Roles of Host Gene and Non-coding RNA Expression in Virus Infection (Current Topics in Microbiology and Immunology Book 419)

"This volume discusses the interactions between viruses and their host cells, and explores the roles of host and viral genes and non-coding RNAs in the virus replication cycle. During infection, viruses express a variety of genes, encoding proteins and RNAs that serve to subjugate the cell -- by redirecting cellular processes to support viral replication and, at the same time, by mitigating the cellular response to infection. In this book, experts discuss these interactions in depth, and elaborate on our current understanding of virus-cell interactions for a diverse range of viruses, including positive and negative sense RNA viruses, DNA viruses, and a vector-borne virus. The roles of non-coding RNAs are also discussed. While each class of viruses has distinct replication requirements, this volume reveals unique features and commonalities in viral replication cycles. Accordingly, it represents a valuable source of information for researchers and clinicians alike."--Back cover Preface 6 Contents 8 25 Host Factors in Coronavirus Replication 9 Abstract 9 1 Introduction 10 2 Host Receptors Involved in Coronavirus Entry 14 3 Translation and the Unfolded Protein Response in Coronavirus-Infected Cells 16 4 Coronavirus-Induced Modification of Host Cell Membranes 18 5 Host Proteins Interacting with the Coronavirus Genome and Its Replication or Expression 21 6 Host Innate Immune Responses Against Coronaviruses, and Viral Countermeasures 24 7 Coronavirus-Induced Deregulation of the Cell Cycle 27 8 The Role of Cyclophilins in Coronavirus Replication 29 9 Systems Biology Approaches to Identifying Host Factors in Coronavirus Replication 31 10 Concluding Remarks 35 References 36 26 Roles of Pro-viral Host Factors in Mosquito-Borne Flavivirus Infections 51 Abstract 51 1 Introduction 52 2 Anti- and Pro-viral Host Factors 52 2.1 Attachment 53 2.1.1 Glycosaminoglycans 53 2.1.2 C-Type Lectin Receptors 53 2.1.3 Phosphatidylserine Receptors 55 2.1.4 Fc Receptors and Antibody-Dependent Enhancement of Attachment and Entry 56 2.1.5 Other Receptor Types 56 2.2 Endocytosis 57 2.3 Uncoating 58 2.4 Viral Translation 58 2.4.1 Translation Initiation 58 2.4.2 RNA Recruitment to the ER 59 2.4.3 Translation Elongation 60 2.4.4 Translation Termination and Recycling 60 2.4.5 Ribosomal Proteins 60 2.4.6 Polyprotein Biogenesis and Processing 61 2.5 Viral RNA Synthesis 62 2.5.1 Replication Complex (RC) Formation and RNA Synthesis 62 2.5.2 RNA-Binding Proteins 63 2.6 Particle Assembly 64 2.7 Particle Egress 65 2.7.1 Glycosylation 66 2.7.2 Furin-like Protease Cleavage 66 Acknowledgements 66 References 67 29 Role of Innate Genes in HIV Replication 76 Abstract 76 1 Introduction 77 2 Sensors of the Innate Response 78 2.1 TLR Sensors 78 2.2 Cytosolic Sensors 78 3 HIV-1 Utilizes or Avoids Cellular Factors to Escape Sensing 82 3.1 Cloaking of HIV-1 Cargo 82 3.2 Exploitation of a Cellular Nuclease 83 3.3 Active Exploitation of NLRX1 83 3.3.1 NLRX1—A Regulator of Innate Signaling 83 3.3.2 NLRX1—A Negative Regulator of HIV-1 Sensing 86 3.3.3 Localization of NLRX1 and Signal Components 87 3.3.4 Possible Impact of NLRX1 