Viruses Chapter

e21
Viruses, Living or Nonliving?....e517

Viral Life Cycles..........................e518

Viruses, Living or Nonliving? Diversity of Viruses....................e519
Great debate still ensues over the living or nonliving nature of viruses. RNA Viruses................................e519
Even though viruses contain genetic information, they still require a
host cell and host cell proteins to replicate as virus particles themselves Subviral Infectious Agents.......e521
are inert. Therefore, they are in fact genetic entities as opposed to liv-
Infectious Proteins....................e521
ing organisms. Viral genomes can be made of either type of nucleic
acid and exhibit great diversity. The Key Concepts for this chapter are
discussed more thoroughly below.

l Virus particles consist of genetic information (the virus genome)

enclosed in protein shells (the capsid).

Viruses are made of some genetic information packaged into a pro-

tein coating called the capsid. The genetic information may be either
DNA or RNA and carries the genes needed to make more virus particles.
The capsid is only made of protein. Viruses do not contain membranes,
although some animal viruses have another coating derived from a host
cell’s membrane called an envelope. The capsid is present to help protect
the nucleic acid while the virus particle is in the environment and inert.

l Viruses must enter and take over a host cell in order to replicate.

Viruses cannot replicate on their own. They are parasitic, more

specifically, obligate intracellular parasites. Once inside a host cell,
viruses hijack a host cell’s replication and protein synthesis machinery
and subvert them into making more virus particles.
The general overview of a viral life cycle involves, first, the attach-
ment of the virus to the host cell followed by entry of the viral genome
into the cell. The host cell’s machinery replicates the viral genome, man-
ufactures viral proteins, and assembles new virus particles called virions.
Finally, the virions are released from the host cell and are free to infect
new cells.

l Viruses that infect bacteria are known as bacteriophage.

Molecular Biology, Second Edition Study Guide.

© 2013 Elsevier Inc.
Academic Cell is an imprint of Elsevier Inc. e517
e518 CHAPTER TWENTY-ONE • Viruses

Even though bacteria are small, they are not immune to viruses. There are sev-
eral examples of viruses that are capable of infecting bacterial cells. These viruses are
called bacteriophage, or phage for short. When phage infect a new cell, they simply
inject their nucleic acid through the bacterial cell wall and leave behind the protein
coating. Some bacteriophage resemble a lunar-lander.

l Viruses may use either DNA or RNA as their genetic material.

The genetic information for viruses may either be DNA or RNA. Additionally,
the nucleic acid can exist as either double-stranded or single-stranded, linear or circu-
lar. For single-stranded RNA viral genomes, the RNA may either be the sense strand
or the antisense strand. The nucleic acids of viruses are discussed in more detail below.

Viral Life Cycles

l Some viruses integrate into the chromosomes of their host cells and are main-
tained in a largely inactive state.

Two major life cycles exist for viruses. The lytic cycle occurs when viruses infect a
host cell, manufacture a large number of viral genomes and capsids, and then release
a large number of virions. In the lysogenic cycle, the viral genome replicates in sync
with the host cell’s genome and no new virions are manufactured or released from
the host. The cell containing the virus is called a lysogen. Usually, the lysogenic virus
integrates into the host cell’s genome, and is replicated as “self” concurrently with the
host. An integrated virus is called a provirus, or prophage (for bacteriophages). Often,
integrated viruses are needed for survival of some endosymbionts of insects.

Kent BN and Bordenstein SR (2010). Phage WO of Wolbachia: lambda of
the endosymbiont world. Trends Microbiol 18:173–182.
Wolbachia is a bacterial endosymbiont of many arthropods and
nematodes. This bacterium is an obligate, intracellular bacterium whose genome is
streamlined due to the easy acquisition of nutrients from the host, which means it
no longer requires the genes for biosynthesis of compounds. The bacteriophage WO
FOCUS ON
RELEVANT RESEARCH
This phage can undergo both lytic and lysogenic viral life cycles. The
mechanism that drives the lytic cycle for phage WO is not known. The authors also
suggest that this phage is transferable among the various bacterial phyla.
In terms of the tripartite relationships among WO, Wolbachia, and
arthropods, it appears that several genes involved in scavenging nutrients, toxin/anti-
toxin systems, and entry of Wolbachia into new hosts are present.
Overall, the association between Wolbachia, WO, and the arthropod
host are important to human health through two routes. Vectorborne diseases often
involve an insect vector. Vector control programs could potentially utilize engineered
Wolbachia and WO to curb the spread of the vector. Additionally, diseases such as
river blindness, lymphatic filiariasis, and heartworm are associated with Wolbachia
symbionts. Perhaps therapies targeting the symbionts would be more effective at
treating these diseases.

