Autophagy in Immunity and Infection : A Novel Immune Effector

by Editor: Vojo Deretic (University of New Mexico, Albuquerque, USA)

• ISBN13: 9783527314508
• ISBN10: 3527314504
• Format: Hardcover
• Copyright: 2006-10-01
• Publisher: Blackwell Pub

Summary

This first book to cover this new topic at the interface of cell biology, immunology and infection biology offers a unique insight as to how the innate and possibly the adaptive immune system are shaped by cellular mechanisms. Following a comprehensive introduction to autophagy, the work features cellular mechanisms and medical implications, structured according to all major pathogens, while also covering emerging infectious diseases, such as tuberculosis. Edited by one of the authors of a groundbreaking paper on this topic.

Author Biography

Vojo Deretic is full professor and vice-chair at the Department of Molecular Genetics and Microbiology of the University of New Mexico Health Sciences Center. From 1997 to 1999 he was Foundation Lecturer of the American Society for Microbiology. He published one of the groundbreaking papers on this topic in CELL.

Table of Contents

Preface	xii
Foreword	xv
List of Contributors	xix
Colour Plates	xxiii
Part I Introduction to Autophagy
Overview of Autophagy	3	(16)
Julie E. Legakis
Daniel J. Klionsky
Overview of Autophagy	3	(2)
The Discovery of Autophagy	5	(2)
Mechanistic Aspects of Autophagy	7	(6)
Induction	9	(1)
Cargo Selection and Packaging	10	(1)
Vesicle Nucleation	11	(1)
Vesicle Expansion and Completion	11	(1)
Retrieval	12	(1)
Targeting, Docking and Fusion of the Vesicle with the Lysosome/Vacuole	12	(1)
Breakdown of the Vesicle and its Cargo	12	(1)
Autophagy and Immunity	13	(6)
References	14	(5)
Cell Biology and Biochemistry of Autophagy	19	(36)
Edmond Chan
Robert Kochl
Sharon A. Tooze
Introduction	19	(1)
Autophagic Pathway	20	(7)
Formation of Autophagosomes	20	(2)
Fusion of AV with Endocytic Pathways and Maturation	22	(3)
Endosomes and Lysosomes	25	(2)
Regulation of Mammalian Autophagy by Amino Acids and Hormones	27	(14)
Amino Acids	28	(2)
Hormones	30	(1)
Longer-term Regulation	31	(1)
The Nutrient Sensor Target of Rapamycin (TOR)	32	(4)
Upstream of TOR	36	(2)
Downstream of TOR	38	(3)
Methods to Measure Autophagy	41	(14)
Microscopic Methods	42	(1)
Electron Microscopy	42	(1)
Light Microscopy	42	(3)
Biochemical Methods	45	(1)
Formation and Induction	45	(1)
Fusion	46	(1)
Purification of Autophagosomes from Rat Liver	47	(1)
Inhibition of Autophagy	47	(1)
Common Questions	48	(1)
Summary and Outlook	48	(1)
References	49	(6)
Transgenic Models of Autophagy	55	(14)
Noboru Mizushima
Molecular Mechanism of Mammalian Autophagy	55	(3)
Atg12 Conjugation System	55	(1)
Atg8/Microtubule-associated Protein 1 Light Chain 3 (LC3) Conjugation System	56	(1)
Class III Phosphatidylinositol-3-kinase (PI3K) Complex	57	(1)
Atg1 Kinase Complex	57	(1)
Other Factors	58	(1)
Autophagy Indicator Mice: Green Fluorescent Protein (GFP)-LC3 Transgenic Mice	58	(2)
Mouse Models Deficient for Autophagy-related Genes	60	(4)
Atg5-deficient Mice	61	(2)
Atg7-deficient Mice	63	(1)
Beclin 1-deficient Mice	63	(1)
Concluding Remarks	64	(5)
References	64	(5)
Autophagy in Disease and Aging	69	(36)
Marta Martinez-Vicente
Susmita Kaushik
Ana Maria Cuervo
Introduction	69	(1)
Autophagy in Neurodegenerative Disorders	70	(9)
Protein Misfolding and Aggregation	71	(2)
Parkinson's Disease	73	(2)
Alzheimer's Disease	75	(1)
Huntington's Disease	76	(1)
Prion Diseases	77	(1)
