We compared the membrane proteins of autolysosomes isolated from leupeptin-administered rat liver with those of lysosomes. In addition to many polypeptides common to the two membranes, the autolysosomal membranes were found to be more enriched in endoplasmic reticulum lumenal proteins (protein-disulfide isomerase, calreticulin, ER60, BiP) and endosome/Golgi markers (cation-independent mannose 6-phosphate receptor, transferrin receptor, Golgi 58-kDa protein) than lysosomal membranes. The autolysosomal membrane proteins include three polypeptides (44, 35, and 32 kDa) whose amino-terminal sequences have not yet been reported. Combining immunoblotting and reverse transcriptase-polymerase chain reaction analyses, we identified the 44-kDa peptide as the intact subunit of betaine homocysteine methyltransferase and the 35-and 32-kDa peptides as two proteolytic fragments. Pronase digestion of autolysosomes revealed that the 44-kDa and 32-kDa peptides are present in the lumen, whereas the 35-kDa peptide is not. In primary hepatocyte cultures, the starvation-induced accumulation of the 32-kDa peptide occurs in the presence of E64d, showing that the 32-kDa peptide is formed from the sequestered 44-kDa peptide during autophagy. The accumulation is induced by rapamycin but completely inhibited by wortmannin, 3-methyladenine, and bafilomycin. Thus, detection of the 32-kDa peptide by immunoblotting can be used as a streamlined assay for monitoring autophagy.Autophagy is a universal process by which cellular proteins are degraded via a lysosomal/vacuolar system. Depending on the extracellular nutrient conditions, the rate of autophagic protein degradation fluctuates between 1-1.5% and 4 -5% of total cell proteins per hour (1, 2). There are two pathways of autophagy, microautophagy and macroautophagy (for reviews, see Refs. 3 and 4). In microautophagy, relatively small portions of the cytoplasm are directly enclosed by invaginating lysosomal membranes for subsequent sequestration and degradation. Degradation of bulky cell constituents by the lysosome/vacuole system occurs via macroautophagy. In the initial step of macroautophagy, various cytosolic proteins, as well as cytoplasmic organelles such as mitochondria, endoplasmic reticulum (ER), 1 and peroxisomes, are sequestered in the lumen of double-membraned autophagosomes. Autophagosomes then fuse with endosomes or lysosomes to become mature, single-membraned autolysosomes. Acidification of the lumen and acquisition of lysosomal hydrolytic enzymes enable this specialized membrane system to degrade sequestered cytoplasmic components.The origin of the autophagosomal membrane is a subject of controversy. Extensive morphological analyses by Dunn (5) indicated that the autophagosomal membrane derives from the rough ER. However, the post-Golgi membrane, as well as a unique de novo synthesized membrane, the phagophore, have also been proposed as sources (6, 7). In recent morphological studies on yeast autophagy (8, 9), autophagosomal membranes were found to have features distinct from th...