(PDF) Autophagy, Infection, and the Immune Response by William T. Jackson

This is the PDF eBook version for Autophagy, Infection, and the Immune Response by William T. Jackson, Michele Swanson

Table of Contents

Contributors xiii Preface xvii Acknowledgments xix 1 AUTOPHAGY AND IMMUNITY 1 Xu Liu and Daniel J. Klionsky 1.1 Introduction 1 1.2 Autophagy 2 1.2.1 Types of autophagy 2 1.2.2 Morphology 3 1.2.3 Molecular machinery 3 1.2.4 Physiological roles 5 1.3 Autophagy and immunity 6 1.3.1 Xenophagy: autophagic clearance of intracellular microorganisms 6 1.3.2 Autophagy and cryptides 9 1.3.3 Autophagy and pattern recognition receptors (PRRs) 9 1.3.4 Autophagy and MHC antigen presentation 10 1.3.5 Autophagy regulation by immune signaling molecules 11 1.3.6 Autophagy, inflammation, and autoimmunity 11 1.4 Conclusion 12 References 12 2 TECHNIQUES FOR STUDYING AUTOPHAGY 19 Isei Tanida and Masato Koike 2.1 Introduction 19 2.2 Reagents and tools for studying autophagy 21 2.2.1 Reagents to monitor the lysosomal flux of LC3-II 21 2.2.2 Reagents that induce autophagy 21 2.2.3 Reagents and recombinant tools that inhibit autophagy 22 2.3 Detection of LC3-I AND LC3-II by immunoblotting 22 2.4 Immunofluorescent analyses of endogenous LC3 23 2.5 Monitoring autophagy using fluorescent protein-tagged LC3 23 2.6 Morphological analyses of autophagosomes and autolysosomes by TEM 24 2.6.1 Reagents or stock solutions 26 2.6.2 Resin embedding of cell pellets or microbes 26 2.6.3 Resin flat embedding of cells grown on glass or plastic coverslips 27 2.7 Techniques for immunoelectron microscopy 28 References 29 3 ROLE OF AUTOPHAGY IN DNA VIRUS INFECTIONS IN VIVO 33 Xiaonan Dong and Beth Levine 3.1 Introduction 33 3.2 In vivo interplay between autophagy and DNA viruses in plants and invertebrates 34 3.3 In vivo interplay between autophagy and DNA viruses in vertebrates 35 3.3.1 Autophagy is an essential antiviral mechanism that protects against HSV-1 in vivo 35 3.3.2 The autophagy-HBV interplay in vivo: a balance between viral exploitation and tumor suppression 40 3.3.3 Autophagy may suppress -herpesvirus persistent infection 42 3.4 Conclusion 43 Acknowledgments 44 References 44 4 STUDYING RNA VIRUSES AND AUTOPHAGY IN VIVO 49 Mehrdad Alirezaei and J. Lindsay Whitton 4.1 Introduction 49 4.2 In vivo interactions between autophagy and RNA viruses in plants and invertebrates 50 4.2.1 Plants 50 4.2.2 Invertebrates 50 4.3 In vivo Interactions between autophagy and RNA viruses in vertebrates 51 4.3.1 Togaviridae 51 4.3.2 Caliciviridae 51 4.3.3 Orthomyxoviridae 53 4.3.4 Flaviviridae 53 4.3.5 Picornaviridae 54 4.4 Conclusion 62 Acknowledgments 63 References 63 5 AUTOPHAGY AND PICORNAVIRUS INFECTION 67 Tom Wileman, Zhigang Zhou, Matthew Whelband, Eleanor Cottam, Stephen Berryman, Terry Jackson and Rebecca Roberts 5.1 Introduction 67 5.2 Selective autophagy involves autophagy receptors with LC3-interacting domains 69 5.3 Autophagy is activated during virus infection 69 5.4 Picornaviruses and autophagy 69 5.4.1 Poliovirus 70 5.4.2 Coxsackievirus 72 5.4.3 Human enterovirus 71 73 5.4.4 Encephalomyocarditis virus 73 5.4.5 Foot-and-mouth disease virus 74 5.4.6 Human rhinoviruses 75 5.5 Caution in interpretation of induction of LC3 puncta and double-membraned vesicles in the context of autophagy 75 5.5.1 LC3 puncta 75 5.6 Conclusions and future research 77 References 78 6 FLAVIVIRUSES AND AUTOPHAGY 81 Tristan X. Jordan and Glenn Randall 6.1 Introduction 81 6.1.1 Autophagy 81 6.2 Flaviviruses 83 6.3 Dengue virus 83 6.3.1 Autophagosomes as a platform for replication? 