Retrovirus-Cell Interactions

Description

Retrovirus-Cell Interactions provides an up-to-date review of the interactions between retroviruses and the cells they infect, offering a comprehensive understanding of how retroviruses hijack cellular factors to facilitate virus replication. Drugs targeting viral enzymes have been developed to treat HIV; the next challenge is to inhibit virus-cell interactions as next generation treatment strategies. Organized according to the retrovirus' replication cycle, this book does not focus exclusively on HIV, but rather includes important findings in other retroviral systems, including animal retroviruses, retrotransposons, and endogenous retroelements to allow broad comparisons on important commonalities and differences. Cover Front-Matter_2018_Retrovirus-Cell-Interactions Retrovirus-Cell Interactions Copyright_2018_Retrovirus-Cell-Interactions Copyright Dedication_2018_Retrovirus-Cell-Interactions Dedication Contents List-of-Contributors_2018_Retrovirus-Cell-Interactions List of Contributors Author-Biographies_2018_Retrovirus-Cell-Interactions Author Biographies Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Preface_2018_Retrovirus-Cell-Interactions Preface Introduction_2018_Retrovirus-Cell-Interactions Introduction References Chapter-1---Retrovirus-Receptor-Interactions-an_2018_Retrovirus-Cell-Interac 1 - Retrovirus Receptor Interactions and Entry Envelope Glycoproteins: Domain Structure Retrovirus Entry Receptors Virus Attachment The Basics of Membrane Fusion Do Receptor Interactions Contribute to the Envelope Proteins Functions That Drive Entry The Triggers Conserved Motifs in Envelope Proteins Are Critical to Regulation of Fusion Regulation by Control of the Conformation of Surface Subunit Regulation by Control of Disulfide Bond Isomerization and Surface Subunit Conformation Lentiviruses: Receptor-Triggered Conformational Changes in the Surface Subunit Gammaretroviruses: Receptor- and Cellular Protease–Driven Disulfide Bond Isomerization Alpharetroviruses: Receptor- and Low pH-Driven Disulfide Bond Isomerization Do Env–Receptor Interactions Contribute to Pathogenesis? CD4+ T-Cell Depletion and AIDS Neurological Damage and HAM/TSP Mutations That Adapt Virus to Low Receptor Levels Can Also Increase Pathogenicity Envelope Protein–Driven Neoplasia in Betaretrovirus Infection Host Defenses That Inhibit Retroviral Entry Also Drive Envelope Protein Variation Challenges in Vaccine Development Interferon-Induced Transmembrane Proteins and Envelope Proteins Variation Coevolution of Virus and Receptor Captured Retroviral Envelope Proteins in the Development of Mammalian Placenta and Male Muscle Mass References Chapter-10---The-Role-of-Lipids-in-Retroviral-R_2018_Retrovirus-Cell-Interac 10 - The Role of Lipids in Retroviral Replication Introduction Composition of Cellular Membranes Composition of Viral Membranes Membrane Microdomains Lipids in Retroviral Entry Role of Cholesterol in Retroviral Entry Role of Sphingolipids in Retroviral Entry Role of Phospholipids in Retroviral Entry Retroviral Assembly Trafficking of Gag and Sites of Retroviral Assembly Gag–Membrane Interactions Lipids in Retroviral Assembly Role of Cholesterol in Retroviral Assembly Role of PI(4,5)P2 in Retroviral Assembly Gag Binding to Giant Unilamellar Vesicles Lipids in Retroviral Cell–Cell Transfer Retroviral Accessory Proteins and Lipid Microdomains Inhibition of Retroviral Replication With Lipid-Modifying Agents Cholesterol Modifying Agents Inhibitors of Sphingolipid Synthesis Concluding Remarks References Chapter-11---Cellular-Immune-Responses-to-Retro_2018_Retrovirus-Cell-Interac 11 - Cellular Immune Responses to Retroviruses Introduction Steps of the Retrovirus Infection Pathway Targeted by the Host Intrinsic/Innate Response Host Pathways Implicated in Cellular Control of Retrovirus Infection Subversion of Cellular Immune Responses by Retroviruses Conclusions References Chapter-12---Noncoding-RNAs-in-Retrovirus-Repl_2018_Retrovirus-Cell-Interact 12 - Noncoding RNAs in Retrovirus