25
The Viruses
CHAPTER OVERVIEW
This chapter describes the life cycles of viruses of all types and specificities. Viruses are grouped by the type
of genome they possess and the details of replication for each type is given. Important examples from each
group are used for illustration and to introduce broader concepts such as latency and virulence.
CHAPTER OBJECTIVES
After reading this chapter you should be able to:




classify viruses based on the type of genome they possess
discuss the differences between DNA phages and RNA phages in terms of their life cycles and their
interactions with their hosts
discuss the establishment and maintenance of lysogeny by temperate phages
understand the life cycle of important pathogens such as HIV, influenza virus, and herpesviruses
CHAPTER OUTLINE
I.
II.
Virus Taxonomy and Phylogeny
A. Almost 2,000 viral species have been placed in 3 orders, 73 families, and 287 genera; genome type,
capsid structure, and envelope are used for classification
B. Some viruses are known to possess positive- or negative-strand RNA or DNA genomes, while
others have double-stranded DNA or RNA genomes; seven groups of viruses are defined by life
cycle, and this system is used here
C. While some evolutionary relationships are emerging through comparative genomics, it remains
difficult to follow viral phylogenies
Viruses with Double-Stranded DNA Genomes (Group I)
A. Largest group of known viruses; mainly bacteriophages with dsDNA genomes; includes
herpesviruses and poxviruses; rely on host DNA and RNA polymerases
B. Bacteriophage T4: A virulent bacteriophage
1. Virulent phages can only undergo the lytic cycle in several stages
a. Attachment (adsorption) and penetration
1) Viruses attach to specific receptor sites on the host cell using tail fibers and
baseplate settles on surface
2) Tail sheath contracts, injecting DNA into the host cell, leaving an empty capsid
outside
b. Synthesis of phage nucleic acids and proteins
1) mRNA molecules transcribed early in the infection (early mRNA) are synthesized
using host RNA polymerase; early proteins, made at the direction of early mRNA
molecules, direct the synthesis of protein factors and enzymes required to take over
the host cell
2) Transcription of viral genes then follows an orderly sequence due to the
modification of the host RNA polymerase and changes in sigma factors
3) Later in the infection viral DNA is replicated using a virus-encoded DNA
polymerase
232
C.
D.
E.
(i) Synthesis of viral DNA requires the initial synthesis of alternate bases; these are
used to protect the phage DNA from host enzymes (restriction endonucleases) that
would otherwise degrade the viral DNA and thereby protect the host
(ii) T4 can form concatemers (long chains) of the DNA genome are formed; these are
later cleaved during assembly
c. Assembly of phage particles
1) Late mRNA molecules (those made after viral nucleic acid replication) direct the
synthesis of capsid proteins and other proteins involved in assembly (e.g.,
scaffolding proteins) and release of the virus
2) Assembly proceeds sequentially by subassembly lines, which assemble different
structural units (e.g., baseplate, tail tube); these are then put together to make the
complete virion
3) DNA packaging is accomplished with a protein complex called the packasome,
which includes the terminase complex that fills in gaps at the end of concatemers
d. Release of phage particles—host is lysed by damaging the cell wall or the cytoplasmic
membrane with T4 lysozyme and holin enzyme
Bacteriophage lambda: A temperate bacteriophage
1. Temperate phages are capable of lysogeny, a nonlytic relationship with their hosts (virulent
phages lyse their hosts)
a. In lysogeny, the viral genome (called a prophage) remains in the host (usually integrated
into the host chromosome) but does not kill (lyse) the host cell; the cells are said to be
lysogenic (or are called lysogens)
b. It may switch to the lytic cycle at some later time; this process is called induction
2. Most bacteriophages are temperate; it is thought that being able to lysogenize bacteria is
advantageous; supporting this is the observation that certain conditions favor the establishment
of lysogeny
3. Lysogenic conversion is a change that is induced in the host phenotype by the presence of a
prophage, and that is not directly related to the completion of the viral life cycle; examples
include:
a. Modification of lipopolysaccharide structure in infected Salmonella
b. Production of diphtheria toxin only by lysogenized strains of Corynebacterium
diphtheriae
4. Establishment of lysogeny
a. Two sets of viral promoters are available to host RNA polymerase
b. A repressor protein (lambda repressor) may be made from genes adjacent to one of these
promoters
c. If the lambda repressor binds to its target operator before the other promoter is used, that
promoter is blocked and lysogeny is established
d. If genes associated with that second promoter (Cro protein) are expressed before the
lambda repressor can bind to the operator, the lytic cycle is established
e. Induction (the termination of lysogeny and entry into the lytic cycle) will occur if the
level of lambda repressor protein decreases; this is usually in response to environmental
damage to host DNA
f.
