Autophagy, Infection, and the Immune Response.
- 1st ed.
- 1 online resource (364 pages)
Cover -- Title Page -- Copyright -- Contents -- Contributors -- Preface -- Acknowledgments -- Chapter 1 Autophagy and Immunity -- 1.1 Introduction -- 1.2 Autophagy -- 1.2.1 Types of autophagy -- 1.2.2 Morphology -- 1.2.3 Molecular machinery -- 1.2.4 Physiological roles -- 1.3 Autophagy and immunity -- 1.3.1 Xenophagy: autophagic clearance of intracellular microorganisms -- 1.3.2 Autophagy and cryptides -- 1.3.3 Autophagy and pattern recognition receptors (PRRs) -- 1.3.4 Autophagy and MHC antigen presentation -- 1.3.5 Autophagy regulation by immune signaling molecules -- 1.3.6 Autophagy, inflammation, and autoimmunity -- 1.4 Conclusion -- References -- Chapter 2 Techniques for Studying Autophagy -- 2.1 Introduction -- 2.2 Reagents and tools for studying autophagy -- 2.2.1 Reagents to monitor the lysosomal flux of LC3-II -- 2.2.2 Reagents that induce autophagy -- 2.2.3 Reagents and recombinant tools that inhibit autophagy -- 2.3 Detection of LC3-I AND LC3-II by immunoblotting -- 2.4 Immunofluorescent analyses of endogenous LC3 -- 2.5 Monitoring autophagy using fluorescent protein-tagged LC3 -- 2.6 Morphological analyses of autophagosomes and autolysosomes by TEM -- 2.6.1 Reagents or stock solutions -- 2.6.2 Resin embedding of cell pellets or microbes -- 2.6.3 Resin flat embedding of cells grown on glass or plastic coverslips -- 2.7 Techniques for immunoelectron microscopy -- References -- Chapter 3 Role of Autophagy in DNA Virus Infections in vivo -- 3.1 Introduction -- 3.2 In vivo interplay between autophagy and DNA viruses in plants and invertebrates -- 3.3 In vivo interplay between autophagy and DNA viruses in vertebrates -- 3.3.1 Autophagy is an essential antiviral mechanism that protects against HSV-1 in vivo -- 3.3.2 The autophagy-HBV interplay in vivo: a balance between viral exploitation and tumor suppression. 3.3.3 Autophagy may suppress r-herpesvirus persistent infection -- 3.4 Conclusion -- Acknowledgments -- References -- Chapter 4 Studying RNA viruses and autophagy in vivo -- 4.1 Introduction -- 4.2 In vivo interactions between autophagy and RNA viruses in plants and invertebrates -- 4.2.1 Plants -- 4.2.2 Invertebrates -- 4.3 In vivo Interactions between autophagy and RNA viruses in vertebrates -- 4.3.1 Togaviridae -- 4.3.2 Caliciviridae -- 4.3.3 Orthomyxoviridae -- 4.3.4 Flaviviridae -- 4.3.5 Picornaviridae -- 4.4 Conclusion -- Acknowledgments -- References -- Chapter 5 Autophagy and picornavirus infection -- 5.1 Introduction -- 5.2 Selective autophagy involves autophagy receptors with LC3-interacting domains -- 5.3 Autophagy is activated during virus infection -- 5.4 Picornaviruses and autophagy -- 5.4.1 Poliovirus -- 5.4.2 Coxsackievirus -- 5.4.3 Human enterovirus 71 -- 5.4.4 Encephalomyocarditis virus -- 5.4.5 Foot-and-mouth disease virus -- 5.4.6 Human rhinoviruses -- 5.5 Caution in interpretation of induction of LC3 puncta and double-membraned vesicles in the context of autophagy -- 5.5.1 LC3 puncta -- 5.6 Conclusions and future research -- References -- Chapter 6 Flaviviruses and Autophagy -- 6.1 Introduction -- 6.1.1 Autophagy -- 6.2 Flaviviruses -- 6.3 Dengue virus -- 6.3.1 Autophagosomes as a platform for replication? -- 6.3.2 Modulation of lipid metabolism -- 6.3.3 Potential role for the autophagy-related proteins USP10 and USP13 in DENV virion maturation -- 6.3.4 Cytoprotective autophagy -- 6.3.5 The role of autophagy in an ADE model of monocyte infection -- 6.3.6 Autophagy in DENV infections in mice -- 6.4 Other Flaviviruses -- 6.4.1 Japanese encephalitis virus -- 6.4.2 Modoc virus -- 6.4.3 West Nile virus -- 6.5 Concluding remarks -- Acknowlegments -- References -- Chapter 7 Autophagy: a home remodeler for Hepatitis C Virus. 7.1 Introduction -- 7.1.1 Autophagy -- 7.1.2 Hepatitis C virus (HCV) disease, genome and replication -- 7.2 HCV induces a proviral autophagy -- 7.3 How does HCV trigger autophagy vesicle accumulation? -- 7.4 Dynamic membrane remodeling by autophagy -- 7.5 Interlinkage of autophagy with the innate immune response -- 7.6 Autophagy and cell death -- 7.7 Removal of aberrant deposits and organelles by autophagy: implications for liver injury associated with chronic hepatitis C -- 7.7.1 Autophagy and lipid metabolism -- 7.7.2 Mitophagy and HCV persistence -- 7.8 Conclusions and future directions -- Acknowledgments -- References -- Chapter 8 Modulating Autophagy to Cure Human Immunodeficiency Virus type-1 -- 8.1 Introduction -- 8.2 HIV subverts autophagy to promote its own replication -- 8.3 HIV infection inhibits autophagy during permissive infection while induction of autophagy leads to