on Latent Reservoirs 88 4 Restriction Factors as Effectors of the Innate Response 89 5 SAMHD1—HIV-1 is Passively Avoiding Restriction 89 5.1 Discovery of SAMHD1 89 5.2 SAMHD1 Enzymatic Functions 96 5.3 SAMHD1 Involved in Innate Immunity 98 6 Conclusion 100 Acknowledgements 100 References 100 27 Host Factors Involved in Ebola Virus Replication 119 Abstract 119 1 Introduction 120 2 Host Factors Required for Cell Entry and Fusion 120 2.1 Attachment Factors 121 2.2 Endosomal Uptake 123 2.3 Glycoprotein Processing and Fusion 123 3 Host Factors Required for Viral Transcription and Translation 124 3.1 Viral Gene Expression and Genome Replication 125 3.2 Viral Protein Synthesis 126 4 Host Factors Required for Assembly and Egress 127 5 Antagonism of Antiviral Responses 129 5.1 Innate Immune Antagonism 130 5.2 Adaptive Immune Antagonism 132 6 Cell and Tissue-Specific Host Factors Involved in Pathogenesis 133 7 Conclusion 138 References 139 30 Role of Host Genes in Influenza Virus Replication 157 Abstract 157 1 Introduction 158 2 Approaches to Identify Host Factors Required by Viruses 159 2.1 Screening Approaches for Host Dependency Factors 159 2.2 Methods to Identify Interaction Partners of Viral Proteins 161 2.3 Additional Methods to Identify Host Factors Related to Virus Infection 162 3 Host Factors Involved in the Influenza Virus Entry Process 164 3.1 Binding and Internalization of Influenza A Virus 167 3.2 Endosomal Trafficking and Fusion 168 3.3 Uncoating and Nuclear Import of the vRNPs 170 4 Host Factors Involved in Viral Replication and Transcription 171 4.1 Genome-Wide “OMIC” Studies on the Replication Complex 172 4.2 Requirements for Transcription 172 4.3 Requirements for Viral RNA Synthesis 173 4.4 Requirements for Replication 174 4.5 Requirements for Viral mRNA Splicing 174 5 Host Factors Involved in Nuclear Export, Trafficking, and Budding 175 5.1 Nuclear Export of RNPs 176 5.2 Trafficking to the Plasma Membrane 178 5.2.1 Cytoplasmic Transport of RNPs 178 5.2.2 Transport of Viral Membrane Proteins 179 5.2.3 Budding and Release of Virus Particles 180 6 The Role of Host Factors in Zoonotic Transmission of Influenza Virus 180 6.1 Restriction of Zoonotic Transmission by Host-Specific Distribution of Sialic Acids 181 6.2 Restriction of Zoonotic Transmission by the Host Protein ANP32A 182 7 Host Factors for Antiviral Drug Development 183 References 183 28 A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease 196 Abstract 196 1 Introduction of Henipaviruses 197 1.1 Discovery and Classification 197 1.2 Natural Reservoir and Other Novel Henipaviruses 199 2 Functional Genomics Analysis of Henipavirus Infection 199 2.1 Platforms for Functional Genomics and Challenges for Studying BSL-4 Pathogens 199 2.2 Functional Genomics Studies on Henipaviruses 200 3 The Reliance of Henipavirus Infection on Nuclear and Nucleolar Proteins 201 3.1 Genome-Wide RNAi Screening 201 3.2 Fibrillarin and Its Role in Henipavirus Infection 202 3.3 Modulation of Translation in Henipavirus Infection 204 4 Viral Targets Within the Host Cell Nucleus 205 4.1 Role of the M Protein in the Henipavirus in Infection Cycle 205 4.2 The Impact of M-Binding Host Proteins on Hendra Virus Infection 206 5 Host Proteins Targeted by