Virus Infected Cells

✍ Scribed by Swetha Vijayakrishnan; Yaming Jiu; J. Robin Harris

• Publisher: Springer Nature
• Year: 2023
• Tongue: English
• Leaves: 460
• Category: Library

✦ Synopsis

Virus-infected Cells is a comprehensive and technical exploration of the intricate interactions between viruses and host cells. This book delves into the molecular and cellular aspects of viral infections, providing a wealth of knowledge about various viruses and their effects on cellular mechanisms. The first part of the book covers general/technical aspects, introducing the reader to the field of virology and providing an overview of the techniques used to study virus-infected cells. It covers topics such as the visualisation of virus-infected cells by cryo-electron tomography and the assessment of necroptosis, a type of programmed cell death, in virus-infected cells. In addition, the book explores the role of apoptosis and phagocytosis as antiviral mechanisms, as well as the intricate process of viral membrane fusion and penetration. It also discusses the tracking of viral entry into living cells and the use of correlative cryo-imaging to study the biology of viruses in cells and tissues. Finally, the book examines the cytopathic effect induced by viruses, shedding light on the damage caused to infected cells. The second section of the book explores specific viruses and their interactions with host cells. Each chapter focuses on a specific virus and provides an in-depth look at its behaviour within infected cells. The book covers a wide range of viruses, including human papillomavirus, respiratory syncytial virus, Japanese encephalitis virus, African swine fever virus, coronavirus, influenza A virus and human endogenous retroviruses. Each chapter examines unique aspects of virus-host interactions, such as viral assembly, impact on the cytoskeleton, critical host-virus interactions mediated by viral RNA, mechanisms of cell entry, and the involvement of cholesterol in virus budding and scission. This volume in the Subcellular Biochemistry series is a valuable resource for researchers, virologists and students interested in understanding the complex dynamics between viruses and the cells they infect. With its detailed exploration of general and specific aspects of virus-host interactions, this book provides a comprehensive understanding of the molecular and cellular mechanisms involved in viral infections.