85 6.3.2 Modulation of lipid metabolism 86 6.3.3 Potential role for the autophagy-related proteins USP10 and USP13 in DENV virion maturation 87 6.3.4 Cytoprotective autophagy 88 6.3.5 The role of autophagy in an ADE model of monocyte infection 89 6.3.6 Autophagy in DENV infections in mice 89 6.4 Other Flaviviruses 90 6.4.1 Japanese encephalitis virus 90 6.4.2 Modoc virus 90 6.4.3 West Nile virus 90 6.5 Concluding remarks 92 Acknowlegments 92 References 93 7 AUTOPHAGY: A HOME REMODELER FOR HEPATITIS C VIRUS 101 Marine L.B. Hillaire, Elodie Decembre, and Marlene Dreux 7.1 Introduction 101 7.1.1 Autophagy 101 7.1.2 Hepatitis C virus (HCV) disease, genome and replication 103 7.2 HCV induces a proviral autophagy 111 7.3 How does HCV trigger autophagy vesicle accumulation? 111 7.4 Dynamic membrane remodeling by autophagy 113 7.5 Interlinkage of autophagy with the innate immune response 114 7.6 Autophagy and cell death 115 7.7 Removal of aberrant deposits and organelles by autophagy: implications for liver injury associated with chronic hepatitis C 116 7.7.1 Autophagy and lipid metabolism 116 7.7.2 Mitophagy and HCV persistence 117 7.8 Conclusions and future directions 118 Acknowledgments 119 References 119 8 MODULATING AUTOPHAGY TO CURE HUMAN IMMUNODEFICIENCY VIRUS TYPE-1 127 Stephen A. Spector and Grant R. Campbell 8.1 Introduction 127 8.2 HIV subverts autophagy to promote its own replication 129 8.3 HIV infection inhibits autophagy during permissive infection while induction of autophagy leads to inhibition of HIV 130 8.4 HIV-induced autophagy in bystander CD4 T cells results in cell death 130 8.5 Modulation of autophagy as a mechanism for HIV-associated neurocognitive impairment 132 8.6 How can autophagy be exploited to control and eradicate HIV? 134 Acknowledgments 137 References 138 9 AUTOPHAGY IN THE INFECTED CELL: INSIGHTS FROM PATHOGENIC BACTERIA 143 Andrea Sirianni and Serge Mostowy 9.1 Introduction 143 9.2 Autophagy bacteria interactions 143 9.2.1 Salmonella typhimurium 144 9.2.2 Mycobacterium tuberculosis 145 9.2.3 Legionella pneumophila 146 9.2.4 Listeria monocytogenes 147 9.2.5 Shigella flexneri 149 9.2.6 Mycobacterium marinum 150 9.3 Conclusions 151 Acknowledgments 151 References 152 10 Rab PROTEINS IN AUTOPHAGY: STREPTOCOCCUS MODEL 159 Takashi Nozawa and Ichiro Nakagawa 10.1 Introduction 159 10.2 Rab GTPase 160 10.3 Rab GTPases in starvation-induced autophagy 160 10.4 Rab localization in autophagy during Streptococcus infection 161 10.5 Involvement of Rab7 in the initial formation of GcAV 163 10.6 Requirement of Rab23 for GcAV formation 163 10.7 Facilitation by Rab9A of GcAV enlargement and lysosomal fusion 164 10.8 Conclusion and perspective 165 References 167 11 HELICOBACTER PYLORI INFECTION CONTROL BY AUTOPHAGY 171 Laura K. Greenfield, Frances Dang, and Nicola