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9.1 General Properties of Viruses
Virus: genetic element that cannot replicate independently of a living (host) cell Virology: the study of viruses Virus particle (virion): extracellular form of a virus Exists outside host and facilitates transmission from one host cell to another Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material © 2012 Pearson Education, Inc.
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9.1 General Properties of Viruses
Viral Genomes (Figure 9.1) Either DNA or RNA genomes Some circular, but most linear © 2012 Pearson Education, Inc.
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dsDNA (Hepadnaviruses)
Figure 9.1 RNA DNA viruses DNA viruses RNA viruses Viral Class ssRNA (Retroviruses) dsDNA (Hepadnaviruses) Viral Genome ssDNA dsDNA ssRNA dsRNA Figure 9.1 Viral genomes. © 2012 Pearson Education, Inc.
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9.2 Nature of the Virion Viral Structure
Capsid: the protein shell that surrounds the genome of a virus particle (Figure 9.2) Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid Capsomere: subunit of the capsid Smallest morphological unit visible with an electron microscope © 2012 Pearson Education, Inc.
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Structural subunits (capsomeres)
Figure 9.2 18 nm Structural subunits (capsomeres) Virus RNA Figure 9.2 The arrangement of nucleic acid and protein coat in a simple virus, tobacco mosaic virus. © 2012 Pearson Education, Inc.
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9.2 Nature of the Virion Viral Structure (cont’d)
Nucleocapsid: complete complex of nucleic acid and protein packaged in the virion (Figure 9.3) Enveloped virus: virus that contains additional layers around the nucleocapsid © 2012 Pearson Education, Inc.
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Naked virus Enveloped virus Envelope Nucleocapsid Capsid Nucleic acid
Figure 9.3 Nucleocapsid Envelope Capsid Nucleic acid Nucleic acid Capsid (composed of capsomeres) Figure 9.3 Comparison of naked and enveloped virus particles. Naked virus Enveloped virus © 2012 Pearson Education, Inc.
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9.2 Nature of the Virion Nucleocapsids constructed in highly symmetric ways Helical symmetry: rod-shaped viruses (e.g., tobacco mosaic virus) Length of virus determined by length of nucleic acid Width of virus determined by size and packaging of protein subunits Icosahedral symmetry: spherical viruses (e.g., human papillomavirus; Figure 9.4) Most efficient arrangement of subunits in a closed shell © 2012 Pearson Education, Inc.
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Symmetry 5-Fold 3-Fold 2-Fold Cluster of 5 units Figure 9.4
Figure 9.4 Icosahedral symmetry. Cluster of 5 units © 2012 Pearson Education, Inc.
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9.2 Nature of the Virion Enveloped Viruses (Figure 9.5a)
Have membrane surrounding nucleocapsid Lipid bilayer with embedded proteins Envelope makes initial contact with host cell Complex Viruses (Figure 9.5b) Virions composed of several parts, each with separate shapes and symmetries Bacterial viruses contain complicated structures Icosahedral heads and helical tails © 2012 Pearson Education, Inc.
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Head Collar Tail Tail pins Endplate Tail fibers Figure 9.5
Figure 9.5 Electron micrographs of animal and bacterial viruses. Endplate Tail fibers © 2012 Pearson Education, Inc.
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9.2 Nature of the Virion Some virions contain enzymes critical to infection Lysozyme Makes hole in cell wall Lyses bacterial cell Nucleic acid polymerases Neuraminidases Enzymes that cleave glycosidic bonds Allows liberation of viruses from cell © 2012 Pearson Education, Inc.
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9.3 The Virus Host Viruses replicate only in certain types of cells or in whole organisms Bacterial viruses are easiest to grow; model systems Animal viruses (and some plant viruses) can be cultivated in tissue or cell cultures Plant viruses typically are most difficult because study often requires growth of whole plant © 2012 Pearson Education, Inc.
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9.4 Quantification of Viruses
Titer: number of infectious units per volume of fluid Plaque assay: analogous to the bacterial colony; one way to measure virus infectivity (Figure 9.6) Plaques are clear zones that develop on lawns of host cells Lawn can be bacterial or tissue culture (Figure 9.7) Each plaque results from infection by a single virus particle © 2012 Pearson Education, Inc.
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Pour mixture onto solidified nutrient agar plate
Figure 9.6 Pour mixture onto solidified nutrient agar plate Nutrient agar plate Mixture containing molten top agar, bacterial cells, and diluted phage suspension Let solidify Plaques Sandwich of top agar and nutrient agar Incubate Figure 9.6 Quantification of bacterial virus by plaque assay using the agar overlay technique. Phage plaques Lawn of host cells © 2012 Pearson Education, Inc.