inhabits Wolbachia and the authors suggest that the arthropod-Wolbachia  -phage WO
system is a great model for studying mobile elements in obligate intracellular bacteria
since they are unusually susceptible to high levels of mobile elements, which includes
transposons and viruses.
These bacteria forge both mutualistic and parasitic relationships with
their hosts. They are inherited through maternal lineages and play roles in such proc-
esses as host oogenesis, larval development, resistance against RNA viruses, locomo-
tion, and iron metabolism.
Bacteriophage WO was initially identified in Wolbachia found in cer-
tain species of mosquitos. Phage WO has contributed to significant genetic diversity
within Wolbachia that is not necessarily limited to phage genes, but also includes
genes for insertional sequences, transposons, and other mobile elements.
Conceptual questions
1. What are the two predominant life cycles for viruses?
2. What is a bacteriophage?
3. How is Phage WO involved in pathogenesis of its host organsms?
Discussion points
The authors mention that Wolbachia is a more streamlined bacte-
rium and contains unusually high numbers of mobile elements, including transposons
and viruses. First of all, why do you think Wolbachia is more streamlined that other
bacteria? What would have been the selecting agent for this? Secondly, what role do
bacteriophages play in the relationships (good or bad) with the host cells?
 RNA Viruses e519

Diversity of Viruses
l Viruses are extremely diverse in the structures of both their particles and their
genomes as well as in their modes of replication.
l Viruses may have anywhere from three to just over a thousand genes.

Viruses are very diverse in their target host, as well as in their overall external
structure, genome arrangement, and method of replication.
Viruses can invade animal, plant, protists, bacterial cells…and even other viruses!
See Box 21.2 for more details on Sputnick.
Some viruses have only three genes. These are the smallest known viruses. The
largest viruses have over a thousand genes. The largest known virus is called Mimivirus.
Viral replication is usually by some form of rolling circle replication (see Chapter 20
for more explanation on this). Viruses with linear genomes usually circularize them prior
to replication. Additionally, those viruses with single-stranded genomes synthesize the
second strand prior to replication. RNA viruses are even more challenged than DNA
viruses in that they must provide an RNA polymerase called RNA replicase to replicate
their genomes.
l Complex bacterial viruses have a head and tail structure and contain double-
stranded DNA.

Complex viruses have an intricate external structure consisting of a head, tail,

and tail fibers. Usually the genome of this virus is linear, double-stranded DNA and is
packaged within the head portion. The tail is used to inject the viral genome through
the bacterial cell wall and into the cytoplasm. The tail fibers are used to adhere the
virus to the outer surface of the bacterial cell. Examples of complex viruses include the
bacteriophage T4, Lambda, and Mu, all of which are used in molecular biology tech-
niques for bacteria.
l Poxviruses are the most complex animal viruses. Unlike most viruses, which
replicate in the nucleus, pox viruses replicate in the cytoplasm inside subcellular
factories.

Poxviruses infect animal cells and are some of the largest viruses. In fact, some
can be viewed with a compound light microscope. Their genome is made of double-
stranded DNA and is replicated within subcellular compartments called inclusion
bodies in the cytoplasm of the host cell.

l Mimivirus and its relatives are the largest viruses known and some may have
1000 genes. They infect primitive eukaryotes.

Mimiviruses and relatives have diameters of about 0.75 μm and contain a large
icosahedral capsid surrounded by filaments. Mimiviruses are the largest known
viruses in terms of physical and genome size. Their genomes contain about 1.2 Mbp of
double-stranded DNA and is larger than the genomes of several bacteria. Poxviruses
and Mimiviruses belong to the same division of viruses which includes several other
large viruses. Like poxviruses, Mimiviruses are replicated inside subcellular compart-
ments in the host cell’s cytoplasm. The hosts of Mimiviruses are usually protists.
Virophages are viruses that infect other viruses. Mimivirus is the target for a
virophage called Sputnik. Sputnik, and related virus particles, are actually defective
viruses that require a helper virus to replicate. Mimivirus serves as the helper.