Henipaviruses for Immune Evasion 207 5.1 Immune Modulating Function of P-Encoded Proteins 207 5.2 Targeting of STAT by Henipaviruses 210 5.3 Novel Function of the M Protein in Immune Evasion 211 6 The Impact of Host-Encoded MicroRNAs on Henipavirus Infection 211 6.1 Role of MicroRNAs in Viral Infection 211 6.2 Host-Encoded MicroRNAs and Henipavirus Infection 212 7 Concluding Remarks 213 References 214 32 Roles of Non-coding RNAs in Respiratory Syncytial Virus (RSV) Infection 219 Abstract 219 1 RSV 220 1.1 Etiology and Management 220 1.2 RSV Genome 221 2 Organization and Classification of Non-coding RNAs in the Human Genome 221 2.1 microRNAs (miRNAs) 223 2.1.1 miRNA Biogenesis 224 2.1.2 Mechanism of miRNA Action 224 2.1.3 Theater of miRNA Function 224 2.2 Transfer RNA Fragments (tRFs) 225 3 Non-coding RNA Function in RSV Replication 226 3.1 miRNA Regulation of Host Gene Expression 226 3.2 Viral Regulators of Host miRNA Expression 228 3.3 miRNA Biomarkers of RSV Disease 229 3.4 Biogenesis and Function of transfer RNA Fragments During RSV Infection 230 4 miRNA Regulation of the Immune Response 232 4.1 Innate Immune Response 232 4.2 Adaptive Immune Response 233 5 Future Directions 235 References 235 31 Roles of Non-coding RNAs During Herpesvirus Infection 246 Abstract 246 1 Introduction 248 2 Non-coding RNAs Made by Herpesviruses 248 2.1 Herpesvirus-Encoded MiRNAs: The Short of It 249 2.2 Biogenesis of Viral MicroRNAs 252 2.3 Other Herpesvirus Small NcRNAs 253 2.4 The Long(er) Non-coding RNAs 254 3 Functions of Viral LncRNAs 256 3.1 Roles in Metabolic Processes and Apoptosis 257 3.2 Viral Long NcRNAs Modify Viral Gene Expression 257 4 Small Silencers of Viral Gene Expression 259 4.1 Host Silencers of Viral Gene Expression 260 5 Viral MiRNA Regulation of Transcription Factors 261 6 Mimicry of Host MiRNA Function 262 7 Cataloging Targets Reveals Diversity in Networks Regulated by Viral MiRNAs 263 8 Combinatorial Targeting and MiRNA Synergy 265 9 Unique Interplay Between Herpesviruses and Cellular MiRNAs 266 10 In Vivo Phenotypes of Herpesvirus NcRNAs 267 10.1 Viral Small NcRNA Phenotypes in Natural Hosts 268 10.2 In Vivo Phenotypes of LncRNA Knockouts 270 11 Summary and Outlook 271 Acknowledgements 272 References 272 Front Matter ....Pages i-vii Host Factors in Coronavirus Replication (Adriaan H. de Wilde, Eric J. Snijder, Marjolein Kikkert, Martijn J. van Hemert)....Pages 1-42 Roles of Pro-viral Host Factors in Mosquito-Borne Flavivirus Infections (Rafael K. Campos, Mariano A. Garcia-Blanco, Shelton S. Bradrick)....Pages 43-67 Role of Innate Genes in HIV Replication (Kerstin Schott, Maximilian Riess, Renate König)....Pages 69-111 Host Factors Involved in Ebola Virus Replication (Angela L. Rasmussen)....Pages 113-150 Role of Host Genes in Influenza Virus Replication (Megan L. Shaw, Silke Stertz)....Pages 151-189 A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease (Cameron R. Stewart, Celine Deffrasnes, Chwan Hong Foo, Andrew G. D. Bean, Lin-Fa Wang)....Pages 191-213 Roles of Non-coding RNAs in Respiratory Syncytial Virus (RSV) Infection (Ralph A. Tripp, Abhijeet A. Bakre)....Pages 215-241 Roles of Non-coding RNAs During Herpesvirus Infection (Meaghan H. Hancock, Rebecca L. Skalsky)....Pages 243-280