Integrated Gene Regulatory Network Analysis Reveals Coordinated Transcriptional Reprogramming in the Arabidopsis...

Mutualistic interactions between plants and beneficial fungi rely on extensive transcriptional reprogramming in both partners, yet the underlying regulatory mechanisms coordinating these responses remain incompletely understood. Here, we combined a transcriptomics analysis with a gene regulatory network (GRN) inference to dissect the interaction between Arabidopsis thaliana and the growth-promoting fungus Trichoderma atroviride. At an early but established stage of colonization (72 h post-inoculation), we identified widespread transcriptional changes in both of the organisms, including host activation of hypoxia, stress and root development-related pathways in Arabidopsis, and fungal reprogramming of membrane transport and primary metabolism. Using DNA-binding motifs and GENIE3-based regulatory inference, we reconstructed interaction-specific GRNs for each species. The subnetworks focused on the main differentially expressed biological processes and uncovered ERF-, WRKY-, NAC- and DOF-centered modules linking hypoxia responses with developmental remodeling in the plant, whereas the putative orthologs of TFs involved in developmental and stress-related TFs in fungi, such as CrzA, RME1, NsdC, PacC and RPN4, formed a regulatory core coordinating fungal transport and metabolic adjustment. In parallel, we uncovered contrasting sRNA dynamics between the partners. While the Arabidopsis sRNA changes were limited, T. atroviride exhibited a strong induction of 20-22 nt sRNAs, including a small set of high-confidence sRNA-mRNA interactions targeting host genes involved in root function and immunity. Together, our results extend previous pathway-based descriptions of the Arabidopsis-Trichoderma mutualism and provide a systems-level, testable framework for how coordinated regulatory programs in both of the partners support the interaction.