RNA Viruses
l Viruses with RNA genomes mutate rapidly and possess relatively few genes.
l Positive-stranded RNA viruses make giant polyproteins that are cleaved into

individual proteins.
e520 CHAPTER TWENTY-ONE • Viruses

l Negative-strand RNA viruses make the complementary (sense) strand upon

entering their host cell.

RNA viruses have the smallest genomes and the highest mutation rates, in some
cases 100-fold higher than viruses with DNA genomes. High mutation rates are
advantageous because the virus is able to quickly mutate gene products and evade
host defense systems. Not surprisingly, an example of an RNA virus is influenza.
RNA viruses may have one of three genome arrangements: double-stranded
RNA, positive single-stranded RNA, or negative single-stranded RNA. Positive single-
stranded RNA refers to an RNA molecule that is the coding strand whereas the nega-
tive RNA is the noncoding strand.
The positive-stranded RNA virus is able to make proteins directly from the
genomic RNA as this constitutes the mRNA strand. Positive-stranded RNA viruses
are challenged following entry into a eukaryotic host cell. First, the positive strand is
not modified in a way that is conducive for translation. That is, there is no 5 cap or
3 poly(A) tail. A protein is attached to the 5 end of the viral RNA to serve as the
cap. Second, the viral mRNA contains all of the genes for the viral proteins and
eukaryotic ribosomes do not synthesize polycistronic mRNAs. The virus circumvents
this by having one large, open reading frame that is synthesized as one continuous
polyprotein, which is then cleaved into the individual proteins.
The negative-strand RNA virus requires the synthesis of a complementary
strand following entry into the host cell. Following entry into the host cell, a negative-
stranded RNA virus first synthesizes double-stranded RNA using the negative strand
as a template. The two strands then serve as templates for production of more negative
strands (from the newly synthesized positive strand) for the genomes of the next gen-
eration, and production of more positive strands, which are used in protein synthesis.

Ho BC, Yu SL, Chen JJ, Chang SY, Yan BS, Hong QS, Singh S, Kao CL, Chen
HY, Su KY, Li KC, Cheng HW, Lee JY, Lee CN, and Yang P (2010). Enterovirus-
induced miR-141 contributes to shutoff of host protein translation by targeting
the translation initiation factor eIF4E. Cell Host Microbe 9:58–69.
The genomes of picornaviruses contain positive single-stranded
RNA and use an internal ribosome entry site for translation initiation. For translation,
They describe a new mechanism for shutting down host cell translation by using a
microRNA, miR-141, that targets eIF4E for shutdown.
Expression of miR-141 is induced upon infection by an enterovirus.
The authors investigated 27 potential targets of miR-141 that were predicted based
on computer programs. Of the 27 predicted targets, eIF4E was the only one with any
involvement in translation. The authors determined that infection by enterovirus likely
upregulated the expression of miR-141, which posttranscriptionally repressed the eIF4E
gene. Since the eIF4E is key to cap-dependent translation, this translation was shut down.

Conceptual questions
FOCUS ON 1. What are the genome arrangements for RNA viruses?
RELEVANT RESEARCH 2. What challenges do RNA genomes pose for the virus?
3. How are positive and negative strands of RNA dealt with following entry into the
host cell?

picornaviruses utilize the host cell machinery, but in a cap-independent mechanism
that also shuts down host translation. This occurs via proteolytic cleavage of eukaryo-
tic initiation factors, eIF4GI and eIF4GII, by viral proteases.
The authors of this paper used miRNA profiles of enterovirus-infected
cells to investigate the role of miRNAs in cellular functions, such as protein synthesis.
Discussion points
The authors discuss a mechanism to not only ensure that viral RNAs
are translated, but to also shut down the translation of host proteins. What is the
significance for the virus of shutting down host translation? What types of proteins
might a host cell need to synthesize during a viral infection?

l Retroviruses use both RNA and DNA for their genome at different stages of
their lifecycle.

Human immunodeficiency virus (HIV) is the virus that causes AIDS and
is a well-known retrovirus. The overall structure of retroviruses consist of a
 Infectious Proteins e521

single-stranded RNA genome inside two protein coatings and surrounded by an enve-
lope. The envelope is derived from the animal host’s plasma membrane.
Following cell entry, the retrovirus genome is converted to a double-stranded
complementary DNA copy using reverse transcriptase. The retroviral DNA perma-
nently integrates into the host cell’s genome and is replicated along with host cell rep-
lication and division. Reverse transcriptase is essential for retrovirus survival, but it is
also an enzyme that has many applications in molecular biology and biotechnology
research.

