William T. Jackson is Assistant Professor of Microbiology at the Medical College of Wisconsin in Milwaukee, Wisconsin, USA Michele S. Swanson is Professor of Microbiology and Immunology at the University of Michigan Medical School, Ann Arbor, Michigan, USA

• Contributors xiiiPreface xviiAcknowledgments xix1 Autophagy and Immunity 1Xu Liu and Daniel J. Klionsky1.1 Introduction 11.2 Autophagy 21.2.1 Types of autophagy 21.2.2 Morphology 31.2.3 Molecular machinery 31.2.4 Physiological roles 51.3 Autophagy and immunity 61.3.1 Xenophagy: autophagic clearance of intracellular microorganisms 61.3.2 Autophagy and cryptides 91.3.3 Autophagy and pattern recognition receptors (PRRs) 91.3.4 Autophagy and MHC antigen presentation 101.3.5 Autophagy regulation by immune signaling molecules 111.3.6 Autophagy, inflammation, and autoimmunity 111.4 Conclusion 12References 122 Techniques for Studying Autophagy 19Isei Tanida and Masato Koike2.1 Introduction 192.2 Reagents and tools for studying autophagy 212.2.1 Reagents to monitor the lysosomal flux of LC3-II 212.2.2 Reagents that induce autophagy 212.2.3 Reagents and recombinant tools that inhibit autophagy 222.3 Detection of LC3-I and LC3-II by immunoblotting 222.4 Immunofluorescent analyses of endogenous LC3 232.5 Monitoring autophagy using fluorescent protein-tagged LC3 232.6 Morphological analyses of autophagosomes and autolysosomes by TEM 242.6.1 Reagents or stock solutions 262.6.2 Resin embedding of cell pellets or microbes 262.6.3 Resin flat embedding of cells grown on glass or plastic coverslips 272.7 Techniques for immunoelectron microscopy 28References 293 Role of Autophagy In DNA Virus Infections in Vivo 33Xiaonan Dong and Beth Levine3.1 Introduction 333.2 In vivo interplay between autophagy and DNA viruses in plants and invertebrates 343.3 In vivo interplay between autophagy and DNA viruses in vertebrates 353.3.1 Autophagy is an essential antiviral mechanism that protects against HSV-1 in vivo 353.3.2 The autophagy-HBV interplay in vivo: a balance between viral exploitation and tumor suppression 403.3.3 Autophagy may suppress γ-herpesvirus persistent infection 423.4 Conclusion 43Acknowledgments 44References 444 Studying RNA Viruses and Autophagy in Vivo 49Mehrdad Alirezaei and J. Lindsay Whitton4.1 Introduction 494.2 In vivo interactions between autophagy and RNA viruses in plants and invertebrates 504.2.1 Plants 504.2.2 Invertebrates 504.3 In vivo Interactions between autophagy and RNA viruses in vertebrates 514.3.1 Togaviridae 514.3.2 Caliciviridae 514.3.3 Orthomyxoviridae 534.3.4 Flaviviridae 534.3.5 Picornaviridae 544.4 Conclusion 62Acknowledgments 63References 635 Autophagy and Picornavirus Infection 67Tom Wileman, Zhigang Zhou, Matthew Whelband, Eleanor Cottam, Stephen Berryman, Terry Jackson and Rebecca Roberts5.1 Introduction 675.2 Selective autophagy involves autophagy receptors with LC3-interacting domains 695.3 Autophagy is activated during virus infection 695.4 Picornaviruses and autophagy 695.4.1 Poliovirus 705.4.2 Coxsackievirus 725.4.3 Human enterovirus 71 735.4.4 Encephalomyocarditis virus 735.4.5 Foot-and-mouth disease virus 745.4.6 Human rhinoviruses 755.5 Caution in interpretation of induction of LC3 puncta and double-membraned vesicles in the context of autophagy 755.5.1 LC3 puncta 755.6 Conclusions and future research 77References 786 Flaviviruses and Autophagy 81Tristan X. Jordan and Glenn Randall6.1 Introduction 816.1.1 Autophagy 816.2 Flaviviruses 836.3 Dengue virus 836.3.1 Autophagosomes as a platform for replication? 856.3.2 Modulation of lipid metabolism 866.3.3 Potential role for the autophagy-related proteins USP10 and USP13 in DENV virion maturation 876.3.4 Cytoprotective autophagy 886.3.5 The role of autophagy in an ADE model of monocyte infection 896.3.6 Autophagy in DENV infections in mice 896.4 Other Flaviviruses 906.4.1 Japanese encephalitis virus 906.4.2 Modoc virus 906.4.3 West Nile virus 906.5 Concluding remarks 92Acknowlegments 92References 937 Autophagy: A Home Remodeler for Hepatitis C Virus 101Marine L.B. Hillaire, Elodie Décembre, and Marlène Dreux7.1 Introduction 1017.1.1 Autophagy 1017.1.2 Hepatitis C virus (HCV) disease, genome and replication 1037.2 HCV induces a proviral autophagy 1117.3 How does HCV trigger autophagy vesicle accumulation? 