For lambda and most temperate phages, if lysogeny is established, the viral genome
integrates into the host chromosome; however, some temperate phages can establish
lysogeny without integration
Archaeal viruses
1. All known archaeal viruses have dsDNA genomes; some have unusual morphologies
2. Some archaeal viruses are virulent, while others are temperate
Herpesviruses
1. Family of human pathogens with dsDNA genome; cause chicken pox, shingles, genital herpes,
cold sores; include cytomegalovirus and Epstein-Barr virus
2. Enveloped pleomorphic virus with spikes; genome contains 50 to 100 genes in an icosahedral
capsid
233
3.
First exposure leads to productive herpes infections that generate many new virions leading to
host cell death; infected neurons develop latent infections that can be reactivated
4. Receptor-mediated viral binding to host cell herpesvirus entry mediators (HVEMs) leads to
capsid penetration and movement of the viral particle to the nucleus; the viral genome is
expressed using host cell machinery and produce early gene products required for replication;
late gene expression directs production of viral proteins
5. Exit from the cell starts with viral budding through the inner nuclear membrane; the virus
moves to the plasma membrane for exocytosis in an vesicle derived from the Golgi
F. Nucleo-cytoplasmic large DNA (NCLD) viruses
1. A group of large enveloped icosahedral virions with a large dsDNA genome that includes
members from several virus families (e.g., Poxviridae and Phycodnaviridae); some are the size
of small bacteria
2. Large genome houses many genes needed for viral replication and assembly
3. Poxviruses are large brick-shaped virions with a dumbbell-shaped core; enter through
receptor-mediated endocytosis; early and late genes are expressed during the life cycle
III. Viruses with Single-Stranded DNA Genomes (Group II)
A. Bacteriophages X174 and fd
1. X174 is plus-strand DNA virus—virus genome that has the same sequence as the viral
mRNA
a. The single-stranded genome is converted to a double-stranded replicative form (RF) by
the host DNA polymerase
b. The RF directs synthesis of more RF, RNA, and +strand DNA genome
c. Phages are released by lysis of host cell
2. Filamentous phage fd—plus-strand DNA virus
a. Phage DNA enters via the host cell’s sex pilus and an RF is synthesized
b. The RF directs mRNA synthesis and DNA replication via the rolling-circle method
c. Phages are released without lysing the host cell; instead they are released by a secretory
process
B. Parvoviruses
1. Group of viruses of eukaryotic cells, including Human parvovirus B19
2. Naked icosahedral virions with mainly negative-strand DNA genomes; among simplest DNA
viruses, codes for no enzymatic proteins
3. Enter by receptor-mediated endocytosis and move to the nucleus; viral genomes have
palindromic ends that act as sites for DNA polymerase binding and rolling-circle replication
IV. Viruses with Double-Stranded RNA Genomes (Group III)
A. Many viruses with RNA genomes carry RNA-dependent RNA polymerase (replicase), an enzyme
not found in host cells
B. Bacteriophage 6
1. Enveloped dsRNA virus with segmented genome; uses pilus for entry through fusion with the
outer membrane, viral enzymes degrade peptidoglycan allowing entry
2. Inside host, viral RNA polymerase generates mRNA and viral genomes; host cells are lysed to
release mature virions
C. Rotaviruses
1. Human pathogens causing severe diarrhea; survive in the environment
2. Naked dsRNA viruses with a segmented genome and a wheel-like capsid with three-layers of
proteins
3. Outer protein layer lost during penetration releasing double-layered particle (DLP); viral genes
expressed and viral proteins accumulate in cytoplasmic inclusions called viroplasm; viral
envelope arises from endoplasmic reticulum
V. Viruses with Plus-Strand RNA Genomes (Group IV)
A. Replicate in host cell cytoplasm using viral RNA-dependent RNA polymerase to generate
replicative form; progeny viruses assembled in replication complexes; includes most plant viruses
and some human pathogens
234
B.
