Principles of Virology. Jane Flint

cell line?

      3 The S (spike) glycoprotein of coronaviruses can engage receptors by the N-terminal domain, the C-terminal domain, or both. The C-terminal domains of both human SARS coronaviruses bind ACE2 (angiotensin-converting enzyme 2) whereas that of MERS-CoV binds DDP4 (dipeptidyl peptidase 4). In contrast, in mouse hepatitis coronavirus (MHV) the N-terminal domain of S binds CEACAM (cell adhesion molecule 1). You have identified a novel coronavirus with an S protein that displays similarity to MHV at the N terminus and to SARS at the C terminus. What are the molecules most likely to function as receptors and how will you test this?

      4 Viral fusion proteins mediate fusion between the viral and cellular membranes. This process begins with the insertion of fusion peptides or loops into the target cellular membrane; however, this step alone is not sufficient to complete the fusion process. Describe how additional conformational changes drive fusion.

      5 Which of the following statements is correct?Non-enveloped virus entry does not depend on binding to a receptor.For enveloped viruses with multiple envelope proteins on their surface, all envelope proteins engage cell surface receptors.Viral fusion proteins on the surface of enveloped viruses cannot engage a receptor.Fusion of enveloped viruses can occur at the plasma membrane or at compartments of the endosomal pathway.

      6 What experiments would you perform to determine whether endosome acidification is required for entry by a particular virus?

      7 You produce a viral fusion protein in cells and cocultivate them with cells expressing the receptor. Would you observe cell-to-cell fusion? If you don’t observe this result, what are the possible explanations?

      8 Describe the ways in which viral and subviral particles can be transported inside the cell.

      9 What are the potential disadvantages for a virion reaching the lysosome?

      10 Which of the following pathways would achieve delivery of the viral genome to the nucleus?Delivery of the viral genome to the cytoplasmic side of the nuclear poreHaving a capsid smaller than 39 nmDocking of a partially uncoated capsid to the nuclear pore that does not result in further uncoating or transport through the poreInteraction of the capsid with components of the nuclear pore that leads to subsequent transport and uncoating in the nucleus

      11 For retroviruses that rely on cell division to access the host chromatin, how does the viral genome remain in the nucleus once cell division is completed?

6 Synthesis of RNA from RNA Templates

        Introduction

        The Nature of the RNA Template Secondary Structures in Viral RNA Naked or Nucleocapsid RNA

        The RNA Synthesis Machinery Identification of RNA-Dependent RNA Polymerases Three-Dimensional Structures of RNA-Dependent RNA Polymerases

        Mechanisms of RNA Synthesis Initiation Capping Elongation Functions of Additional Polymerase Domains RNA Polymerase Oligomerization Template Specificity Unwinding the RNA Template Role of Cellular Proteins

        Paradigms for Viral RNA Synthesis (+) Strand RNA Synthesis of Nested Subgenomic mRNAs (−) Strand RNA Ambisense RNA Double-Stranded RNA Unique Mechanisms of mRNA and Genome Synthesis of Hepatitis Delta Virus Do Ribosomes and RNA Polymerases Collide?

        Origins of Diversity in RNA Virus Genomes Misincorporation of Nucleotides Segment Reassortment and RNA Recombination RNA Editing

        Perspectives

        References

        Study Questions

      LINKS FOR CHAPTER 6

       Video: Interview with Dr. Karla Kirkegaard http://bit.ly/Virology_Kirkegaard

       A swinging gate http://bit.ly/Virology_Twiv330

When a thing has been said and said well, have no scruple. Take it and copy it.

      ANATOLE FRANCE

Introduction

The genomes of RNA viruses may be unimolecular or segmented; single stranded of (+), (−), or ambisense polarity; double stranded; or circular. These structurally diverse viral RNA genomes share a common requirement: they must be copied efficiently within the infected cell to provide both genomes for assembly into progeny virus particles and messenger RNAs (mRNAs) for the synthesis of viral proteins. The production of these RNA molecules is a unique process that has no parallel in the cell. The genomes of all RNA viruses except retroviruses and hepatitis delta virus encode an RNA-dependent RNA polymerase (RdRP) (Box 6.1) to catalyze the synthesis of new genomes and mRNAs.

      Virus particles that contain (−) strand or double-stranded RNA genomes must contain the RdRP, because the incoming viral RNA can be neither translated nor copied by the cellular machinery. Consequently, the deproteinized genomes of (−) strand and double-stranded RNA viruses are not infectious. In contrast, viral particles containing a (+) strand RNA genome lack a viral polymerase; the deproteinized RNAs of these viruses are infectious because they are translated in cells to produce, among other viral proteins, the viral RNA polymerase. An exception is the retrovirus particle, which contains a (+) stranded