L. Jones 11.1 Helicobacter pylori 171 11.2 H. pylori and evasion of host immune responses 176 11.3 Autophagy 178 11.4 Acute H. pylori infection: induction of autophagy in gastric epithelial cells 180 11.5 Chronic H. pylori infection: suppression of autophagy in gastric epithelial cells 184 11.6 H. pylori induction of autophagy in immune cells 185 11.7 Host genetics affecting autophagic clearance of H. pylori 185 11.8 H. pylori disrupted autophagy and gastric cancer 186 11.9 H. pylori therapy: is autophagy a contender? 187 11.10 Concluding remarks 188 Acknowledgments 189 References 189 12 INTERACTIONS BETWEEN SALMONELLA AND THE AUTOPHAGY SYSTEM 201 Teresa L.M. Thurston and David W. Holden 12.1 Introduction 201 12.2 Salmonella s life within the host 201 12.3 Salmonella s survival in a harsh intracellular habitat 202 12.4 Models for studying Salmonella infection 203 12.5 Mechanisms of Salmonella autophagy 204 12.5.1 Salmonella is targeted for antibacterial autophagy 204 12.5.2 Antibacterial autophagy induction 205 12.5.3 Eat-me signals for antibacterial autophagy 206 12.5.4 Autophagy receptors provide cargo specificity 208 12.6 Autophagy of Salmonella in vivo 209 12.7 Bacterial countermeasures 210 12.7.1 Could Salmonella counteract autophagy? 210 12.7.2 Potential autophagy avoidance mechanisms 210 12.7.3 SseL deubiquitinates autophagy-targeted protein aggregates 210 12.7.4 Does Salmonella inhibit selective antibacterial autophagy? 211 12.8 Perspectives 211 References 213 13 HOST FACTORS THAT RECRUIT AUTOPHAGY AS DEFENSE AGAINST TOXOPLASMA GONDII 219 Carlos S. Subauste 13.1 Introduction 219 13.2 CD40, autophagy and lysosomal degradation of T. gondii 220 13.3 Events downstream of CD40 involved in the stimulation of autophagy 222 13.4 Relevance of autophagy during in vivo infection with T. gondii 224 13.5 IFN- and ATG5 in T. gondii infection 224 13.6 T. gondii manipulates host cell signaling to inhibit targeting by LC3 structures and to maintain the nonfusogenic nature of the parasitophorous vacuole 227 13.7 Autophagy machinery within T. gondii 228 13.8 Conclusion 229 Acknowledgments 229 References 229 14 MYCOBACTERIUM TUBERCULOSIS AND THE AUTOPHAGIC PATHWAY 233 Gabriela Maria Recalde and Maria Isabel Colombo 14.1 Mycobacterium tuberculosis, a pathogen that resides in a self-tailored compartment to avoid killing by the host cell 233 14.2 The ESX-1 secretion system 235 14.3 Mycobacterium marinum, a close relative that escapes and forms actin tails in the cytoplasm 235 14.4 Mycobacterium actively modulates autophagy 236 14.5 Mycobacterium tuberculosis, a pathogen also able to escape toward the cytoplasm 239 14.6 Concluding remarks 240 References 241 15 AUTOPHAGY ENHANCES THE EFFICACY OF BCG VACCINE 245 Arshad Khan, Christopher R. Singh, Emily Soudani, Pearl Bakhru, Sankaralingam Saikolappan, Jeffrey D. Cirillo, N. Tony Eissa, Subramanian Dhandayuthapani and Chinnaswamy Jagannath 15.1 Introduction 246 15.2 Induction of autophagy through mTOR enhances antigen presentation via the MHC-II pathway in macrophages and dendritic cells 247 15.2.1 Rapamycin-induced autophagy enhances antigen presentation in APCs 248 15.2.2 Rapamycin and Torin1-induced autophagy