Autophagy as a multi-scale architect of fungal development and pathogenicity: membrane dynamics, multilayer regulation, and cell wall integrity crosstalk

Autophagy is a conserved membrane-trafficking pathway traditionally viewed as a nonspecific nutrient recycling mechanism. However, recent advances across diverse fungal systems, from plant pathogens to human opportunistic fungi and entomopathogenic species, have revealed autophagy as a central regulatory hub that orchestrates fungal development, virulence, and host interaction at multiple biological scales. This review provides a comprehensive and critical synthesis of these emerging insights. At the nanoscale, the discussion explores how autophagosome biogenesis depends on the spatially precise delivery of PtdIns4P by oxysterol-binding proteins, the dual function of the TRAPPIII vesicle-tethering complex, and the retromer-mediated sorting of vacuolar proteases. At the organelle level, the interplay between selective autophagy (mitophagy, lipophagy, pexophagy) and a newly discovered layer of epitranscriptomic, transcriptional, and post-translational regulation, comprising m 5 C RNA methylation of core ATG transcripts, FOX transcription-factor-driven gene activation, and nuclear acetylation of Atg8, respectively, is examined. At the macroscale, the review highlights how autophagy-dependent cell death and ferroptosis cooperate to drive appressorium maturation in Magnaporthe oryzae , and presents direct biochemical evidence for crosstalk between the cell wall integrity MAPK cascade and the autophagy machinery, a paradigm that challenges the long-standing view of these pathways as parallel systems. Further discussion addresses how autophagy deficiency triggers Mincle-dependent host immunity in Cryptococcus neoformans and how entomopathogenic Cordyceps militaris co-opts autophagy for fruiting body morphogenesis. We emphasize that the direct biochemical evidence for several of these mechanisms, notably CWI–MAPK/Atg4 crosstalk and autophagy–ferroptosis coupling, currently derives largely from Magnaporthe oryzae , and we distinguish such established mechanisms from cross-species extrapolations throughout. Finally, Atg4 inhibitors are evaluated as a promising class of broad-spectrum antifungal agents, and key directions for future research, including spatiotemporal imaging, multi-omics validation, and translational antifungal strategies, are identified.