Transcriptional, epigenetic, and post-translational regulation of plant autophagy

Autophagy is a highly conserved intracellular recycling process in eukaryotes that delivers cellular components to the lysosome or vacuole for degradation, thereby maintaining intracellular homeostasis. Acting as a quality control system, autophagy plays a pivotal role in plant growth, development, and adaptation to environmental challenges. The regulation of autophagy under stress conditions involves multi-layered mechanisms, including transcriptional, epigenetic, and post-translational controls. Transcription factors from families such as WRKY, NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON (NAC), and basic leucine zipper (bZIP) directly bind to the promoters of autophagy-related (ATG) genes, thereby integrating stress-responsive signal pathways to orchestrate autophagic activity dynamically. Epigenetic modifications, including histone modifications, DNA methylation, N⁶-methyladenosine (m⁶A) methylation, and microRNA-mediated silencing, further fine-tune expression of ATG genes in response to changing environments. At the post-translational level, modifications such as phosphorylation, ubiquitination, acetylation, persulfidation, and S-nitrosylation serve as rapid regulatory switches that modulate autophagosome formation under stress. This review summarizes recent advances in elucidating these regulatory layers, highlighting how these regulators collectively modulate autophagy to improve plant tolerance to environmental cues. Unraveling these mechanisms will expand our understanding of the autophagy regulatory network in plants and provide potential strategies for improving stress tolerance in crops.