inhibition of HIV -- 8.4 HIV-induced autophagy in bystander CD4+ T cells results in cell death -- 8.5 Modulation of autophagy as a mechanism for HIV-associated neurocognitive impairment -- 8.6 How can autophagy be exploited to control and eradicate HIV? -- Acknowledgments -- References -- Chapter 9 Autophagy in the infected cell: insights from pathogenic bacteria -- 9.1 Introduction -- 9.2 Autophagy-bacteria interactions -- 9.2.1 Salmonella typhimurium -- 9.2.2 Mycobacterium tuberculosis -- 9.2.3 Legionella pneumophila -- 9.2.4 Listeria monocytogenes -- 9.2.5 Shigella flexneri -- 9.2.6 Mycobacterium marinum -- 9.3 Conclusions -- Acknowledgments -- References -- Chapter 10 Rab Proteins in Autophagy: Streptococcus Model -- 10.1 Introduction -- 10.2 Rab GTPase -- 10.3 Rab GTPases in starvation-induced autophagy -- 10.4 Rab localization in autophagy during Streptococcus infection -- 10.5 Involvement of Rab7 in the initial formation of GcAV. 10.6 Requirement of Rab23 for GcAV formation -- 10.7 Facilitation by Rab9A of GcAV enlargement and lysosomal fusion -- 10.8 Conclusion and perspective -- References -- Chapter 11 Helicobacter pylori Infection Control by Autophagy -- 11.1 Helicobacter pylori -- 11.2 H. pylori and evasion of host immune responses -- 11.3 Autophagy -- 11.4 Acute H. pylori infection: induction of autophagy in gastric epithelial cells -- 11.5 Chronic H. pylori infection: suppression of autophagy in gastric epithelial cells -- 11.6 H. pylori induction of autophagy in immune cells -- 11.7 Host genetics affecting autophagic clearance of H. pylori -- 11.8 H. pylori disrupted autophagy and gastric cancer -- 11.9 H. pylori therapy: is autophagy a contender? -- 11.10 Concluding remarks -- Acknowledgments -- References -- Chapter 12 Interactions between Salmonella and the autophagy system -- 12.1 Introduction -- 12.2 Salmonella's life within the host -- 12.3 Salmonella's survival in a harsh intracellular habitat -- 12.4 Models for studying Salmonella infection -- 12.5 Mechanisms of Salmonella autophagy -- 12.5.1 Salmonella is targeted for antibacterial autophagy -- 12.5.2 Antibacterial autophagy induction -- 12.5.3 Eat-me signals for antibacterial autophagy -- 12.5.4 Autophagy receptors provide cargo specificity -- 12.6 Autophagy of Salmonella in vivo -- 12.7 Bacterial countermeasures -- 12.7.1 Could Salmonella counteract autophagy? -- 12.7.2 Potential autophagy avoidance mechanisms -- 12.7.3 SseL deubiquitinates autophagy-targeted protein aggregates -- 12.7.4 Does Salmonella inhibit selective antibacterial autophagy? -- 12.8 Perspectives -- References -- Chapter 13 Host Factors That Recruit Autophagy As Defense Against Toxoplasma Gondii -- 13.1 Introduction -- 13.2 CD40, autophagy and lysosomal degradation of T. gondii. 13.3 Events downstream of CD40 involved in the stimulation of autophagy -- 13.4 Relevance of autophagy during in vivo infection with T. gondii -- 13.5 IFN-r and ATG5 in T. gondii infection -- 13.6 T. gondii manipulates host cell signaling to inhibit targeting by LC3+ structures and to maintain the nonfusogenic nature of the parasitophorous vacuole -- 13.7 Autophagy machinery within T. gondii -- 13.8 Conclusion -- Acknowledgments -- References -- Chapter 14 Mycobacterium tuberculosis and the autophagic pathway -- 14.1 Mycobacterium tuberculosis, a pathogen that resides in a self-tailored compartment to avoid killing by the host cell -- 14.2 The ESX-1 secretion system -- 14.3 Mycobacterium marinum, a close relative that escapes and forms actin tails in the cytoplasm -- 14.4 Mycobacterium actively modulates autophagy -- 14.5 Mycobacterium tuberculosis, a pathogen also able to escape toward the cytoplasm -- 14.6 Concluding remarks -- References -- Chapter 15 Autophagy enhances the efficacy of BCG vaccine -- 15.1 Introduction -- 15.2 Induction of autophagy through mTOR enhances antigen presentation via the MHC-II pathway in macrophages and dendritic cells -- 15.2.1 Rapamycin-induced autophagy enhances antigen presentation in APCs -- 15.2.2 Rapamycin and Torin1-induced autophagy enhances both antigen presentation and IL-1B secretion from BCG infected APCs -- 15.3 Intracellular mechanisms of autophagic routing of particulate BCG vaccine and secreted Ag85B into autophagosomes and enhanced MHC-II mediated antigen presentation -- 15.3.1 Overexpression of secreted Ag85B in BCG vaccine leads to aggresome formation in the cytosol of APCs -- 15.3.2 Overexpressed Ag85B from BCG vaccine forms aggresomes, which enhance antigen presentation through autophagy -- 15.3.3 Discussion: in vitro studies on autophagy and antigen presentation. 15.4 Rapamycin activation of dendritic cells enhances efficacy of DC-BCG vaccine.