✦ Table of Contents

Preface
Contents
Part I: General/Technical Aspects
Chapter 1: In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview
Introduction
Sample Preparation
Data Collection and Image Processing
Integrative Techniques
Cryo-serial Block Face Scanning Electron Microscopy
Cryo-soft X-Ray Tomography
Cryo-correlative Light and Electron Microscopy
Cryo-ET Studies of Enveloped Viruses and Their Interactions Within the Host Cell
Cryo-ET of Purified Enveloped Viruses
Human Immunodeficiency Virus (HIV-1)
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Other Enveloped Viruses
In Situ Cellular Cryo-ET Enables Peering into the Cell
Probing Enveloped Viral Infections and Molecular Mechanisms of Virus-Host Interactions
Viral Disassembly and Genome Release
Viral Factories Are Sites of Viral Replication
Enveloped Positive-Strand RNA Viruses
Enveloped Negative-Strand RNA Viruses
Viral Assembly and Egress
Concluding Remarks and Perspectives
References
Chapter 2: Approaches to Evaluating Necroptosis in Virus-Infected Cells
Introduction
Necroptosis Pathway and Players
Necroptosis Inhibitors
In Vitro Necroptosis in Cultured Cells
In Vivo Models of Necroptosis
Cellular Patterns and Methods to Evaluate Necroptosis
Metabolic Viability Assays
Membrane Integrity Assays
Necroptosis Morphology
Immuno-techniques
The Viruses That Activate or Inhibit Necroptosis
DNA Viruses
Herpesviruses
Murine Cytomegalovirus
Human Cytomegalovirus
Herpes Simplex Viruses
Poxviruses
RNA Viruses
Influenza A
Reovirus
Respiratory Syncytial Virus
SARS-CoV-2
Flaviviruses
Rotavirus
Conclusion
References
Chapter 3: Apoptosis and Phagocytosis as Antiviral Mechanisms
Introduction
Virus Life Cycle, Classification, and Infection
Changes in Host Cells After Viral Infection
Alteration of Gene Expression
Changes in Cell Surface Structures
Apoptosis and Viral Resistance to Apoptosis
Cellular and Humoral Immune Responses Against Virus Infection and the Possible Induction of Cytokine Storm
Roles for Phagocytosis in the Prevention and Progression of Viral Diseases
Phagocytosis of Virus-Infected Cells as Innate Immune Response
Consequences of Apoptosis-Dependent Phagocytosis of Virus-Infected Cells
Perspectives
References
Chapter 4: The Art of Viral Membrane Fusion and Penetration
General Terminology and Mechanisms of How Viruses Cross Host Membranes
Viral Membrane Fusion and Membrane Fusion Proteins
Conformational States of Viral Fusion Proteins
Membrane Penetration by Non-enveloped Viruses
Proteinaceous Pore-Forming Viruses
Viruses Utilizing Lytic Peptide-Driven Membrane Penetration
Lipid-Modifying Membrane Rupturing Viruses
Visualization of Viral Membrane Fusion and Penetrations Using Cryo-electron Tomography
Endosomal Lipids as Regulators of Membrane Fusion
Effect of Lipid Curvature
Effect of Lipid Charge
Host Restriction Factors Controlling Viral Membrane Fusion and Penetration by Modulating the Endosomal Lipid Composition
Role of Viral Uncoating in Membrane Fusion
Inhibitors of Viral Membrane Fusion
Conclusion
Glossary
References
Chapter 5: Single-Particle Tracking of Virus Entry in Live Cells
Introduction
Dynamic Entry of Viruses into Host Cells
Virus-Receptor Interactions
Virus Internalization
Virus Transport
Virus Uncoating
Fluorescent Labeling of Viruses and Cellular Components
Fluorescent Proteins
Organic Dyes
Quantum Dots
Microscopy Methods and Image Processing
Microscopy Configurations
Image Processing
Concluding Remarks
References
Chapter 6: Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues
Soft X-Ray Technique
SXT Principles and Advantages
SXT Data Collection
Use of SXT in Viral Studies
Extending the Information Content of SXT Data in the Context of Correlative Microscopy Schemes
Sample Preparation and B24 Experimental Workflow
SXT Correlative Schemes in the Service of Virus Research
Reovirus
Hepatitis C Virus
Challenges and Prospects
References
Chapter 7: The Virus-Induced Cytopathic Effect
Introduction
Cytopathic Effects across Viral Species
Approaches to Studying the Cytopathic Effect
Bright-Field Microscopy
Fluorescence Microscopy
Immunofluorescence Assay (IFA)
Labeling with Fluorescent Dyes
Plaque Assay
Monitoring of the Cytopathic Effect and Its Relevance
Cellular Tropism Evaluation
Antiviral Drug Screening
Neutralizing Antibodies Assessment
Conclusions
References
Part II: Specific Viruses
Chapter 8: Human Papilloma Virus-Infected Cells
Introduction
HPV Entry into Its Target Cells
HPV Endocytosis as a Journey to the Nucleus
Replication and Transcription of the HPV Genome
Exocytosis and Exit toward a New Infection
Conclusions
References
Chapter 9: Defining the Assembleome of the Respiratory Syncytial Virus
Respiratory Syncytial Virus Infection Is a Global Health Problem
The Genetic Structure of RSV
RSV Particle Morphogenesis at the Assembleome
Interactions between the Virus Membrane Structural Proteins at the Assembleome
RSV Particles Form as Filamentous Structures at the Assembleome on Infected Cells
The Assembleome Forms at Lipid Raft Microdomains on the Surface of Infected Cells
Filamentous Actin (F-Actin) Remodeling at Lipid Raft Microdomains at the Assembleome Drives Virus Filament Formation
Trafficking of the rac1 and rhoA Proteins to the Assembleome Is Required for Virus Filament Formation
Future Perspectives
