The ubiquitously distributed MAP1S is a homologue of the exclusively neuronal distributed microtubule-associated protein 1A and 1B (MAP1A/B). They give rise to multiple isoforms through similar post-translational modification. Isoforms of MAP1S have been implicated in microtubule dynamics and mitotic abnormalities and mitotic cell death. Here we show that ablation of the Map1s gene in mice caused reduction in the B-cell CLL/lymphoma 2 or xL (Bcl-2/xL) and cyclin-dependent kinase inhibitor 1B (P27) protein levels, accumulation of defective mitochondria, and severe defects in response to nutritive stress, suggesting defects in autophagosomal biogenesis and clearance. Furthermore, MAP1S isoforms interacted with the autophagosome-associated light chain 3 of MAP1A/B (LC3), a homologue of yeast autophagy-related gene 8 (ATG8), and recruited it to stable microtubules in a MAP1S and LC3 isoformdependent mode. In addition, MAP1S interacted with mitochondrion-associated leucine-rich PPR-motif containing protein (LRPPRC) that interacts with the mitophagy initiator and Parkinson disease-related protein Parkin. The three-way interactions of MAP1S isoforms with LC3 and microtubules as well as the interaction of MAP1S with LRPPRC suggest that MAP1S isoforms may play positive roles in integration of autophagic components with microtubules and mitochondria in both autophagosomal biogenesis and degradation. For the first time, our results clarify roles of MAP1S in bridging microtubules and mitochondria with autophagic and mitophagic initiation, maturation, trafficking, and lysosomal clearance. Defects in the MAP1S-regulated autophagy may impact heart disease, cancers, neurodegenerative diseases, and a wide range of other diseases.Autophagy, or self-digestion, is a process that begins with the formation of isolation membranes that engulf substrates to form autophagosomes. Then autophagosomes fuse with lysosomes to generate autolysosomes in which substrates are degraded (1). The initiation of autophagy is regulated by the mammalian target of rapamycin (mTOR) pathway. Autophagy will be shut down through either the phosphatidylinositol 3-kinase (PI3K)-v-akt murine thymoma viral oncogene (AKT)-mTOR pathway in response to signals from growth factors or the serine/threonine kinase 11 (LKB1)-AMP-activated protein kinase (AMPK) 2 -mTOR pathway in response to signals from nutrients and metabolites. The anti-apoptotic protein Bcl-2 and Bcl-xL exhibit opposite functions in autophagy initiation. They inhibit autophagy initiation through the PI3K-AKTmTOR pathway by sequestering the BCL2 interacting protein (Beclin 1) or activate autophagy initiation through the LKB1-AMPK-mTOR pathway by increasing P27 levels (2, 3).After initiation, the metabolism of LC3 has emerged as a key biochemical marker for tracking of autophagy and autophagosomes (4, 5). The 22-kDa full-length LC3 (4) is proteolytically modified into LC3I form by ATG4, resulting in exposure of a C-terminal glycine (5). LC3I is first conjugated with the ubiquitin activating enzyme (E1)-...