Autophagy is a process where double-membrane autophagosomes sequester and degrade cellular components, such as organelles or damaged proteins, in response to stress or nutrient deprivation. The process is regulated by a network of genes and signaling pathways, including the target of rapamycin (TOR) pathway, which integrates input from various upstream signals and negatively regulates autophagy under nutrient-rich conditions. Key autophagy-related (Atg) proteins, such as Atg1, Atg9, and Atg8/LC3, play crucial roles in induction, cargo recognition, vesicle formation, and autophagosome-lysosome fusion. Selective autophagy, which targets specific cargos like mitochondria, ribosomes, and peroxisomes, is mediated by specific receptor proteins. The molecular machinery of autophagy involves complex interactions between Atg proteins and other cellular components, including the secretory and endocytic pathways, and the cytoskeleton. Signaling pathways that regulate autophagy include nutrient signaling (TOR and Ras-cAMP-PKA pathways), insulin/growth factor pathways, energy sensing (AMPK), stress response (ER stress, hypoxia, oxidative stress), and pathogen infection. Transcriptional and epigenetic mechanisms also contribute to the regulation of autophagy, with transcription factors like FoxO and eIF2α kinase playing important roles.Autophagy is a process where double-membrane autophagosomes sequester and degrade cellular components, such as organelles or damaged proteins, in response to stress or nutrient deprivation. The process is regulated by a network of genes and signaling pathways, including the target of rapamycin (TOR) pathway, which integrates input from various upstream signals and negatively regulates autophagy under nutrient-rich conditions. Key autophagy-related (Atg) proteins, such as Atg1, Atg9, and Atg8/LC3, play crucial roles in induction, cargo recognition, vesicle formation, and autophagosome-lysosome fusion. Selective autophagy, which targets specific cargos like mitochondria, ribosomes, and peroxisomes, is mediated by specific receptor proteins. The molecular machinery of autophagy involves complex interactions between Atg proteins and other cellular components, including the secretory and endocytic pathways, and the cytoskeleton. Signaling pathways that regulate autophagy include nutrient signaling (TOR and Ras-cAMP-PKA pathways), insulin/growth factor pathways, energy sensing (AMPK), stress response (ER stress, hypoxia, oxidative stress), and pathogen infection. Transcriptional and epigenetic mechanisms also contribute to the regulation of autophagy, with transcription factors like FoxO and eIF2α kinase playing important roles.