Bacteriophages MS2 and Q—small, tailless, icosahedral virions with very simple genomes; use
pili to reach cell membrane and then insert genome; uses viral RNA polymerase to generative
replicative form and produce new virions that are released by host cell lysis
C. Poliovirus
1. Naked plus-strand RNA virus causes polio in humans
2. Enters host cell by ingestion; genome acts as mRNA but without a 5' cap an internal ribosome
binding site mediates recognition
3. A polyprotein is produced that self-cleaves into capsid proteins, RNA polymerase, and others;
mature virions are released through host cell lysis
D. Tobacco mosaic virus (TMV)
1. Plant viruses are mainly plus-strand RNA viruses
2. TMV is a helical filamentous virion that resembles animal viruses and bacteriophages
a. Penetration through the plant cuticle through wounds or by the action of biting insects
b. The virus uses either a cellular or a virus-specific RNA-dependent RNA polymerase
c. The virus produces proteins, which then spontaneously assemble
d. Viral spread is through the plant vascular system or to adjacent cells through
plasmodesmata
e. The virus causes many cytological changes, such as the formation of inclusion bodies and
the degeneration of chloroplasts
VI. Viruses with Minus-Strand RNA Genomes (Group V)
A. Spherical or pleomorphic, enveloped virions having segmented or unsegmented genomes; includes
Rabies virus, Ebola virus, influenza viruses, and Measles virus
B. Must carry RNA-dependent RNA polymerase to generate mRNA from minus-strand RNA genome
C. Influenza
1. Causes three major types of flu; has segmented genome
2. Uses surface neuraminidase and hemagglutinin spikes to enter cells through receptor-mediated
endocytosis; membrane fusion with endosome releases capsid to cytoplasm; mature virions
released through cell lysis
VII. Viruses with Single-Stranded RNA Genomes (Group VI—Retroviruses)
A. Contain positive-strand RNA genomes that do not act as mRNA; ssRNA genome converted to
dsDNA using reverse transcriptase; dsDNA genome can then integrate into the host cell
chromosome
B. Human immunodeficiency virus (HIV)
1. Causative agent of AIDS; enveloped virion with two RNA genomes and enzymes including
reverse transcriptase and integrase
2. Surface GP120 protein binds to host CD4+ T-helper cells and other immune cells; entrance is
by receptor-mediated endocytosis
3. Reverse transcriptase copies the RNA genome into dsDNA that integrates as a provirus into
the host cell chromosome; mature viruses bud from host cell surface; eventually the host cell is
killed
VIII. Viruses with Gapped DNA Genomes (Group VII)
A. Hepadnaviruses include Hepatitis B virus, a spherical virion with a circular genome
B. One strand of the dsDNA genome is nicked, while the complementary strand has a large gap which
is repaired by host cell enzymes; viral replication involves reverse transcription of progenome RNA
formed from the minus-strand DNA
235
TERMS AND DEFINITIONS
Place the letter of each term in the space next to the definition or description that best matches it.
____ 1.
____
____
____
____
2.
3.
4.
5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
n.
The term that describes the time immediately after infection during which no infective virions are
released
The place on the surface of a host cell where a phage can attach
The mRNA that is made before viral nucleic acid has been replicated
The mRNA that is made after viral nucleic acid has been replicated
A dsDNA or dsRNA that is produced by a phage with a single-stranded genome; it acts as a
template for the synthesis of mRNA and genomic nucleic acid
The switching of an infected bacterial lysogen to the active production of viral progeny
Long DNA molecules consisting of several genomes linked together in a row
An RNA-dependent RNA polymerase
An enzyme that synthesizes RNA using a DNA template
An enzyme carried by retroviruses that promotes the addition of the dsDNA copy of the virus
genome to the host cell chromosome
A protein important in recombination reactions and DNA repair
An enzyme that synthesizes DNA using a DNA template
An enzyme that synthesizes RNA using an RNA template
A protein that catalyzes the synthesis of viral genomes during replication
concatemers
DNA-dependent DNA polymerase
DNA-dependent RNA polymerase
early mRNA
induction
integrase
late mRNA
latent period
receptor site
RecA protein
replicase
replicative form
reverse transcriptase
RNA-dependent RNA polymerase
FILL IN THE BLANK
1.
2.
3.
4.
5.
Virus-specific mRNA that is synthesized before viral nucleic acid is replicated is called ____________
mRNA, while that produced after viral replication is called ____________ mRNA.
T4 DNA replication produces
, long strands of several genome copies linked together.
The latent form of the genome that exists when a phage establishes lysogeny is called a ____________.
This can be integrated into the host chromosome or may exist independently. The viral enzyme that
catalyzes integration is called
.
Phages having single-stranded genomes begin their replicative process by synthesizing a double-stranded
molecule called a
. The virally encoded enzyme
catalyzes this
synthesis in ssRNA viruses.