Niemann-Pick Type C	78	(1)
Autophagy and Cancer	79	(6)
Proteolysis of long-lived Proteins and Effect of Nutrient Deprivation in Cancer Cells	79	(1)
Autophagic Cell Death in Response to Anticancer Treatment	80	(2)
Molecular Mechanisms	82	(1)
Beclin 1	82	(1)
PI3K-Akt-mTOR Pathway	82	(2)
Possible Therapeutic Attempts	84	(1)
Myopathies	85	(3)
Danon Disease	85	(1)
XMEA	86	(1)
Rimmed Vacuolar Myopathies	86	(1)
Other Myopathies	87	(1)
Cardiomyopathies and Myocardial Cell Death	87	(1)
Liver Diseases	88	(1)
Diabetes Mellitus	89	(1)
Aging	90	(4)
Changes in Protein Degradation with Age	90	(1)
Age-related Changes in Autophagy	91	(2)
Consequences of the Failure of Autophagy in Aging	93	(1)
Slowing Down Aging?	94	(1)
Concluding Remarks and Pending Questions	94	(11)
References	95	(10)
The Dual Roles for Autophagy in Cell Death and Survival	105	(24)
Yayanta Debnath
Christopher Fung
Introduction	105	(1)
Types of Programmed Cell Death	106	(2)
Type 1 Programmed Cell Death	106	(1)
Type 2 Programmed Cell Death	106	(1)
Type 3 Programmed Cell Death	107	(1)
Other Types of Programmed Cell Death	107	(1)
The Contribution of Autophagy to Programmed Cell Death	108	(2)
Death Processes That Require atg Genes	108	(2)
The Combined Activation of Autophagy and Apoptosis during Programmed Cell Death	110	(2)
Emerging Relationships between Apoptosis and Autophagy	112	(1)
Autophagy and Cell Survival	113	(5)
Autophagy is Cytoprotective during Nutrient Depletion in Mammalian Cells	114	(1)
Autophagy and Neuroprotection	115	(1)
Cytoprotective Roles of Autophagy in the Response to Infectious Pathogens	116	(2)
Autophagy and Organism Survival	118	(1)
Concluding Remarks	119	(10)
Acknowledgments	119	(1)
References	120	(9)
Part II Autophagy and Bacteria
Autophagy and Mycobacterium tuberculosis	129	(10)
James Harris
Sergio De Haro
Vojo Deretic
Introduction	129	(1)
M. tuberculosis Blocks Phagolysosome Biogenesis in Macrophages	130	(1)
Autophagy and the Host Response to M. tuberculosis	131	(2)
Regulation of Autophagy by the Immune System	133	(1)
p47 GTPases and Autophagy	134	(1)
Future Directions	135	(4)
References	136	(3)
Autophagy Eliminates Group A Streptococcus Invading Host Cells	139	(12)
Atsuo Amano
Tamotsu Yoshimori
Group A Streptococcus (GAS; Streptococcus pyogenes)	139	(1)
Adherence to Host Cells by GAS	139	(1)
Invasion of Host Cells by GAS	140	(1)
Survival of Intracellular Bacteria	141	(1)
Streptolysin O (SLO) Enables GAS to Escape form Phagocytic/Endocytic Degradation	141	(1)
Autophagy	142	(1)
Intracellular GAS is Trapped by Autophagosome-like Compartments	142	(2)
Atg5 is Required for Capture and Killing of GAS	144	(3)
GcAVs Fuse with Lysosomes for Degradation	147	(1)
Conclusion and Perspective	147	(4)
References	149	(2)
Shigella Invasion of Host Cells and Escape from Autophagy	151	(10)
Michinaga Ogawa
Chihiro Sasakawa
Shigella Invasion of Epithelia	151	(1)
Shigella Disseminate among Epithelial Cells	152	(2)
Shigella Infection Elicits an Inflammatory Response	154	(1)
Shigella that do not Produce IcsB Undergo Autophagic Degradation	154	(2)
Shigella VirG is a Target for Autophagy, but is Camouflaged by its IcsB	156	(1)
Perspective	157	(4)
References	158	(3)
Listeria monocytogenes: A Model System for Studying Autophagy	161	(18)
Kathryn A. Rich
Paul Webster
Listeriosis	161	(1)
Invasion of Mammalian Cells by L. monocytogenes	161	(3)
Autophagy	164	(1)
The Ideal Target for Studying the Early Stages of Autophagy	165	(2)
