Regulation of the autophagy pro-survival mechanism by ULK1

Autophagy (from Greek to mean self‐eating) is a highly conserved pro‐survival pathway found in almost every type of eukaryotic cell. Autophagy occurs constitutively but also serves as an important stress induced cellular response in multiple contexts. Dysfunction of the autophagic pathway is strongly associated with numerous human pathologies such as cancer and neurodegeneration driving the need for better overall understanding of the fundamental mechanisms. The Uncoordinated 51‐like kinases (ULK1/2) are essential autophagy regulators that function in complex with several additional regulatory proteins. ULK complexes are critically positioned early during the signalling pathway controlling autophagosome biogenesis, receiving and integrating information from the upstream nutrient sensors mechanistic target of rapamycin (MTOR) and AMP‐activated protein kinase (AMPK).Specific roles for ULK1 as compared to its related, but less understood family member,ULK2, were unclear. However, this issue needed to be resolved to better understandhow to target this kinase pathway to block autophagy. Therefore, within this thesis, it has been investigated ULK1 and ULK2 might differentially regulate autophagic activation was investigated. Findings within this thesis support functional redundancy between ULK1 and ULK2 for nutrient-dependent initiation of autophagy. In addition, these data have indicated unexpectedly that glucose starvation fails to induce canonical autophagy as observed in amino acid withdrawal, therefore highlighting the differential autophagy responses that arise following amino acid‐dependent MTOR vs. glucose‐dependent AMPK signalling events. Finally, this thesis aimed to understand regions of ULK1 that were critical for autophagy function, focussing on C‐terminal (early autophagy tethering "EAT") domain. The findings indicate that small helical sub‐regions of the EAT are sufficient to mediate binding to its accessory protein Atg13 and also for binding to membranes. However, more complete regions of the EAT are needed for ULK1 function in cells. Data also suggests that ULK1 interacts with specialized membrane micro‐domains known as lipid rafts.Overall, these combined approaches offered definitive evidence for ULK1/ULK2 functional redundancy in vivo, evidence of distinct MTOR and AMPK nutrient sensing pathways for autophagy; and lastly, further definition of distinct regions within the ULK1/2 EAT regulatory domain. These basic findings further support the developmentof novel inhibitors that could provide similar effects to modulate autophagy in applied settings.Autophagy (from Greek to mean self‐eating) is a highly conserved pro‐survival pathway found in almost every type of eukaryotic cell. Autophagy occurs constitutively but also serves as an important stress induced cellular response in multiple contexts. Dysfunction of the autophagic pathway is strongly associated with numerous human pathologies such as cancer and neurodegeneration driving the need for better overall understanding of the fundamental mechanisms. The Uncoordinated 51‐like kinases (ULK1/2) are essential autophagy regulators that function in complex with several additional regulatory proteins. ULK complexes are critically positioned early during the signalling pathway controlling autophagosome biogenesis, receiving and integrating information from the upstream nutrient sensors mechanistic target of rapamycin (MTOR) and AMP‐activated protein kinase (AMPK).Specific roles for ULK1 as compared to its related, but less understood family member,ULK2, were unclear. However, this issue needed to be resolved to better understandhow to target this kinase pathway to block autophagy. Therefore, within this thesis, it has been investigated ULK1 and ULK2 might differentially regulate autophagic activation was investigated. Findings within this thesis support functional redundancy between ULK1 and ULK2 for nutrient-dependent initiation of autophagy. In addition, these data have indicated unexpectedly that glucose starvation fails to induce canonical autophagy as observed in amino acid withdrawal, therefore highlighting the differential autophagy responses that arise following amino acid‐dependent MTOR vs. glucose‐dependent AMPK signalling events. Finally, this thesis aimed to understand regions of ULK1 that were critical for autophagy function, focussing on C‐terminal (early autophagy tethering "EAT") domain. The findings indicate that small helical sub‐regions of the EAT are sufficient to mediate binding to its accessory protein Atg13 and also for binding to membranes. However, more complete regions of the EAT are needed for ULK1 function in cells. Data also suggests that ULK1 interacts with specialized membrane micro‐domains known as lipid rafts.Overall, these combined approaches offered definitive evidence for ULK1/ULK2 functional redundancy in vivo, evidence of distinct MTOR and AMPK nutrient sensing pathways for autophagy; and lastly, further definition of distinct regions within the ULK1/2 EAT regulatory domain. These basic findings further support the developmentof novel inhibitors that could provide similar effects to modulate autophagy in applied settings