The Hepatitis B virus has a circular genome that is
dsDNA. After its synthesis, the enzyme
associates with the RNA progenome and generates a
-strand
DNA molecule.
236
6.
7.
8.
9.
10.
11.
12.
13.
The HIV virus, the causative agent of
has a genome made from
and is within
a group of viruses called
. The virus genome integrates into the host cell chromosome as a
during the
phase of the virus life cycle.
The influenza virus uses the envelope spikes
and
to mediate binding to host
cells. Once inside the cell, a complementary RNA strand must be synthesized from ssRNA genome using
a
.
Because their genome is complementary to their mRNA,
-strand RNA viruses must employ
a virion-associated ____________ to synthesize mRNA.
Plant viruses typically have
genomes. The viruses often enter
through
or through biting
and spread through plant
.
When rotaviruses enter cells they lose their outermost protein layer generating a
. These collect in the cytoplasm creating
. The maturing virions
acquire their lipid envelope from the
.
The negative-strand DNA genome of Parvoviruses is complementary to viral
. The ends of the
parvovirus genome are
sequences that fold back on themselves to initiate replication with
a
.
Under some conditions, E. coli cells infected with lambda phage will change from the lysogenic state and
enter the lytic cycle. A decrease in the level of
triggers the switch, which is
referred to as ____________.
Two of the first proteins to appear after infection with lambda are the
, which blocks
transcription of proteins required for the lytic cycle, and
, which blocks establishment
of lysogeny. The fate of the virus in the host depends on which protein first reaches high levels. Lysogeny
is established if
wins the race.
MULTIPLE CHOICE
For each of the questions below select the one best answer.
1.
2.
3.
4.
5.
Which of the following is least important in classifying bacteriophages?
a.
phage morphology
b.
host range
c.
type of nucleic acid (DNA or RNA)
d.
strandedness of nucleic acid (single or double stranded)
Which of the following does NOT serve as phage receptor sites?
a.
lipopolysaccharides
b.
teichoic acids
c.
proteins
d.
All of the above serve as phage receptor sites.
In T-even phages, which of the following makes the initial contact with the appropriate receptor site?
a. tail fiber
b. base plate
c. collar
d. tail tube
What is the function of virus-specific enzymes produced before viral nucleic acid replication?
a. degradation of host DNA
b. modification of host RNA polymerase to recognize viral promoters
c. production of any unusual bases required by the virus for DNA replication
d. All of the above are functions performed by virus-specific enzymes.
The sequence of genes in each T4 virus within a population starts with a different gene at the 5 end. If
each of these linear pieces is coiled into a circle, the gene sequences are identical. What is the term used
to describe T4 DNA?
a. linear circle
b. linearly permuted
c. circularly permuted
237
6.
7.
8.
9.
10.
11.
12.
13.
14.
d. linearly circular
Which of the following is NOT a function of the replicative form (dsDNA) of the ssDNA phage X174?
a. synthesis of more RF copies
b. synthesis of minus-strand DNA
c. synthesis of plus-strand DNA
d. synthesis of mRNA
Which of the following is NOT a translation product of late mRNA?
a. phage structural proteins
b. phage assembly proteins that are not incorporated in the capsid
c. phage proteins needed to replicate the phage nucleic acid
d. phage release proteins
What is unique about bacteriophage 6, a phage that infects Pseudomonas phaseolicola?
a. It has a dsRNA genome.
b. It has a membranous envelope.
c. Both of the above are correct.
d. None of the above is correct.
Where are poliovirus receptors found?
a. in cells of all tissues
b. in spinal cord anterior horn cells only
c. in nasopharynx, gut, and spinal cord anterior horn cells
d. in gut cells only
Which of the following is the most important agent of plant virus transmission?
a. soil nematodes feeding on plant roots
b. parasitic fungi
c. pollen
d. insects that feed on plant leaves
For viruses that enter the cell by endocytosis, what usually triggers uncoating?
a. lysosomal enzymes
b. low endosomal pH
c. Both (a) and (b) are correct.
d. Neither (a) nor (b) is correct.
How do enveloped viruses acquire their envelopes?
a. by budding through the plasma membrane
b. by budding through internal cellular membranes
c. For some viruses (a) is correct; for other viruses (b) is correct.
d. Neither (a) nor (b) is correct.
Which of the following is responsible for the establishment and maintenance of lysogeny in cells infected
with bacteriophage lambda?
a. lactose repressor
b. lambda repressor
c. lambda lysogeny protein
d. lysogeny maintenance protein
Which enzyme is responsible for the escape of the lambda genome from the host chromosome when
induction occurs?
a. integrase
b. RNA replicase
c. excisionase
d. lambda repressor
TRUE/FALSE
____ 1.
When the single-stranded DNA phage X174 infects a cell, transcription must take place before
replication can occur.