Why Other Organisms may not be as Useful to Study the Autophagic Process	167	(2)
Assembly of AVs may Result from Fusion of Cytoplasmic Membrane Structures	169	(2)
Pathogenic Cytoplasmic Bacteria can avoid the Autophagic Pathway	171	(2)
Cellular Fate of Metabolically Inhibited L. monocytogenes	173	(6)
References	174	(5)
Coxiella burnetii Hijacks the Autophagy Pathway to Survive	179	(20)
Maximiliano G. Gutierrez
Maria I. Colombo
Introduction	179	(1)
Coxiella burnetii	179	(1)
Bacterium Morphology and Phylogeny	180	(1)
Lipopolysaccharide (LPS) and Phases	180	(1)
Genome and Genetics	181	(1)
Host Response and Immunity	181	(2)
Developmental Cycle of C. burnetii: Small Cell Variant (SCV) and Large Cell Variant (LCV)	183	(1)
C. burnetii Type IV Secretion System	184	(1)
Interaction with the Endocytic and Autophagic Pathways	185	(4)
Contribution of Autophagy to RV Development	189	(3)
Autophagy and Bacterial Differentiation from SCVs to LCVs	192	(2)
Unanswered Questions and Future Perspectives	194	(5)
Acknowledgments	195	(1)
References	195	(4)
Utilization of Endoplasmic Reticulum Membranes to Establish a Vacuole that Supports Replication of Legionella pneumophila	199	(14)
Mary-Pat Stein
Craig R. Roy
Introduction	199	(2)
Evidence that Legionella Utilizes the Autophagy Machinery for Biogenesis of a Replicative Organelle	201	(4)
Induction of Autophagy	201	(1)
Formation of Autophagosomes	202	(2)
Maturation of Autophagosomes and Fusion with Lysosomes	204	(1)
Evidence that the Host Autophagy Machinery is not Essential for Transport or Growth of Legionella	205	(2)
Dictyostelium discoideum Autophagy Mutants Support Legionella Growth	205	(1)
Morphological Differences between LCVs and Autophagosomes	205	(1)
Differences Between Legionella and Other Bacteria that Utilize Autophagy for Intracellular Survival	206	(1)
Creation of an ER-derived Vacuole that Supports Legionella Replication by Subversion of the Host Secretory Pathway	207	(1)
Conclusion	208	(5)
References	209	(4)
Part III Autophagy and Viruses
Endogenous Major Histocompatibility Complex Class II Antigen Processing of Viral Antigens	213	(14)
Dorothee Schmid
Christian Munz
Introduction	213	(1)
Classical Pathways of Antigen Processing for MHC Presentation	214	(1)
Endogenous MHC Class II Antigen Processing of Viral Antigens	215	(1)
Autophagic Delivery of Antigens for Lysosomal Degradation and MHC Class II Presentation	216	(2)
Similarities Between Sources of MHC Class II Ligands and Autophagy Substrates	218	(1)
Overlap Between the Vesicular Transport Pathways of Autophagosomes and MHC Class II Loading Compartments	219	(1)
Possible Functions of MHC Class II Presentation after Autophagy in the Immune Control of Viral Infections	220	(1)
Future Directions of Research into Endogenous MHC Class II Antigen Processing	221	(1)
Summary	222	(5)
Acknowledgments	222	(1)
References	222	(5)
Autophagy in Antiviral Host Defense	227	(15)
Beth Levine
Introduction	227	(1)
Role of Antiviral Signaling Pathways in Autophagy Regulation	227	(4)
PKR is Required for Virus-induced Autophagy	227	(3)
IFN-y Stimulates Autophagy	230	(1)
Role of Mammalian Autophagy Genes in Antiviral Host Defense	231	(2)
Role of Plant Autophagy Genes in Antiviral Host Defense	233	(1)
Evasion of Autophagy by Viruses	234	(2)
How Might Viral Evasion of Autophagy Contribute to Viral Pathogenesis?	236	(1)
Autophagy and Antigen Presentation	237	(1)
Concluding Remarks	238	(4)
References	239	(3)
Addendum	242	(1)
Jennifer Sparks
Mark R. Denison
Subject Index	243