Otto, Neil2016-04-142016-04-142014-02https://hdl.handle.net/11299/178934University of Minnesota Ph.D. dissertation. February 2014. Major: Biochemistry, Molecular Bio, and Biophysics. Advisor: Do-Hyung Kim. 1 computer file (PDF); viii, 112 pages.Autophagy, an evolutionarily conserved process through which cellular components or organelles are degraded through lysosomes, is induced when eukaryotic cells are under nutrient starvation or cellular stress conditions. The ULK1 (UNC-51 like kinase 1) complex consisting of ULK1, Atg13, FIP200, and Atg101 plays a key role in mediating cellular nutritional status to the regulation of autophagy. Despite the recent advance in our understanding of the ULK1 functions, how the ULK1 complex regulates autophagy induction remains unclear. Here, we identify that the ULK1 complex interacts with mammalian Atg8 homologs via Atg13 and the interaction is important for autophagosome formation. Through a yeast two-hybrid screen, we identified a clone harboring the full length GATE-16 (Golgi-associated ATPase enhancer of 16 kDa) as an Atg13 binding protein. Through co-immunoprecipitation and in vitro binding assays, we confirmed that Atg13 directly interacts with GATE-16, as well as GABARAP (Gamma-aminobutyric acid receptor-associated protein) and GABARAPL1 (GABA-A receptor-associated protein-like 1), but not LC3B (Microtubule-associated protein1B-light chain 3), via a conserved LC3 interacting region (LIR) near its C-terminus. The Atg13-Atg8 interaction was greatly increased when cells were induced to accumulate protein aggregates or mitochondrial damage, but not by nutrient starvation, implying that the interaction might respond to selective autophagy inducing conditions. The LIR-disrupting mutation of Atg13 suppressed the degradation of p62/sequestosome 1, poly-ubiquitinated protein aggregates, and damaged mitochondria. These results suggest that Atg13 might participate in autophagy, especially selective autophagy, via interacting with GABARAP subfamily Atg8 proteins. p62 is a protein involved in selective autophagy that also interacts with Atg8 proteins via its LIR motif. My study revealed that ULK1 binds and phosphorylates p62. Several phosphorylation sites of p62 were identified by mass spectrometry. Mutational approaches revealed that some of the identified phosphorylations are important for colocalization of p62 with LC3 and for autophagic clearance of mutant huntingtin aggregates. The culmination of this work suggests that the ULK1 complex recruits GABARAP subfamily proteins and phosphorylates p62 in the pathway of autophagy induction.enAtg13Atg8AutophagyLIRULK1Thesis or Dissertation