Multi-omics reveals PKA as a central regulator of lignocellulolytic response in Trichoderma reesei

The filamentous fungus Trichoderma reesei is a chief industrial producer of holocellulases, renowned for its capacity to secrete enzymes that depolymerize cellulose into glucose, a key step in biofuel production. The synthesis of these holocellulolytic enzymes is finely regulated by nutrient-sensing pathways, notably the cyclic AMP-Protein Kinase A (PKA) signaling pathway. Here, we investigated the role of the PKA catalytic subunit (PKAc1) in controlling enzyme production and metabolic adaptation in T. reesei. We employed a multi-omics approach (RNA-seq transcriptomics, quantitative proteomics, and phosphoproteomics) to compare the QM9414 and Delta pkac1 mutant strains under carbon-repressing (glucose) and inducing (sugarcane bagasse) conditions. Deletion of pkac1 strongly reduced cellulase activity, severely impaired growth on lignocellulosic substrate, and collapsed the induction of the transcriptional activator XYR1 and its associated repertoire of carbohydrate-active enzymes (CAZymes). Proteomic analyses further showed that most CAZymes were markedly less abundant in Delta pkac1, in line with the transcriptional defects. Furthermore, phosphoproteomic profiling identified extensive changes in signaling networks: the Delta pkac1 mutant strain exhibited global hypophosphorylation of many proteins and altered phosphorylation of specific transcription factors and transporters. Notably, multiple PKA consensus motif sites lost phosphorylation in the mutant, and in silico docking of peptides from these sites into the PKAc1 structure suggested several proteins (e.g., the Golgi regulator Sec7) as direct PKA targets. Thus, we conclude that PKAc1 is a crucial positive regulator of the lignocellulolytic response in T. reesei, orchestrating the metabolic transition from carbon catabolite repression to biomass degradation.