238
____ 2.
____ 3.
____ 4.
____ 5.
____ 6.
____ 7.
____ 8.
____ 9.
____ 10.
____ 11.
____ 12.
____ 13.
____ 14.
____ 15.
____ 16.
____ 17.
____ 18.
The single-stranded genome of RNA phages serves both as a template for its own replication and as
mRNA.
Filamentous fd phages are released by secretion through the host plasma membrane, leaving the host
relatively undamaged and able to continue to release more phage particles.
The tail tube of a complex bacteriophage may interact with the plasma membrane to form a pore
through which the DNA passes.
Noncapsid proteins that aid in the assembly of virion structures are referred to as
scaffolding proteins.
Bacteriophage genomes diverged as a whole from a common ancestor.
All viruses, except parvoviruses, use some virus-specific enzymes for replication. Therefore, some
viral proteins must enter the cell with the viral nucleic acid.
Unlike bacteriophages, most animal viruses do not cause degradation of host DNA.
All of the DNA viruses use host RNA polymerase to transcribe at least early genes.
The parvovirus genome is so small that it must use overlapping genes (i.e., a single sequence of
bases read in different reading frames) to encode the three proteins that are its only gene products.
Poxviruses have a complex infectious cycle in which partial uncoating occurs followed by early
gene expression. One of these early gene products is an enzyme that completes the uncoating
process prior to DNA replication.
RNA viruses are more uniform in their replication strategies than DNA viruses.
Unlike other enveloped viruses that use altered cellular membranes as their envelope source,
herpesviruses use the nuclear membrane in envelope formation.
Some plant viruses that require insect vectors for transmission can actually be cultivated in insect
cells.
All of the known plant viruses are RNA viruses.
Tobacco mosaic virus mRNA arises by complex processing of genomic RNA, even though the
genome is plus stranded and could conceivably function as mRNA directly.
Poxviruses use actin microfilaments to escape from host cells without damaging the cell.
The tobacco mosaic virus is the only virus incapable of self-assembly.
239
PHAGE REPLICATION
Fill in the requested information in the table below.
Stage or
Event
Adsorption
to host cell
and
penetration
mRNA
synthesis
Description of
Stage or Event
dsDNA
ssDNA
phages (e.g., phages (e.g.,
T4)
X174)
dsRNA
phages (e.g.,
6)
plus-strand
ssRNA
phages (e.g.,
MS2)
minus-strand
ssRNA
phages (e.g.,
influenza)
Genome
synthesis
Protein
synthesis
Assembly
Release
240
retroviruses
(e.g., HIV)
Gapped DNA
phages (e.g.,
HBV)
CRITICAL THINKING
1.
Describe the life cycle of the HIV viruses being sure to include the replication process. Why do you think
that a retrovirus like HIV might be difficult to treat? What features of the viral replication cycle are
unique to the virus and hence could make good targets to anti-HIV drugs?
2.
Describe the differences between temperate and virulent phages. What survival advantages are offered by
each life cycle? How might you expect human disease caused by each class of virus to differ from each
other?
ANSWER KEY
Terms and Definitions
1. h, 2. i, 3. d, 4. g, 5. l, 6. e, 7. a, 8. m, 9. c, 10. f, 11. j, 12. b, 13. n, 14. k
Fill in the Blank
1. early; late 2. concatemers 3. prophage; integrase 4. replicative form; RNA replicase 5. gapped; reverse
transcriptase; minus 6. AIDS; ssRNA; retrovirus; provirus; latent 7. hemagglutinin; neuraminidase; RNAdependent RNA polymerase 8. negative; transcriptase 9. plus-strand RNA; wounds; insects; vasculature 10.
double-layered particle (DLP); viroplasm; endoplasmic reticulum 11. mRNA; palindromic; DNA polymerase
12. lambda repressors; induction 13. lambda repressor; cro protein; lambda repressor
Multiple Choice
1. b, 2. d, 3. a, 4. d, 5. c, 6. b, 7. c, 8. c, 9. c, 10. d, 11. d, 12. c, 13. b, 14. c
True/False
1. F, 2. T, 3. T, 4. T, 5. T, 6. F, 7. F, 8. T, 9. F, 10. T, 11. T, 12. F, 13. T, 14. T, 15. F, 16. T, 17. T, 18. F
241