Protein–protein interaction network analysis of the phaseolus vulgaris factorome reveals AP2/ERF, WRKY, and NAC as key regulators in defense against colletotrichum lindemuthianum race 65

Transcription factors (TFs) act as key regulators of gene expression during plant stress responses. Despite extensive studies in model species, the transcriptional regulation of immune responses in crop plants such as common bean ( Phaseolus vulgaris ) remains poorly understood. The hemibiotrophic fungus Colletotrichum lindemuthianum race 65 severely impacts bean productivity, yet the regulatory circuits underlying incompatible interactions remain incipient. Here, we integrated differentially expressed transcription factors (TFDex) and coexpressed transcription factors (TFCoDex) from RNA-seq data of P. vulgaris challenged with C. lindemuthianum to explore TF-centered protein–protein interaction (PPI) networks. Our analysis highlights WRKY, NAC, and AP2/ERF families as central network hubs potentially associated with defense responses. Temporal dynamics between early (48 hpi) and late (96 hpi) infection stages suggest a shift from salicylic acid (SA)- to jasmonate/ethylene (JA/ethylene)-mediated signaling pathways. Network motifs such as feed-forward loops and autoregulatory circuits suggest potential regulatory configurations that may contribute to robustness and fine-tuning of defense responses. The integration of components from PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI), including NB-LRRs and receptor-like kinases, reveals a coordinated network of predicted functional associations potentially converging on transcriptional regulation, hormonal crosstalk, and modulation of reactive oxygen species. Modules enriched for circadian rhythm, secondary metabolism, and cell wall-related processes further support a multilayered and dynamic defense response. By identifying TF hubs and putative regulatory connections within predicted PPIs, this study provides systems-level insights into transcriptional regulation of immunity in P. vulgaris and establishes a framework for future functional validation and resistance breeding strategies.