9.1 General Properties of Viruses Virus: genetic element that cannot replicate independently of a...

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.

9.1 General Properties of Viruses

• Viral Genomes (Figure 9.1)– Either DNA or RNA genomes

– Some circular, but most linear


Figure 9.1

Viral Class

Viral Genome

DNA viruses RNA virusesRNA DNA

viruses

ssDNA dsDNA ssRNA dsRNAssRNA

(Retroviruses)dsDNA

(Hepadnaviruses)


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


Figure 9.218 nm

Virus RNA

Structural subunits(capsomeres)



• 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


Figure 9.3

Nucleocapsid

Nucleicacid

Capsid(composed ofcapsomeres)

Envelope

Capsid

Nucleic acid

Naked virus Enveloped virus



• 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


Figure 9.4

5-Fold 3-Fold 2-FoldSymmetry

Cluster of5 units



• 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


Figure 9.5

Collar

Tail

Endplate

Tail pins

Tail fibers

Head



• 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


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


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


Figure 9.6

Nutrient agarplate

Sandwich of topagar andnutrient agar

Lawn of hostcells

Phageplaques

Plaques

Mixture containingmolten top agar,bacterial cells, anddiluted phagesuspension

Pour mixture ontosolidified nutrientagar plate

Let solidify

Incubate


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


Figure 9.8

Protein coatremains outside

Viral DNA enters

Virion

DNA

Cell (host)

Virions

Attachment(adsorption)

Penetration(injection)

Synthesis ofnucleic acidand protein

Assembly andpackaging

Release(lysis)


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


Figure 9.9

Eclipse Maturation

Earlyenzymes

Nucleicacid

Proteincoats

Virusadded

Latent period

Assemblyandrelease

Time

Rel

ativ

e vi

rus

cou

nt

(pla

qu

e-fo

rmin

g u

nit

s)


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



• 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



• 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


Figure 9.10

Tailfibers

Tail pins

Outermembrane

Peptidoglycan

Cytoplasmicmembrane

Cytoplasm

Taillysozyme

T4 genome



• 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



• 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



• Viral mechanisms to evade bacterial restriction systems– Chemical modification of viral DNA (glycosylation

or methylation)

– Production of proteins that inhibit host cell restriction system


Figure 9.11

dsDNA () virusClass I

Class VII

ssDNA () virus

Class II

dsRNA () virus

Class III

ssRNA () virus

Class IV

ssRNA () virus

Class V

ssRNA () retrovirusClass VI

dsDNA intermediate

dsDNA intermediate

Synthesis ofother strand

Transcriptionof minus strand




Used directlyas mRNA

Reversetranscription

mRNA () mRNA ()

Genomereplication: Class I, Class II,

Class VII, DNA viruses

Genomereplication: Class III, Class IV, Class V, Class VI,

RNA viruses

classical semiconservativeclassical semiconservative,discard () strand transcription followed byreverse transcription

make ssRNA () and transcribe from this to give ssRNA () partnermake ssRNA () and transcribe from this to give ssRNA () genomemake ssRNA () and transcribe from this to give ssRNA () genomemake ssRNA () genome by transcription of () strand of dsDNA


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



• 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



• Retroviruses: animal viruses responsible for causing certain types of cancers and acquired immunodeficiency syndrome (AIDS)– Class VI and VII viruses

– Require reverse transcriptase



• 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



• Production of Viral Proteins (cont’d)– Late proteins

• Synthesized later • Include proteins of virus coat• Typically structural components• Synthesized in larger amounts


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


Figure 9.12

RNA

ssDNA

dsDNA

MS2ss ds 6

174fd, M13

T3, T7

MuLambda T2, T4


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


Figure 9.16Temperate virus

Lytic pathway Lysogenic pathway

Induction

Viral DNA

Host DNA

Cell (host)

Lysogenized cell

Attachment

Injection

Viral DNAreplicates

Coat proteinssynthesized;virus particlesassembled

Viral DNAis integratedinto host DNA

Lysis Celldivision

Prophage


Figure 9.17

Capsid

Tail


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


Figure 9.21

DNA viruses RNA viruses

Nonenveloped Enveloped Nonenveloped Enveloped all ssRNA

ssDNAParvovirus

dsDNAPapovavirus

dsDNA

Adenovirus

dsDNA

Iridovirus

partiallydsDNA

Hepadnavirus

dsDNA

Poxvirus

dsDNA

Herpesvirus

100 nm

100 nm

dsRNA

ssRNAPicornavirus

Reovirus

Rhabdovirus

Togavirus

Orthomyxovirus

Bunyavirus Coronavirus

Arenavirus RetrovirusParamyxovirus


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


Figure 9.22

Transformation

Lysis

Persistentinfection

Latentinfection

Cell

Virus

Attachmentand penetration

Virusmultiplication

May

rev

ert

to ly

tic

infe

ctio

n

Transformationinto tumor cell

Tumorcelldivision

Cellfusion

Death ofcell andreleaseof virus

Slow releaseof virus withoutcell death

Virus presentbut not replicating


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


Figure 9.23a

Surface envelope protein

Transmembraneenvelope protein

RNAEnzymes(reversetranscriptase,integrase,protease)

Lipidmembranebilayer

Core shellprotein

Core protein


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


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


Figure 9.24Retrovirus virioncontaining ssRNA(two copies)

R RssRNA

LTR

LTRdsDNA

Host DNA

LTR LTRProvirus

ssRNAR R Viral mRNA and

genomic RNA

ssRNA Nucleocapsid

Host cytoplasmicmembrane

Progenyretrovirus virions

Entrance

Uncoating

Reverse transcription

Travel to nucleus andintegration into host DNA

Transcription

Encapsidation

Budding

Release


IV. Subviral Entities

• 9.13 Defective Viruses• 9.14 Viroids• 9.15 Prions


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


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


Figure 9.25


Figure 9.26


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)


Figure 9.28Neuronal cell

Nucleus

DNA

Normalfunction

Abnormalfunction

PrPSc

(misfolded prion)

PrPc

(normal prion)

PrPSc-inducedmisfolding

TranslationTranscription

Prnp


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


9.1 General Properties of Viruses Virus: genetic element that cannot replicate independently of a...

Documents

Transcript of 9.1 General Properties of Viruses Virus: genetic element that cannot replicate independently of a...