These authors contributed equally to this work.Keywords: autophagy, autophagosome, BECN1, LC3, PtdIns3KAbbreviations: ATG, autophagy related; BafA1, bafilomycin A 1 ; BCL2L1/Bcl -xL, BCL2-like 1; BECN1, Beclin 1, autophagy related; BECN1P1/BECN2, Beclin 1, autophagy related, pseudogene 1; EM, electron microscopy; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFP, green fluorescent protein; KO, knockout; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; MAP1LC3-I/LC3-I, soluble, proteolytically processed microtubule-associated protein 1 light chain 3; MAP1LC3-II/LC3-II, proteolytically processed and lipid-modified microtubule-associated protein 1 light chain 3; MAP1LC3B/LC3B, microtubule-associated protein 1 light chain 3 b; PtdIns3K, phosphatidylinositol 3-kinase; PIK3C3/VPS34, phosphatidylinositol 3-kinase, catalytic subunit type 3; PIK3R4/VPS15, phosphoinositide-3-kinase, regulatory subunit 4; SQSTM1/p62, sequestosome 1; TUBB, tubulin, b class I; TALEN, transcription activator-like effector nuclease; UVRAG, UV radiation resistance associated; ZFYVE1/DFCP1, zinc finger, FYVE domain containing 1.BECN1/Beclin 1 is regarded as a critical component in the class III phosphatidylinositol 3-kinase (PtdIns3K) complex to trigger autophagy in mammalian cells. Despite its significant role in a number of cellular and physiological processes, the exact function of BECN1 in autophagy remains controversial. Here we created a BECN1 knockout human cell line using the TALEN technique. Surprisingly, the complete loss of BECN1 had little effect on LC3 (MAP1LC3B/LC3B) lipidation, and LC3B puncta resembling autophagosomes by fluorescence microscopy were still evident albeit significantly smaller than those in the wild-type cells. Electron microscopy (EM) analysis revealed that BECN1 deficiency led to malformed autophagosome-like structures containing multiple layers of membranes under amino acid starvation. We further confirmed that the PtdIns3K complex activity and autophagy flux were disrupted in BECN1 ¡/¡ cells. Our results demonstrate the essential role of BECN1 in the functional formation of autophagosomes, but not in LC3B lipidation.