Subviral Infectious Agents

l Subviral infectious agents include various defective viruses as well as viroids
and prions.

Subviral infectious particles often have RNA genomes and are defective in some
way. In some cases, they are defective by a few genes needed to form the capsid. They
may also be defective in replication and assembly.
Examples of subviral infectious particles include satellite viruses, viroids, and prions.
Each is discussed in more detail below.

l Satellite viruses are defective viruses that rely on other, intact, viruses to pro-
vide missing functions.

Sputnik is classified as a subviral infectious particle because it relies on a helper

virus for replication and viral assembly. Satellite viruses are not simply defunct helper
viruses and often have no sequence homology or similarity to them.

l Viroids are short molecules of infectious RNA that lack protein coats and
have no protein coding sequences.

Viroids are even more strange because they are simply naked, infectious RNA.
The genomes of viroids are small and contain only single-stranded, circular RNA. The
single-stranded RNA folds over on itself to produce a rod-shaped structure that is
more protected from degradation in the environment. Additionally, the RNA acts as a
ribozyme and catalyzes some reactions.
They initially infect a plant through cells with damaged cell walls and membranes.
From there, they can be passed to other cells through cell junctions. Replication of
the RNA occurs via rolling circle mechanism. Damage to the plant may be minor or
extensive.

Infectious Proteins
l Prions are infectious proteins that exist in two alternative conformations and
lack nucleic acids in their infectious form.

Infectious prions are responsible for some cases of nervous system diseases
including scrapie in sheep, bovine spongiform encephalopathy (also known as “mad
cow”) in cattle, Creutzfeldt-Jacob disease and related diseases in humans, and chronic
wasting disorder in sheep.
Infectious prions are simply proteins and do not contain any nucleic acid. They
are misfolded proteins that direct the misfolding of natural prions found on the out-
side of nerve cells. Eventually, the misfolded proteins form aggregates. The result is a
slow degeneration of the nervous system and eventual death.
Prion disease occurs by three routes: spontaneous, inherited, and transmissible.
e522 CHAPTER TWENTY-ONE • Viruses
Halfmann R, Alberti S, and Lindquist S (2010). Prions, protein homeosta-
sis, and phenotypic diversity. Trends in Cell Biology Vol.20:125–134.
Prions usually receive bad attention due to the degenerative nerv-
ous system diseases they often cause. However, there are significantly underplayed
roles for prions in phenotypic diversity of organisms, particularly in yeast such as
Saccharomyces cerevisiae. The authors of this opinion article suggest that the prions
in yeast allow the cells to adapt quickly to stressful environments and might also be
a source of new traits.
FOCUS ON
RELEVANT RESEARCH
Usually when one hears the word “prion,” images of deadly neurode-
generative diseases come to mind for cattle, sheep, deer, and humans. Recent evidence
suggests, however, that prions are more numerous and present in lower eukaryotes such
as yeast. Although some cause disease, others are benign and some are beneficial. The
essence of this article was to focus on prions, not as disease-causing entities, but rather
as protein-based genetic elements and their ability to drive phenotypic diversity.
The authors suggest that prions act as “bet-hedging” devices that
allow organisms to switch phenotypes in fluctuating environments, thus increasing
reproductive fitness. One of the first prions characterized for such an activity was
[PSI*], the prion form of Sup35. This prion allowed translation to occur when envi-
ronmental conditions included heavy metals or toxic chemicals, or with different
carbon and nitrogen sources. Also, the prion state can potentially be lost during cell
division, thus switching the cell back to a more normal phenotype for the growth con-
ditions. Additionally, Ure2, a nitrogen catabolite repressor in its prion state [URE3]
allows cells to constitutively use poor nitrogen sources.
Prions might also be capacitors of evolutionary change and responsi-
ble for solidifying the beneficial phenotypes for the yeast cells. In addition, the prions
are heritable, and therefore can be passed to the next generation, which allows sur-
vival of those progeny under environmental stresses.
Conceptual questions
1. What are prions? How are they different from infectious prions?
2. How are prions different from other genetic elements?
3. What diseases do infectious prions cause?
Discussion points
This paper outlines an area that is often surprising for many people.
Most people who have heard of prions, have heard of them as disease-causing enti-
ties to fear. From this paper, what other purposes do prions serve? How do you think
they are responsible for phenotypic diversity? Do you think it is possible that animal
prions are also responsible for phenotypic diversity?