Replication Introduction Host RNAs Packaged Into Virions Transfer RNAs 7SL RNA U Small Nuclear RNA Y RNA Vault RNA High-Throughput RNA-Sequencing Studies Long Noncoding RNA and Endogenous Retroviruses NRON: HIV-1 NEAT1: HIV-1 Large Intergenic RNA–p21: HIV-1 Antisense Protein RNA: HIV-1 Long Noncoding RNA 00173: HIV-1 ASP RNA: HTLV-1 Bic: ALV and His-1: MLV Endogenous Retroviruses Functional Transactivating Response Element RNAs RNA Interference and miRNAs RNAi, miRNA, and siRNA Production Cellular MicroRNAs Made in Response to Viral Infections Viral MicroRNAs Encoded Within Genomes Viral Suppressors of RNA Silencing Therapeutics Concluding Remarks Acknowledgments References Chapter-13---Cellular-Control-of-Endogenous-Retrovi_2018_Retrovirus-Cell-Int 13 - Cellular Control of Endogenous Retroviruses and Retroelements Introduction Background Long Terminal Repeat Retrotransposons and Endogenous Retroviruses Fig. 13.1 Non-Long Terminal Repeat Retrotransposons Long Interspersed Elements Short Interspersed Elements Chimeric Short Interspersed Elements Pseudogenes Activity Frequencies of Retrotransposition Retroelement Activities and Impacts Control of Retroelement Expression Retroelement Transcription Patterns Favor Self-Preservation Regulation of Retroelements in Somatic Cells by RNA Interference Fig. 13.2 Regulation of Retroelements in Germline and Embryonic Stem Cells Sequence-Specific Suppression of Retroelements Neuronal Activity of Retroelements Roles for Retroelements in Cancer Initiation and Progression Regulation of Retroelements by the Innate Immune System Regulation of Innate Immunity by Endogenous Retrovirus Sequences Fig. 13.3 Sensing of Retroelements by Innate Immunity Direct Control of Retroelements by Innate Immunity Perspectives Acknowledgments References Chapter-14---Strategies-to-Discover-Novel-Cellular-Fac_2018_Retrovirus-Cell- 14 - Strategies to Discover Novel Cellular Factors Involved in Retrovirus Replication Introduction Identifying Protein–Protein Interactions in Retroviruses Using Two-Hybrid Screens Using Gag Proteins as Bait Using Integrase as Bait Additional Retroviral Proteins Used as Bait Mass Spectrometry Approaches to Discovery of Retrovirus–Cell Protein–Protein Interactions Mass Spectrometry to Identify Proteins Packaged Into Virus Particles Mass Spectrometry to Identify Host Proteins Interacting With HIV-1 Proteins Affinity Purification Approaches Liquid Chromatography Coupled to Tandem Mass Spectrometry Multidimensional Protein Identification Technology Mass Spectrometry Mass Spectrometry Using Viral DNA as Bait HIV-1 5′ Untranslated Regions as Bait Mass Spectrometry Using Viral RNA as Bait HIV-1 Subgenomic RNAs as Bait Retroviral 5′Untranslated Regions as Bait Full-Length HIV-1 RNA Used as Bait RNA Interference and Genome-Wide Screens to Assess the Contribution of Host Factors to Virus Replication Small Interfering RNA Screens Short Hairpin RNA Screens Metaanalysis of siRNA Screens in HIV-1 Replication Targeted RNAi Screens Genome-Wide Analysis of Retrotransposition in Yeast Host Genome Editing Using CRISPR/Cas-9 to Find Retrovirus Dependency Genes Gain-of-Function Genetic Approaches Using cDNA Overexpression Screens Identification of Cellular RNAs That Interact With Retroviruses Host RNAs Packaged Into Retrovirus Particles RNA Sequencing Techniques Concluding Remarks Acknowledgments References Chapter-2---Cellular-Factors-That-Regulate-Retrovirus-_2018_Retrovirus-Cell- 2 - Cellular Factors That Regulate Retrovirus Uncoating and Reverse Transcription A Brief Description of Early Events of Infection Monitoring the Course of Infection in Early Stages Monitoring Viral Nucleic Acids Monitoring Incoming Viral Proteins Imaging Host Factors Promoting Early Events of Infection Breaking and Entering: Subcortical Actin Factors Affecting Reverse Transcription Cytoskeleton and Motors: Trafficking Cyclophilin A, a Host Factor Binding Capsid Modifications of Viral Proteins During Infection Host Factors Restricting Infection in Early Stages of Infection Fv1, a Gene