1117.4 Dynamic membrane remodeling by autophagy 1137.5 Interlinkage of autophagy with the innate immune response 1147.6 Autophagy and cell death 1157.7 Removal of aberrant deposits and organelles by autophagy: implications for liver injury associated with chronic hepatitis C 1167.7.1 Autophagy and lipid metabolism 1167.7.2 Mitophagy and HCV persistence 1177.8 Conclusions and future directions 118Acknowledgments 119References 1198 Modulating Autophagy to Cure Human Immunodeficiency Virus Type-1 127Stephen A. Spector and Grant R. Campbell8.1 Introduction 1278.2 HIV subverts autophagy to promote its own replication 1298.3 HIV infection inhibits autophagy during permissive infection while induction of autophagy leads to inhibition of HIV 1308.4 HIV-induced autophagy in bystander CD4+ T cells results in cell death 1308.5 Modulation of autophagy as a mechanism for HIV-associated neurocognitive impairment 1328.6 How can autophagy be exploited to control and eradicate HIV? 134Acknowledgments 137References 1389 Autophagy in the Infected Cell: Insights from Pathogenic Bacteria 143Andrea Sirianni and Serge Mostowy9.1 Introduction 1439.2 Autophagy–bacteria interactions 1439.2.1 Salmonella typhimurium 1449.2.2 Mycobacterium tuberculosis 1459.2.3 Legionella pneumophila 1469.2.4 Listeria monocytogenes 1479.2.5 Shigella flexneri 1499.2.6 Mycobacterium marinum 1509.3 Conclusions 151Acknowledgments 151References 15210 Rab Proteins in Autophagy: Streptococcus Model 159Takashi Nozawa and Ichiro Nakagawa10.1 Introduction 15910.2 Rab GTPase 16010.3 Rab GTPases in starvation-induced autophagy 16010.4 Rab localization in autophagy during Streptococcus infection 16110.5 Involvement of Rab7 in the initial formation of GcAV 16310.6 Requirement of Rab23 for GcAV formation 16310.7 Facilitation by Rab9A of GcAV enlargement and lysosomal fusion 16410.8 Conclusion and perspective 165References 16711 Helicobacter Pylori Infection Control by Autophagy 171Laura K. Greenfield, Frances Dang, and Nicola L. Jones11.1 Helicobacter pylori 17111.2 H. pylori and evasion of host immune responses 17611.3 Autophagy 17811.4 Acute H. pylori infection: induction of autophagy in gastric epithelial cells 18011.5 Chronic H. pylori infection: suppression of autophagy in gastric epithelial cells 18411.6 H. pylori induction of autophagy in immune cells 18511.7 Host genetics affecting autophagic clearance of H. pylori 18511.8 H. pylori disrupted autophagy and gastric cancer 18611.9 H. pylori therapy: is autophagy a contender? 18711.10 Concluding remarks 188Acknowledgments 189References 18912 Interactions Between Salmonella and The Autophagy System 201Teresa L.M. Thurston and David W. Holden12.1 Introduction 20112.2 Salmonella’s life within the host 20112.3 Salmonella’s survival in a harsh intracellular habitat 20212.4 Models for studying Salmonella infection 20312.5 Mechanisms of Salmonella autophagy 20412.5.1 Salmonella is targeted for antibacterial autophagy 20412.5.2 Antibacterial autophagy induction 20512.5.3 Eat-me signals for antibacterial autophagy 20612.5.4 Autophagy receptors provide cargo specificity 20812.6 Autophagy of Salmonella in vivo 20912.7 Bacterial countermeasures 21012.7.1 Could Salmonella counteract autophagy? 21012.7.2 Potential autophagy avoidance mechanisms 21012.7.3 SseL deubiquitinates autophagy-targeted protein aggregates 21012.7.4 Does Salmonella inhibit selective antibacterial autophagy? 21112.8 Perspectives 211References 21313 Host Factors That Recruit Autophagy as Defense Against Toxoplasma Gondii 219Carlos S. Subauste13.1 Introduction 21913.2 CD40, autophagy and lysosomal degradation of T. gondii 22013.3 Events downstream of CD40 involved in the stimulation of autophagy 22213.4 Relevance of autophagy during in vivo infection with T. gondii 22413.5 IFN-γ and ATG5 in T. gondii infection 22413.6 T. gondii manipulates host cell signaling to inhibit targeting by LC3+ structures and to maintain the nonfusogenic nature of the parasitophorous vacuole 22713.7 Autophagy machinery within T. gondii 22813.8 Conclusion 229Acknowledgments 229References 22914 