A group of phosphoinositide 3-kinase (PI3K) inhibitors, such as 3-methyladenine (3-MA) and wortmannin, have been widely used as autophagy inhibitors based on their inhibitory effect on class III PI3K activity, which is known to be essential for induction of autophagy. In this study, we systematically examined and compared the effects of these two inhibitors on autophagy under both nutrient-rich and deprivation conditions. To our surprise, 3-MA is found to promote autophagy flux when treated under nutrient-rich conditions with a prolonged period of treatment, whereas it is still capable of suppressing starvation-induced autophagy. We first observed that there are marked increases of the autophagic markers in cells treated with 3-MA in full medium for a prolonged period of time (up to 9 h). Second, we provide convincing evidence that the increase of autophagic markers is the result of enhanced autophagic flux, not due to suppression of maturation of autophagosomes or lysosomal function. More importantly, we found that the autophagy promotion activity of 3-MA is due to its differential temporal effects on class I and class III PI3K; 3-MA blocks class I PI3K persistently, whereas its suppressive effect on class III PI3K is transient. Because 3-MA has been widely used as an autophagy inhibitor in the literature, understanding the dual role of 3-MA in autophagy thus suggests that caution should be exercised in the application of 3-MA in autophagy study.Autophagy refers to an evolutionarily conserved process in which intracellular proteins and organelles are sequestered in autophagosomes and subsequently degraded by lysosomal enzymes for the purpose of recycling cellular components to sustain metabolism during nutrient deprivation and to prevent accumulation of damaged proteins and organelles (1, 2). Autophagy is a dynamic process, consisting of several sequential stages (initiation, nucleation, elongation, and maturation) controlled by a group of autophagy-related genes (Atg genes). So far, more than 30 Atg genes have been identified in yeast, and many of them have homologues in mammalian cells (3). Upstream of ATG proteins, mammalian target of rapamycin (mTOR) 4 has been well studied as the key regulatory molecule (4). mTOR is a serine/threonine protein kinase serving as the convergence point for many of the upstream stimuli and pathways to regulate cell growth, cell proliferation, cell motility, cell survival, protein synthesis, translation, and autophagy (5-7). Abundance of nutrients, including growth factors, glucose, and amino acids will activate mTOR and suppress autophagy, whereas nutrient deprivation will suppress mTOR, leading to activation of autophagy. At present, the molecular mechanisms downstream of mTOR responsible for its anti-autophagic function have not been fully understood. In yeast, TOR directly targets the ATG13-ATG1 complex and suppresses its function at the initiation stage of autophagy (8). In mammalian cells, the complex containing ULK1 (the ATG1 homologue), ATG13, and FIP200 is directly cont...