enhances both antigen presentation and IL-1 secretion from BCG infected APCs 248 15.3 Intracellular mechanisms of autophagic routing of particulate BCG vaccine and secreted Ag85B into autophagosomes and enhanced MHC-II mediated antigen presentation 251 15.3.1 Overexpression of secreted Ag85B in BCG vaccine leads to aggresome formation in the cytosol of APCs 251 15.3.2 Overexpressed Ag85B from BCG vaccine forms aggresomes, which enhance antigen presentation through autophagy 251 15.3.3 Discussion: in vitro studies on autophagy and antigen presentation 253 15.4 Rapamycin activation of dendritic cells enhances efficacy of DC-BCG vaccine 255 15.4.1 Discussion 256 15.5 Rapamycin coadministration with BCG vaccine in mice enhances CD4 and CD8 T cell mediated protection against tuberculosis 256 15.5.1 Discussion 262 15.6 Conclusions 262 Acknowledgments 263 References 263 16 AUTOPHAGY S CONTRIBUTION TO INNATE AND ADAPTIVE IMMUNITY: AN OVERVIEW 267 Christina Bell, Michel Desjardins, Pierre Thibault and Kerstin Radtke 16.1 Autophagy: different routes to the same goal? 267 16.2 Xenophagy: it is a dog-eat-dog world 269 16.3 Autophagy and Toll-like receptors: a mutual turn-on 269 16.4 Autophagy and antigen presentation: a cry for help to clear pathogenic invaders 270 16.5 Autophagy and inflammasomes: Mutual regulation for an effective immune response 273 16.6 Cross-talk between autophagy and cytokines 273 Acknowledgments 275 References 275 17 AUTOPHAGY IN IMMUNE RESPONSES TO VIRUSES 279 Christophe Viret and Mathias Faure 17.1 Innate immunity against viruses 279 17.2 Autophagy in antiviral innate immunity 281 17.2.1 Virus sensing for autophagy induction 281 17.2.2 Role of autophagy in xenophagy of viruses 282 17.2.3 Role of autophagy in antiviral innate immunity signaling 283 17.3 Autophagy manipulation by viruses to resist innate immunity 285 17.3.1 Autophagy manipulation by viruses to prevent IFN-I synthesis 285 17.3.2 Viruses subvert autophagy to interfere with inflammatory responses 286 17.3.3 Autophagy and cell death during virus infection 287 17.4 Autophagy in antiviral adaptive immunity 287 17.4.1 Promotion of adaptive immune responses to viral infection by autophagy 287 17.4.2 MHC class II-restricted presentation of viral epitopes 288 17.4.3 MHC class I-restricted presentation of viral epitopes 290 17.4.4 Autophagy and cross-presentation 292 17.5 Autophagy manipulation by viruses to escape adaptive immunity 294 17.5.1 MHC class II antigen presentation pathway 294 17.5.2 MHC class I antigen presentation pathway 295 17.5.3 Autophagy and antigen-presenting cell function 295 17.6 Concluding remarks 296 Acknowledgments 296 References 297 18 PROCESSING AND MHC PRESENTATION OF ANTIGENS AFTER AUTOPHAGY-ASSISTED ENDOCYTOSIS, EXOCYTOSIS, AND CYTOPLASM DEGRADATION 303 Christian Munz 18.1 Introduction 303 18.2 Substrate recognition by macroautophagy 305 18.3 Antigen processing for MHC class II presentation by macroautophagy 307 18.4 A role of macroautophagy in MHC class I antigen presentation 308 18.5 Antigen release by autophagy-assisted exocytosis 309 18.6 Autophagy-assisted phagocytosis 310 18.7 Conclusions and outlook 312 Acknowledgments 312 References 312 Index 317