Edited by Didier StainierBeclin 1/Atg6 is an essential autophagy gene, and deficiency of this gene in organisms leads to impaired autophagic flux, usually with cell apoptosis; however, the causative mechanism of cell apoptosis is not clear. Here, we knocked out the beclin 1 gene in zebrafish and found that autophagic flux is disrupted in mutants. Beclin 1-deficient zebrafish live through embryogenesis but die at larval stage. We found accumulated protein aggregates and vigorous apoptosis in mutant larvae, predominantly in the liver. The hepatic cell apoptosis in mutants results from an endoplasmic reticulum (ER) stress response; however, it is not the leading cause of mutant larval lethality. Our work proposes that ER stress induces cell apoptosis in Beclin 1-deficient organisms.Autophagy is an ancient self-digestive mechanism in eukaryotic cells, delivering cytoplasmic materials into the lysosome for degradation. The cargoes include damaged organelles, aberrant proteins, invading pathogens, and other cellular contents. The digestive products can be used for macromolecule synthesis and energy production. Therefore, autophagy plays important roles in the maintenance of cellular hemostasis, response to energy deprivation, and clearance of invading microorganism pathogen [1,2]. Among the three types of autophagy, namely microautophagy, chaperone-mediated autophagy, and macroautophagy, macroautophagy draws the most attention [3,4] and is hereafter called autophagy in this study. Autophagy is regulated by a group of genes, known as autophagy-related gene (Atg), with majority of them firstly identified by genetic screens in yeast and highly conserved among species [5]. Beclin 1/Atg6 is an essential for autophagy induction. It directly binds to Vps34 (Pik3c3) through its evolutionarily conserved domain (ECD) forming the class III phosphatidylinositol 3-kinase (PI3KIII) complex to produce phosphatidylinositol 3-phosphate (PtdIns(3)P), an essential lipid-based compound for initial steps of autophagosome formation [6].To study the biological functions of Beclin 1/Atg6, the loss-of-function mutants were generated in many Abbreviations Atg, autophagy-related gene; BH3, Bcl-2 homology-3 domain; CCD, coiled-coil domain; ECD, evolutionarily conserved domain; ER, endoplasmic reticulum; PC, Purkinje cell; PI3KIII, class III phosphatidylinositol 3-kinase; PtdIns(3)P, phosphatidylinositol 3-phosphate; TUDCA, tauroursodeoxycholic acid; VE, visceral endoderm; WISH, Whole-mount in situ hybridization.