for Resistance to the Friend Leukemia Virus TRIM5α, a Major Postentry Block TRIM-Cyp: Evolution of a Restriction Factor by Gene Fusion Mov10 Lv2: An Entry-Specific Block APOBECs, the Cytidine Deaminases SAMHD1, a Nucleotidase MX2, Another Factor Targeting Capsid SUN2 More Restriction Factors? Sensing and Responding to Infection: Innate Immunity TRIM5α as Sensor RIG-I and MDA5 as Retroviral Sensors cGAS Involvement in Sensing Infection IFI16, a DNA Sensor TREX1, a Nuclease Applications for Therapy Conclusions: Parting Words References Chapter-3---Nucleoporins-in-Retroviral-Replication--W_2018_Retrovirus-Cell-I 3 - Nucleoporins in Retroviral Replication: What’s Nup Got to Do with It? Nuclear Pore Complexes, Nucleoporins, and Nucleocytoplasmic Transport Nucleoporins Implicated in Retroviral Replication Normal Cellular Functions of the Nup358/RanBP2 Nuclear Pore Complex Protein Functions of Nu358/RanBP2 in Retroviral Replication Normal Cellular Functions of the Nup214/CAN Nuclear Pore Complex Protein Functions of Nup214/CAN in Retroviral Replication Normal Cellular Functions of the Nup98 Nuclear Pore Complex Protein Functions of Nup98 in Retroviral Replication Normal Cellular Functions of the Nup85 and Nup160 Components of the Nup107–160 Nuclear Pore Complex Functions of the Nup107–160 Complex (Y-Complex) during Retroviral Replication Normal Cellular Functions of the Nup62 Nuclear Pore Complex Protein Functions of Nup62 in Retroviral Replication Normal Cellular Functions of the Nup155 Nuclear Pore Complex Protein Functions of Nup155 in Retroviral Replication Normal Cellular Functions of the Nup153 Nuclear Pore Complex Protein Functions of Nup153 in Retroviral Replication Normal Cellular Functions of the Tetratricopeptide Repeat Nuclear Pore Complex Protein Functions of Tetratricopeptide Repeat in Retroviral Replication Caution: Depletion of Any Single Multifunctional Nup Can Modify Overall NPC Architecture The Importance of FG-Repeat Nups to Disease Viruses Commonly Cause the Displacement of FG–Nups to Remodel NPCs Acknowledgments References Chapter-4---Virus-Host-Interactions-in-Retroviru_2018_Retrovirus-Cell-Intera 4 - Virus–Host Interactions in Retrovirus Integration Introduction Integrase-Interacting Proteins Lentiviruses Lens Epithelium–Derived Growth Factor/p75 Hepatoma-derived Growth Factor LIKE 2 (HDGFL2) Gammaretroviruses Bromodomain and Extra-Terminal Domain Proteins Deltaretroviruses B′-Protein Phosphatase 2A (PP2A) Gag-Interacting Proteins HIV-1 CA–Interacting Proteins Foamy Virus Allosteric IN Inhibitors That Target the LEDGF/p75–IN Interaction Conclusions Acknowledgments References Chapter-5---Transcriptional-Control-and-Latency-o_2018_Retrovirus-Cell-Inter 5 - Transcriptional Control and Latency of Retroviruses Introduction Retroviral Integration Occurs at Transcriptionally Active Sites in Host Genome Transcriptional Regulation by Endogenous Retroviruses Retroviral Elements Are Prominent in All Jawed Vertebrate Genomes Endogenous Retroviruses Can Function as Long-Range Transcriptional Enhancers Endogenous Retroviruses Regulate the Potency of Stem Cells Retroviral Genome Complexity Confers a Benefit for Transcriptional Regulation Transcriptional Regulation in Simple Retroviruses Retroviral Capture of Cellular Genes for Transcription Factors or Signaling Kinases Retroviral Use of Hormone Response Elements in Long Terminal Repeat Enhancer Transcriptional Silencing of Simple Retroviruses Complex Retroviruses Encode Transactivator Proteins Transcriptional Control of HIV-1 Clinical Importance of HIV-1 Proviral Transcription HIV-1 5′ Long Terminal Repeat Contains the Viral Promoter and Enhancer RNA Polymerase II Transcriptional Initiation of the HIV-1 Provirus HIV-1 Tat Activates RNA Polymerase II Elongation Tat and P-TEFb CDK11 and HIV-1 3′ End Processing HIV-1 Latent Infection Establishment of Latent Infection Maintenance of Latent Infection Reactivation of Latent Virus Future Research of Retroviral Transcription HIV-1 Latency and the Need for a Functional Cure Endogenous Retroviruses