Autophagy in Immunity and Infection: A Novel Immune Effector

Preface. Foreword. List of Contributors. Colour Plates. Part I Introduction to Autophagy. 1 Overview of Autophagy (Julie E. Legakis and Daniel J. Klionsky). 1.1 Overview of Autophagy. 1.2 The Discovery of Autophagy. 1.3 Mechanistic Aspects of Autophagy. 1.4 Autophagy and Immunity. References. 2 Cell Biology and Biochemistry of Autophagy (Edmond Chan, Robert Kochl and Sharon A. Tooze). 2.1 Introduction. 2.2 Autophagic Pathway. 2.3 Regulation of Mammalian Autophagy by Amino Acids and Hormones. 2.4 Methods to Measure Autophagy. References. 3 Transgenic Models of Autophagy (Noboru Mizushima). 3.1 Molecular Mechanism of Mammalian Autophagy. 3.2 Autophagy Indicator Mice: Green Fluorescent Protein (GFP)-LC3 Transgenic Mice. 3.3 Mouse Models Deficient for Autophagy-related Genes. 3.4 Concluding Remarks. References. 4 Autophagy in Disease and Aging (Marta Martinez-Vicente, Susmita Kaushik and Ana Maria Cuervo). 4.1 Introduction. 4.2 Autophagy in Neurodegenerative Disorders. 4.3 Autophagy and Cancer. 4.4 Myopathies. 4.5 Liver Diseases. 4.6 Diabetes Mellitus. 4.7 Aging. 4.8 Concluding Remarks and Pending Questions. References. 5 The Dual Roles for Autophagy in Cell Death and Survival (Yayanta Debnath and Christopher Fung). 5.1 Introduction. 5.2 Types of Programmed Cell Death. 5.3 The Contribution of Autophagy to Programmed Cell Death. 5.4 The Combined Activation of Autophagy and Apoptosis during Programmed Cell Death. 5.5 Emerging Relationships between Apoptosis and Autophagy. 5.6 Autophagy and Cell Survival. 5.7 Autophagy and Organism Survival. 5.8 Concluding Remarks. Acknowledgments. References. Part II Autophagy and Bacteria. 6 Autophagy and Mycobacterium tuberculosis (James Harris, Sergio De Haro and Vojo Deretic0. 6.1 Introduction. 6.2 M. tuberculosis Blocks Phagolysosome Biogenesis in Macrophages. 6.3 Autophagy and the Host Response to M. tuberculosis. 6.4 Regulation of Autophagy by the Immune System. 6.5 p47 GTPases and Autophagy. 6.6 Future Directions. References. 7 Autophagy Eliminates Group A Streptococcus Invading Host Cells (Atsuo Amano and Tamotsu Yoshimori). 7.1 Group A Streptococcus (GAS Streptococcus pyogenes). 7.2 Adherence to Host Cells by GAS. 7.3 Invasion of Host Cells by GAS. 7.4 Survival of Intracellular Bacteria. 7.5 Streptolysin O (SLO) Enables GAS to Escape form Phagocytic/Endocytic Degradation. 7.6 Autophagy. 7.7 Intracellular GAS is Trapped by Autophagosome-like Compartments. 7.8 Atg5 is Required for Capture and Killing of GAS. 7.9 GcAVs Fuse with Lysosomes for Degradation. 7.10 Conclusion and Perspective. References. 8 Shigella Invasion of Host Cells and Escape from Autophagy (Michinaga Ogawa and Chihiro Sasakawa). 8.1 Shigella Invasion of Epithelia. 8.2 Shigella Disseminate among Epithelial Cells. 8.3 Shigella Infection Elicits an Inflammatory Response. 8.4 Shigella that do not Produce IcsB Undergo Autophagic Degradation. 8.5 Shigella VirG is a Target for Autophagy, but is Camouflaged by its IcsB. 8.6 Perspective. References. 9 Listeria monocytogenes: A Model System for Studying Autophagy (Kathryn A. Rich and Paul Webster). 9.1 Listeriosis. 9.2 Invasion of Mammalian Cells by L. monocytogenes. 9.3 Autophagy. 9.4 The Ideal Target for Studying the Early Stages of Autophagy. 9.5 Why Other Organisms may not be as Useful to Study the Autophagic Process. 9.6 Assembly of AVs may Result from Fusion of Cytoplasmic Membrane Structures. 9.7 Pathogenic Cytoplasmic Bacteria can avoid the Autophagic Pathway. 9.8 Cellular Fate of Metabolically Inhibited L. monocytogenes. References. 10 Coxiella burnetii Hijacks the Autophagy Pathway to Survive (Maximiliano G. Gutierrez and Maria I. Colombo). 10.1 Introduction. 10.2 Coxiella burnetii. 10.3 Bacterium Morphology and Phylogeny. 10.4 Lipopolysaccharide (LPS) and Phases. 10.5 Genome and Genetics. 10.6 Host Response and Immunity. 10.7 Developmental Cycle of C. burnetii: Small Cell Variant (SCV) and Large Cell Variant (LCV). 10.8 C. burnetii Type IV Secretion System. 10.9 Interaction with the Endocytic and Autophagic Pathways. 10.10 Contribution of Autophagy to RV Development. 10.11 Autophagy and Bacterial Differentiation from SCVs to LCVs. 10.12 Unanswered Questions and Future Perspectives. Acknowledgments. References. 11 Utilization of Endoplasmic Reticulum Membranes to Establish a Vacuole that Supports Replication of Legionella pneumophila (Mary-Pat Stein and Craig R. Roy). 11.1 Introduction. 11.2 Evidence that Legionella Utilizes the Autophagy Machinery for Biogenesis of a Replicative Organelle. 11.3 Evidence that the Host Autophagy Machinery is not Essential for Transport or Growth of Legionella. 11.4 Creation of an ER-derived Vacuole that Supports Legionella Replication by Subversion of the Host Secretory Pathway. 11.5 Conclusion. References. Part III Autophagy and Viruses. 12 Endogenous Major Histocompatibility Complex Class II Antigen Processing of Viral Antigens (Dorothee Schmid and Christian Munz). 12.1 Introduction. 12.2 Classical Pathways of Antigen Processing for MHC Presentation. 12.3 Endogenous MHC Class II Antigen Processing of Viral Antigens. 12.4 Autophagic Delivery of Antigens for Lysosomal Degradation and MHC Class II Presentation. 12.5 Similarities Between Sources of MHC Class II Ligands and Autophagy Substrates. 12.6 Overlap Between the Vesicular Transport Pathways of Autophagosomes and MHC Class II Loading Compartments. 12.7 Possible Functions of MHC Class II Presentation after Autophagy in the Immune Control of Viral Infections. 12.8 Future Directions of Research into Endogenous MHC Class II Antigen Processing. 12.9 Summary. Acknowledgments. References. 13 Autophagy in Antiviral Host Defense (Beth Levine). 13.1 Introduction. 13.2 Role of Antiviral Signaling Pathways in Autophagy Regulation. 13.3 Role of Mammalian Autophagy Genes in Antiviral Host Defense. 13.4 Role of Plant Autophagy Genes in Antiviral Host Defense. 13.5 Evasion of Autophagy by Viruses. 13.6 How Might Viral Evasion of Autophagy Contribute to Viral Pathogenesis? 13.7 Autophagy and Antigen Presentation. 13.8 Concluding Remarks. References. Addendum (Jennifer Sparks and Mark R. Denison). Subject Index.