are activated in leguminous plant root cells. The cell membrane ion channels are triggered and calcium ions flow in, causing characteristic calcium oscillations in root hair cells (especially in the perinuclear region). This is one of the core early events of the symbiotic signaling pathway. Subsequently, cation channels on the nuclear membrane and downstream calmodulin-dependent kinase (CCaMK) are activated one after another. CCaMK serves as a signal "decoder" and is activated by sensing calcium oscillations, and then phosphorylates specific substrates to transmit signals (Ren et al., 2025). The initiation of the symbiotic signaling network ultimately triggers the expression of a large number of nodulation-related genes and drives nodule organ formation. Multiple host genes have been found to play key roles in this process. For example, NIN (nodulation initiating factor) is an early transcription factor that induces the development of root nodule primordium; transcription factors such as NSP1/NSP2 and ERN are involved in the regulation of symbiotic gene expression and the control of the infection process respectively (Gresshoff et al., 2025). In addition, plants also feedback-regulate the number of nodules through CLE signal peptide and so on.
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