in Stem Cells and Cancer Acknowledgments References Chapter-6---Teetering-on-the-Edge--The-Critical-Role-of-_2018_Retrovirus-Cel 6 - Teetering on the Edge: The Critical Role of RNA Processing Control During HIV-1 Replication Introduction Role of hnRNPs in the Regulation of HIV-1 RNA Processing Role of SR Proteins in the Regulation of HIV-1 RNA Processing Manipulation of HIV-1 RNA Processing With Small Molecules Acknowledgments References Chapter-7---Cellular-RNA-Helicases-Support-Early-and-L_2018_Retrovirus-Cell- 7 - Cellular RNA Helicases Support Early and Late Events in Retroviral Replication RNA Helicase and Retroviruses in the Advent of “Omics Technology” Early Events: Reverse Transcription and Integration DHX9/RNA Helicase A Activity in the Genomic RNP MOV10 Activity in Virions Remains Undefined Late Events: Provirus Transcription, Primary RNA Processing, Export, Translation, Formation of Genomic RNP DHX9, Bridging RNA Polymerase to Transcription Coactivators Shuttling RNA Helicase in Nucleocytoplasmic Transport of Retroviral RNA Nuclear Cap–Binding Proteins and RNA Helicase: Translation Evading Nonsense RNA–Mediated Decay Steady-State Translation: Switching 5′Cap–Binding Proteins to Gain eIF4E Therapeutic Targeting at the Interface of RNA Helicase and Cognate Retroviral RNA References Chapter-8---Role-of-Host-Factors-in-the-Subcellular-Traff_2018_Retrovirus-Ce 8 - Role of Host Factors in the Subcellular Trafficking of Gag Proteins and Genomic RNA Leading to Virion Assembly Introduction Nuclear Export of Viral RNAs Unspliced Viral RNA Export in Simple Retroviruses The Constitutive Transport Element of MMTV Export of Unspliced RNA in Rous Sarcoma Virus Spumaretrovirus RNA Nuclear Export Retroviral Genome Trafficking in the Cytoplasm Relationship Between Viral RNA Export and Virus Assembly Transport of Unspliced Viral RNA Through the Cytoplasm to the Assembly Site Dimerization of Retroviral Genomic RNA Retroviral Gag Protein Trafficking Nuclear Trafficking of Retroviral Gag Proteins Foamy Virus Gag Association With Chromatin Transport of Gag Proteins in the Cytoplasm Role of Cytoskeletal Proteins and Microtubule-Organizing Center in Gag Transport Multivesicular Bodies and Endosomal Proteins in Gag Trafficking Role of Myristoylation and Lipid Binding in Gag Membrane Targeting Multivesicular Body and Endosomal Sorting Complexes Required for Transport Pathway Interactions With Gag Late Domains Nedd4 and E3 Ubiquitin Ligases Tsg101 as a Central Player in Wide Range of Gag Late Domain Interactions Alix/AIP-1 Interactions With HIV Gag Proteins Late Domains in EIAV, MLV, and Foamy Virus Gag Proteins Endophilin 2 in Murine Leukemia Virus Gag Trafficking Association of Gag With tRNA Synthetases Factors That Interact With Gag or Viral RNA to Restrict Virus Replication Host Restriction Factors That Interfere With Gag Functions Early or Late in Replication Concluding Remarks Acknowledgments References Chapter-9---Tumor-Suppressor-Gene-101--A-Virus--Multifun_2018_Retrovirus-Cel 9 - Tumor Suppressor Gene 101: A Virus’ Multifunctional Conduit to the ESCRT Trafficking Machinery Introduction The Endosomal Sorting Complex Required for Transport Machinery ESCRT-0 ESCRT-I ESCRT-II ESCRT-III Endosomal Sorting Complexes Required for Transport Participation in Cellular Processes Endosomal Sorting Complexes Required for Transport Participation in Virus Budding Tumor Suppressor Gene 101 Structure Tsg101-UEV Domain Tsg101-UEV PTAP-Binding Pocket Tsg101-UEV Ub-Binding Pocket Ub- and PTAP-Binding Pockets: Is There Cross Talk? Tumor Suppressor Gene 101 Participation Tumor Suppressor Gene 101 Participation in the Cellular Endocytic Pathway Tumor Suppressor Gene 101 Participation in Virus Budding Cellular Factors That Work With Tumor Suppressor Gene 101 Convergence of Tsg101-Ub-Nedd4-Alix Participation Tumor Suppressor Gene 101 Role in Budding of Other Viruses Questions Remaining Acknowledgments References Index_2018_Retrovirus-Cell-Interactions Index A B C D E F G H I J K L M N O P R S T U V X Y Z Backcover