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9.5 General Features of Virus Replication
Phases of Viral Replication (Figure 9.8) Attachment (adsorption) of the virus to a susceptible host cell Entry (penetration) of the virion or its nucleic acid Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus Assembly of capsids and packaging of viral genomes into new virions (maturation) Release of mature virions from host cell © 2012 Pearson Education, Inc.
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Attachment (adsorption)
Figure 9.8 Virion DNA Attachment (adsorption) Cell (host) Protein coat remains outside Penetration (injection) Viral DNA enters Synthesis of nucleic acid and protein Assembly and packaging Figure 9.8 The replication cycle of a bacterial virus. Release (lysis) Virions © 2012 Pearson Education, Inc.
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9.5 General Features of Virus Replication
Virus replication typically characterized by a one-step growth curve (Figure 9.9) Latent period: eclipse + maturation Burst size: number of virions released © 2012 Pearson Education, Inc.
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Relative virus count (plaque-forming units)
Figure 9.9 Eclipse Maturation Early enzymes Nucleic acid Protein coats Relative virus count (plaque-forming units) Virus added Assembly and release Figure 9.9 The one-step growth curve of virus replication. Latent period Time © 2012 Pearson Education, Inc.
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9.6 Viral Attachment and Penetration
Attachment of virion to host cell is highly specific Requires complementary receptors on the surface of a susceptible host and its infecting virus Receptors on host cell carry out normal functions for cell (e.g., uptake proteins, cell to cell interaction) Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or complexes © 2012 Pearson Education, Inc.
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9.6 Viral Attachment and Penetration
The attachment of a virus to its host cell results in changes to both virus and cell surface that facilitate penetration Permissive cell: host cell that allows the complete replication cycle of a virus to occur © 2012 Pearson Education, Inc.
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9.6 Viral Attachment and Penetration
Bacteriophage T4: virus of E. coli; one of the most complex penetration mechanisms (Figure 9.10) Virions attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope Tail fibers retract and tail core makes contact with E. coli cell wall Lysozyme-like enzyme forms small pore in peptidoglycan Tail sheath contracts and viral DNA passes into cytoplasm © 2012 Pearson Education, Inc.
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Tail fibers Tail pins Outer membrane Tail lysozyme Peptidoglycan
Figure 9.10 Tail fibers Tail pins Outer membrane Tail lysozyme Peptidoglycan Figure 9.10 Attachment of bacteriophage T4 to the cell wall of Escherichia coli and injection of DNA. Cytoplasmic membrane Cytoplasm T4 genome © 2012 Pearson Education, Inc.
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9.6 Viral Attachment and Penetration
Many eukaryotes possess mechanisms to diminish viral infections For example, immune defense mechanisms, RNA interference Prokaryotes also possess mechanisms CRISPR Similar to RNA interference Restriction modification system © 2012 Pearson Education, Inc.
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9.6 Viral Attachment and Penetration
Restriction modification systems (cont’d) DNA destruction system; only effective against double-stranded DNA viruses Restriction enzymes (restriction endonucleases) cleave DNA at specific sequences Modification of host’s own DNA at restriction enzyme recognition sites prevents cleavage of own DNA © 2012 Pearson Education, Inc.
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9.6 Viral Attachment and Penetration
Viral mechanisms to evade bacterial restriction systems Chemical modification of viral DNA (glycosylation or methylation) Production of proteins that inhibit host cell restriction system © 2012 Pearson Education, Inc.
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Figure 9.11 RNA viruses mRNA () mRNA ()
dsDNA () virus Class I Class VII ssDNA () virus Class II dsRNA () virus Class III ssRNA () virus Class IV ssRNA () virus Class V ssRNA () retrovirus Class VI Synthesis of other strand Used directly as mRNA Reverse transcription Transcription of minus strand Transcription of minus strand dsDNA intermediate Transcription of minus strand Transcription of minus strand dsDNA intermediate mRNA () mRNA () Genome replication: Class I, Class II, Class VII, DNA viruses Genome replication: Class III, Class IV, Class V, Class VI, RNA viruses classical semiconservative classical semiconservative, discard () strand transcription followed by reverse transcription make ssRNA () and transcribe from this to give ssRNA () partner make ssRNA () and transcribe from this to give ssRNA () genome make ssRNA () and transcribe from this to give ssRNA () genome make ssRNA () genome by transcription of () strand of dsDNA Figure 9.11 Formation of mRNA and new genomes in (a) DNA viruses and (b) RNA viruses. © 2012 Pearson Education, Inc.
