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II TABLE OF CONTENTS  III LIST OF TABLES  V LIST OF FIGURES VI LIST OF ABBREVIATIONS  IX ACKNOWLEDGEMENTS  XIV SOURCES OF FUNDING  XV INTRODUCTION  1 I.1 History of autophagy  1 I.2 Autophagy biogenesis  4 I.2.1 Autophagy initiators  4 I.2.1.1 ULK kinases  4 I.2.1.2 mTORC1  6 I.2.1.3 AMPK  8 I.2.2 Critical autophagy-associated complexes 11 I.2.2.1 The class III phosphoinositide (PtdIns) 3-kinase/VPS34 complex I  12 I.2.2.2 Two ubiquitin-like protein conjugation systems (ATG12–ATG5-ATG16L1 and MAP1LC3 (LC3)  14 I.2.2.3 WIPI proteins  15 I.2.2.4 Transmembrane proteins  15 I.3 Bulk versus selective autophagy  16 I.4 Pathogens versus the host cells  16 I.4.1 Model pathogen  16 I.4.2 Intracellular Salmonella fate  17 I.4.3 Salmonella-mediated induction of inflammation  18 I.4.4 Anti-bacterial autophagy (xenophagy)  19 MATERIALS AND METHODS  21 Antibodies and Reagents  21 Cell Culture 21

AMPK Promotes Xenophagy Through Priming of Autophagic Kinases upon Detection of Salmonella Outer Membrane Vesicles