Mycobacterium Tuberculosis and The Autophagic Pathway 233Gabriela María Recalde and María Isabel Colombo14.1 Mycobacterium tuberculosis, a pathogen that resides in a self-tailored compartment to avoid killing by the host cell 23314.2 The ESX-1 secretion system 23514.3 Mycobacterium marinum, a close relative that escapes and forms actin tails in the cytoplasm 23514.4 Mycobacterium actively modulates autophagy 23614.5 Mycobacterium tuberculosis, a pathogen also able to escape toward the cytoplasm 23914.6 Concluding remarks 240References 24115 Autophagy Enhances yhe Efficacy of BCG Vaccine 245Arshad Khan, Christopher R. Singh, Emily Soudani, Pearl Bakhru, Sankaralingam Saikolappan, Jeffrey D. Cirillo, N. Tony Eissa, Subramanian Dhandayuthapani and Chinnaswamy Jagannath15.1 Introduction 24615.2 Induction of autophagy through mTOR enhances antigen presentation via the MHC-II pathway in macrophages and dendritic cells 24715.2.1 Rapamycin-induced autophagy enhances antigen presentation in APCs 24815.2.2 Rapamycin and Torin1-induced autophagy enhances both antigen presentation and IL-1β secretion from BCG infected APCs 24815.3 Intracellular mechanisms of autophagic routing of particulate BCG vaccine and secreted Ag85B into autophagosomes and enhanced MHC-II mediated antigen presentation 25115.3.1 Overexpression of secreted Ag85B in BCG vaccine leads to aggresome formation in the cytosol of APCs 25115.3.2 Overexpressed Ag85B from BCG vaccine forms aggresomes, which enhance antigen presentation through autophagy 25115.3.3 Discussion: in vitro studies on autophagy and antigen presentation 25315.4 Rapamycin activation of dendritic cells enhances efficacy of DC-BCG vaccine 25515.4.1 Discussion 25615.5 Rapamycin coadministration with BCG vaccine in mice enhances CD4 and CD8 T cell mediated protection against tuberculosis 25615.5.1 Discussion 26215.6 Conclusions 262Acknowledgments 263References 26316 Autophagy’s Contribution to Innate and Adaptive Immunity: An Overview 267Christina Bell, Michel Desjardins, Pierre Thibault and Kerstin Radtke16.1 Autophagy: different routes to the same goal? 26716.2 Xenophagy: it is a dog-eat-dog world 26916.3 Autophagy and Toll-like receptors: a mutual turn-on 26916.4 Autophagy and antigen presentation: a cry for help to clear pathogenic invaders 27016.5 Autophagy and inflammasomes: Mutual regulation for an effective immune response 27316.6 Cross-talk between autophagy and cytokines 273Acknowledgments 275References 27517 Autophagy in Immune Responses to Viruses 279Christophe Viret and Mathias Faure17.1 Innate immunity against viruses 27917.2 Autophagy in antiviral innate immunity 28117.2.1 Virus sensing for autophagy induction 28117.2.2 Role of autophagy in xenophagy of viruses 28217.2.3 Role of autophagy in antiviral innate immunity signaling 28317.3 Autophagy manipulation by viruses to resist innate immunity 28517.3.1 Autophagy manipulation by viruses to prevent IFN-I synthesis 28517.3.2 Viruses subvert autophagy to interfere with inflammatory responses 28617.3.3 Autophagy and cell death during virus infection 28717.4 Autophagy in antiviral adaptive immunity 28717.4.1 Promotion of adaptive immune responses to viral infection by autophagy 28717.4.2 MHC class II-restricted presentation of viral epitopes 28817.4.3 MHC class I-restricted presentation of viral epitopes 29017.4.4 Autophagy and cross-presentation 29217.5 Autophagy manipulation by viruses to escape adaptive immunity 29417.5.1 MHC class II antigen presentation pathway 29417.5.2 MHC class I antigen presentation pathway 29517.5.3 Autophagy and antigen-presenting cell function 29517.6 Concluding remarks 296Acknowledgments 296References 29718 Processing and MHC Presentation Of Antigens After Autophagy-Assisted Endocytosis, Exocytosis, and Cytoplasm Degradation 303Christian Münz18.1 Introduction 30318.2 Substrate recognition by macroautophagy 30518.3 Antigen processing for MHC class II presentation by macroautophagy 30718.4 A role of macroautophagy in MHC class I antigen presentation 30818.5 Antigen release by autophagy-assisted exocytosis 30918.6 Autophagy-assisted phagocytosis 31018.7 Conclusions and outlook 312Acknowledgments 312References 312Index 317