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9.7 Production of Viral Nucleic Acid and Protein
Once a host has been infected, new copies of the viral genome must be made and virus-specific proteins synthesized in order for the virus to replicate Generation of messenger RNA (mRNA) occurs first Viral genome serves as template for viral mRNA In some RNA viruses, viral RNA itself is the mRNA In some cases essential transcriptional enzymes are contained in the virion © 2012 Pearson Education, Inc.
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9.7 Production of Viral Nucleic Acid and Protein
Nomenclature used to describe mRNA is used to describe the configuration of the genome of a single-stranded DNA or RNA virus (mRNA is said to be in plus (+) configuration; its complement is in minus () configuration) Positive-strand RNA virus: single-stranded RNA genome with same orientation as its mRNA Negative-strand RNA virus: single-stranded RNA genome with orientation complementary to its mRNA © 2012 Pearson Education, Inc.
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9.7 Production of Viral Nucleic Acid and Protein
Retroviruses: animal viruses responsible for causing certain types of cancers and acquired immunodeficiency syndrome (AIDS) Class VI and VII viruses Require reverse transcriptase © 2012 Pearson Education, Inc.
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9.7 Production of Viral Nucleic Acid and Protein
Viral Proteins Production follows synthesis of viral mRNA Early proteins synthesized soon after infection necessary for replication of virus nucleic acid typically act catalytically synthesized in smaller amounts © 2012 Pearson Education, Inc.
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9.7 Production of Viral Nucleic Acid and Protein
Production of Viral Proteins (cont’d) Late proteins Synthesized later Include proteins of virus coat Typically structural components Synthesized in larger amounts © 2012 Pearson Education, Inc.
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9.8 Overview of Bacterial Viruses
Bacteriophages are very diverse (Figure 9.12) Best-studied bacteriophages infect enteric bacteria Examples of hosts: E. coli, Salmonella enterica Most phages contain dsDNA genomes Most are naked, but some possess lipid envelopes They are structurally complex, containing heads, tails, and other components © 2012 Pearson Education, Inc.
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RNA ssDNA dsDNA ss MS2 ds 6 174 fd, M13 T3, T7 Mu Lambda T2, T4
Figure 9.12 RNA ss MS2 ds 6 ssDNA 174 fd, M13 dsDNA Figure 9.12 Schematic representations of the main types of bacterial viruses. T3, T7 Mu Lambda T2, T4 © 2012 Pearson Education, Inc.
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9.10 Temperate Bacteriophages, Lambda, and P1
Temperate viruses: can undergo a stable genetic relationship within the host (Figure 9.16) But can also kill cells through lytic cycle Lysogeny: state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome Lysogen: a bacterium containing a prophage Under certain conditions lysogenic viruses may revert to the lytic pathway and begin to produce virions © 2012 Pearson Education, Inc.
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Figure 9.16 Temperate virus Lytic pathway Lysogenic pathway Induction
Host DNA Viral DNA Attachment Cell (host) Injection Lytic pathway Lysogenic pathway Viral DNA replicates Induction Coat proteins synthesized; virus particles assembled Viral DNA is integrated into host DNA Figure 9.16 The consequences of infection by a temperate bacteriophage. Lysogenized cell Prophage Lysis Cell division © 2012 Pearson Education, Inc.
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Capsid Tail Figure 9.17 Figure 9.17 Bacteriophage lambda.
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9.11 Overview of Animal Viruses
Entire virion enters the animal cell, unlike in prokaryotes Eukaryotic cells contain a nucleus, the site of replication for many animal viruses Animal viruses contain all known modes of viral genome replication (Figure 9.21) Many more kinds of enveloped animal viruses than enveloped bacterial viruses exist As animal viruses leave host cell, they can remove part of host cell’s lipid bilayer for their envelope © 2012 Pearson Education, Inc.
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DNA viruses RNA viruses Figure 9.21 Nonenveloped Enveloped
Enveloped all ssRNA partially dsDNA ssDNA Parvovirus Hepadnavirus Rhabdovirus dsDNA ssRNA Papovavirus Picornavirus Togavirus dsDNA Orthomyxovirus dsDNA Poxvirus Adenovirus dsRNA Bunyavirus Coronavirus Reovirus dsDNA dsDNA 100 nm Figure 9.21 Diversity of animal viruses. Herpesvirus Paramyxovirus Iridovirus Retrovirus 100 nm Arenavirus DNA viruses RNA viruses © 2012 Pearson Education, Inc.