References
Chapter 10: Japanese Encephalitis Virus-Infected Cells
Introduction
Epidemiology
Transmission Cycle
Clinical Features
JEV Molecular Biology
Infection Route: A Cellular Overview
Cellular Response to Infection
Alteration of Signalling Pathways
PKR Activation and Formation of Stress Granules
Induction of Oxidative Stress
Activation of the Unfolded Protein Response
Upregulation of Autophagy
Innate Immune Activation
Cell Death Pathways
Downregulation of Cell Adhesion Molecules
Metabolic Reprogramming
Infection Route: A Host Overview
Infection Route in the Periphery
Peripheral Immune Response to Infection
Virus Entry into the CNS
CNS Response to Infection
Perspectives
References
Chapter 11: African Swine Fever Virus Host-Pathogen Interactions
Introduction
Virus Replication
Virion Structure
Virus Entry
Early Steps in Replication
Virus Factories
Membranes
Cytoskeleton
Programmed Cell Death
Autophagy
Interferon Response
Type I Interferons
Induction of Type I Interferon Expression
Interferon Regulatory Factors
Nuclear Factor κB
Transmembrane Pathogen Recognition Receptors
Cytosolic Pathogen Recognition Receptors
IFN-Mediated Signalling
ASFV Modulation of the IFN Response
Inhibition of IFN Induction at the Level of Transcription Factors or Their Activation
Inhibition of Specific PRRs Pathways
Inhibition of IFN-Mediated Signalling
Cellular Stress
Secretory Pathway
Concluding Remarks
References
Chapter 12: Coronavirus and the Cytoskeleton of Virus-Infected Cells
Introduction to the Cytoskeleton
Cytoskeleton
Actin Filaments
Microtubules
Intermediate Filaments
Coronavirus
The Structure and Life Cycle of Coronavirus
SARS-CoV-2 and COVID-19 Infection
Hazards of Other Virus Infections
Response of the Host Cell Cytoskeleton Network Following Coronavirus Infection
Coronavirus Infection Induces Expression Level or Posttranslational Modification Changes of the Cytoskeleton and its Related P...
Coronavirus Infection Induces Actin Filament Rearrangement
Microtubules Are Hijacked by Coronavirus for Trafficking
Detection of Intermediate Filament Changes upon Infection
Host Cytoskeleton Participates in Coronavirus Life Cycle
Host Cytoskeleton Protein Facilitates Coronaviral Internalization
Host Cytoskeleton Affects Coronaviral Replication
Host Cytoskeleton Participates in the Coronaviral Assembly Process
Coronaviral Release Can Be Promoted by Cytoskeleton Proteins
Cytoskeleton and Pathogenesis
The Ciliary Structure Is Involved in the Pathogenic Process
Lung Injury Caused by SARS-CoV-2 Is Related to Endothelial Cell Permeability Regulation
Relationship with the Nervous System
Possibilities of Cytoskeleton-Related Treatment of COVID-19
Summary
References
Chapter 13: Viral RNA Is a Hub for Critical Host-Virus Interactions
Introduction: RNA-Binding Proteins Are at the Core of Virus Infection
RNA-Binding Proteins, Structure and Function
The Expanding Universe of Cellular RNA-Binding Proteins
The Essential Roles of Viral RBPs in Infection
Virus Infection Profoundly Remodels the Cellular RNA-Binding Proteome (RBPome)
How Are Cellular RBPs Regulated by a Virus Infection?
New Methods to Uncover the Viral RNA Interactome
Methods to Uncover the Viral RNA Interactome
Viral RNA Is a Hub for Critical and Conserved Host-Virus Interactions
RBPs Involved in Innate Immunity
RNA Stability and Degradation
Protein Synthesis
Outlook
References
Chapter 14: Influenza A Virus: Cellular Entry
Molecular Mechanisms of Influenza A Virus Entry
Uncoating Reaction In Vitro
Application to Coronavirus Endosomal Uncoating
Conclusions
References
Chapter 15: Human Endogenous Retroviruses in Diseases
HERV Functions
Introduction to ERVs
Classification of HERVs
Human Endogenous Retrovirus-K (HML-2)
HERV-H
Replication of HERVs
HERVs as Transcriptional Regulators
HERVs as Promoters or Enhancers
HERV-Encoded Proteins
HERV-Derived ncRNAs or dsRNAs
HERVs May Alter Gene Structure or Yield Antisense Sequences
HERV Biological Functions
Physiological Functions Involving HERVs
HERVs Involved in Human Diseases
HERV Involvement in Viral Diseases
HERVs Associated with Retroviral Infections
HERVs Associated with RNA Virus Infections
HERVs Associated with DNA Virus Infections
HERVs and Epigenetic Modifications
Retroviruses and Epigenetics
HERVs and DNA Methylation
Epigenetic Suppression of HERV Expression
Epigenetic Activation of HERVs
HERVs and DNA Acetylation
The Mechanisms of HERVs in Antiviral Immunity
The Roles of HERVs in Therapy
Therapies Targeting HERVs
Specific Monoclonal Antibodies (mAbs)
Chimeric Antigen Receptor T Cells (CAR-T)
Epigenetic Modifications
Therapies Utilizing HERV Tools
HERVs as Vaccine Carriers
LTR as a Retrotransposon Homolog
References
Chapter 16: Cholesterol and M2 Rendezvous in Budding and Scission of Influenza A Virus
Introduction
Methods
Experimental Techniques
Theoretical Modeling and Simulation
Biomolecules and Interactions Driving Budding and Scission
Initiation of Budding
Virion Assembly
Scission of the Budding Neck
A Contemporary Hypothesis on the Roles of Cholesterol and M2
Conclusion
References
Further Reading
Correction to: In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview
Correction to: Chapter 1 in: S. Vijayakrishnan et al. (eds.), Virus Infected Cells, Subcellular Biochemistry 106, https://doi....