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9.11 Overview of Animal Viruses
Consequences of Virus Infection in Animal Cells (Figure 9.22) Persistent infections: release of virions from host cell does not result in cell lysis Infected cell remains alive and continues to produce virus Latent infections: delay between infection by the virus and lytic events Transformation: conversion of normal cell into tumor cell Cell fusion: two or more cells become one cell with many nuclei © 2012 Pearson Education, Inc.
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Persistent infection Latent infection
Figure 9.22 Tumor cell division Transformation Transformation into tumor cell Cell Lysis Virus Death of cell and release of virus Attachment and penetration Persistent infection Virus multiplication May revert to lytic infection Slow release of virus without cell death Cell fusion Figure 9.22 Possible effects that animal viruses may have on cells they infect. Latent infection Virus present but not replicating © 2012 Pearson Education, Inc.
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9.12 Retroviruses Retroviruses: RNA viruses that replicate through a DNA intermediate Enveloped viruses (Figure 9.23a) Contain a reverse transcriptase (copies information from its RNA genome into DNA), integrase, and protease Virion contains specific tRNA molecules © 2012 Pearson Education, Inc.
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Surface envelope protein RNA Transmembrane envelope protein
Figure 9.23a Surface envelope protein RNA Transmembrane envelope protein Enzymes (reverse transcriptase, integrase, protease) Lipid membrane bilayer Figure 9.23 Retrovirus structure and function. Core shell protein Core protein © 2012 Pearson Education, Inc.
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9.12 Retroviruses Retroviruses have a unique genome
Two identical ssRNA molecules of the plus (+) orientation Contain specific genes (Figure 9.23b) gag: encode structural proteins pol: encode reverse transcriptase and integrase env: encode envelope proteins © 2012 Pearson Education, Inc.
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9.12 Retroviruses Process of Replication of a Retrovirus (Figure 9.24)
Entrance into the cell Removal of virion envelope at the membrane Reverse transcription of one of the two RNA genomes Integration of retroviral DNA into host genome Transcription of retroviral DNA Assembly and packaging of genomic RNA Budding of enveloped virions; release from cell © 2012 Pearson Education, Inc.
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Figure 9.24 Figure 9.24 Replication process of a retrovirus.
Retrovirus virion containing ssRNA (two copies) Entrance Uncoating R R ssRNA Reverse transcription LTR dsDNA LTR Travel to nucleus and integration into host DNA Host DNA LTR Provirus LTR Transcription R R Viral mRNA and genomic RNA ssRNA Encapsidation Figure 9.24 Replication process of a retrovirus. ssRNA Nucleocapsid Budding Host cytoplasmic membrane Release Progeny retrovirus virions © 2012 Pearson Education, Inc.
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IV. Subviral Entities 9.13 Defective Viruses 9.14 Viroids 9.15 Prions
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9.13 Defective Viruses Defective viruses: viruses that are parasitic on other viruses Require other virus (helper virus) to provide some function Some rely on intact virus of same type Satellite viruses: defective viruses for which no intact version exists; rely on unrelated viruses as helpers © 2012 Pearson Education, Inc.
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9.14 Viroids Viroids: infectious RNA molecules that lack a protein coat Smallest known pathogens (246–399 bp) Cause a number of important plant diseases (Figure 9.25) Small, circular, ssRNA molecules (Figure 9.26) Do not encode proteins; completely dependent on host-encoded enzymes © 2012 Pearson Education, Inc.
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Figure 9.25 Figure 9.25 Viroids and plant diseases.
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Figure 9.26 Figure 9.26 Viroid structure.
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9.15 Prions Prions: infectious proteins whose extracellular form contains no nucleic acid Known to cause disease in animals (transmissible spongiform encephalopathies) Host cell contains gene (PrnP) that encodes native form of prion protein that is found in healthy animals (Figure 9.28) Prion misfolding results in neurological symptoms of disease (e.g., resistance to proteases, insolubility, and aggregation) © 2012 Pearson Education, Inc.
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PrPSc-induced misfolding Abnormal function PrPc (normal prion)
Figure 9.28 Neuronal cell Nucleus Prnp DNA Transcription Translation Normal function PrPSc-induced misfolding Abnormal function PrPc (normal prion) Figure 9.28 Mechanism of prion misfolding. PrPSc (misfolded prion) © 2012 Pearson Education, Inc.
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9.15 Prions Prion disease occurs by three distinct mechanisms:
Infectious prion disease: pathogenic form of prion protein is transmitted between animals or humans Sporadic prion disease: random misfolding of a normal, healthy prion protein in an uninfected individual Inherited prion disease: mutation in prion gene yields a protein that changes more often into disease-causing form © 2012 Pearson Education, Inc.
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