Chapter 8 - Viral Replication Strategies

Negative-sense RNA

genomes have to be converted into the proper form to be made into proteins

infectious RNA

genomes of positive-sense RNA

Plant viruses move from cell to cell within the same plant by

using cytoplasmic connections (plasmodesmata) to infect neighboring cells.

Viruses recognize and attach to host cells by binding to them with their:

Attachment proteins

How are enveloped animal viruses released from a host cell?

Budding

Bgp1a function and virus?

Cell adhesion; MHV-A59

T/F: Nucleic acid entry into the host cell is typically mediated by some kind of protein.

True

Fusion peptide

Fusion at the plasma membrane via a short string of hydrophobic amino acids

Host Range

Host specificity; determined by interactions between the viral attachment proteins and host cell receptors

Membrane fusion occurs only in enveloped animal cells and not in non-enveloped animal viruses. What is the most logical reason for this?

Non-enveloped animal viruses do not have a phospholipid structure to effectively fuse with the host cell membrane.

Class VII: Double-stranded DNA viruses that utilize reverse transcriptase.

The genome serves as a template for the generation of mRNA and full-length RNA molecules. A viral reverse transcriptase generates genomic DNA from this RNA intermediate.

Class V: Negative-sense single-stranded RNA viruses.

The genome serves as the template for formation of mRNA and is referred to as negative-sense (complementary to mRNA). A viral RNA-dependent RNA polymerase produces the mRNA. This enzyme also is required for genome replication, which usually occurs in the cytoplasm.

What step must occur in order for an animal virus genome to enter a host cell for replication?

Uncoating

Which of the following components of viral replication have been targeted by some anti-viral drug?

Viral RNA-dependent RNA polymerase Viral RNA-dependent DNA polymerase Viral reverse transcriptase

What is the relationship between viral attachment proteins and host cell receptors?

Viral attachment proteins bind to proteins, lipids, or sugars on the surface of host cells (host cell receptors). For the virus, binding of the attachment protein to a receptor is the first step toward gaining access to the inside of the host cell.

Endocytosis

Viral envelope fuses with the endocytic vesicle membrane

Describe two ways that viral genomes can become enclosed within capsids during assembly

Viral genomes can have the capsid proteins assemble around them (as is the case with tobacco mosaic virus) where the capsid proteins bind and assemble around specific "packaging sequences" present on the viral genome. Conversely the empty capsids can be pre-assembled from capsomeres and the viral genome can then be inserted into it (as is the case with poliovirus)

Why is it difficult to design antiviral drugs?

Viruses use a wide variety of host cell enzymes, so host cells would also be impacted by the antiviral drug

Once a host cell releases an enveloped animal virus through budding, the host cell membrane is _____.

Weakened and intact

In some temperate bacteriophages, the lytic and lysogenic states are regulated by the interaction of two virally-encoded proteins, cI and cro. How do these regulate the two states?

When cro levels are high, cI expression is blocked, initiating lytic replication

In the Baltimore viral replication system

a. Class I contains double stranded DNA virusea c. Class VII contains double stranded DNA viruses

The influenza virus, like many enveloped RNA viruses, enters host cells via

endocytosis

The process in which the host cell membrane surrounds the entire virus forming an endosome is called:

endocytosis

A fundamental difference between enveloped and non enveloped mammalian viruses is:

enveloped viruses egress by budding off the host cell while non-enveloped viruses egress when the host cell becomes unstable and lyses.

positive-sense RNA

genomes that are ready for immediate translation into proteins

For most bacteriophages, the attachment proteins are...

portions of the tail fibers

Viruses ensure host cell specificity through the interaction of viral ___ and host cell ___.

proteins; receptors

Once successfully attached to a host cell, the virus' genome must enter the host cell in order to begin _____.

replication

In the experiment investigating host specificity for bacteriophages T2 and PP01

researchers switched the attachment proteins on bacteriophages T2 and PP01

positive-sense RNA is also known as

ssRNA(+)

negative-sense RNA is also known as

ssRNA(-)

Mutations in the virus genome can alter the _____.

three-dimensional shape of the virus attachment proteins

Sialic acid function and virus?

various functions; influenza virus

Virulent Phages

viruses the reproduce through the lytic cycle and kill their host cells

How do plant cells get infected with viruses, considering they have a thick cell wall?

An outside force, like an insect. When an insect feeds, it damages the cell wall. If an insect feeds on an infected plant, it can transmit a virus to another plant when it feeds on that plant.

How can antibodies and antiviral drugs play a role in blocking viral attachment to host cells?

Antibodies produced by the host can bind to the viral attachment protein and interfere with viral attachment and entry. Similarly, drugs can be designed to interfere with viral attachment by binding specifically to either the viral attachment protein or the host cell receptor. Maraviroc (Selzentry) is a recently approved drug that binds CCR5, one of the host cell receptors for the HIV 2 virus.

CR2 function and virus?

B cell activation; Epstein-Barr virus

In order to combat bacterial infections, some researchers have studied bacteriophages as a means to combat these infections. Why are bacteriophages a potential option for treatment of bacterial infection?

Bacteriophages lyse bacterial cells upon exit Bacteriophages infect only bacterial cells Bacteriophages use host cells for viral replication

What are the basic criteria for antiviral drugs?

Be easily administered; be easily produced; be relatively affordable; have few side affects; decrease the severity of the disease

Protease Inhibitor

Blocks viral protease enzyme from cutting and assembling proteins to form structural elements of new HIV (6) tipranavir, indinavir, saquinavir, lopinavir, fosamprenavir, ritonavir, darunavir, atazanavir, nelfinavir

ICAM-1 function and virus?

Cell adhesion; rhinovirus

Class I: Double-stranded DNA virus

DNA serves as a template for synthesis of mRNA. Genome replication usually occurs in the nucleus of the host cell and uses the host DNA-dependent DNA polymerase. Some viruses in this class, like the poxviruses, replicate in the cytoplasm, using viral enzymes.

How do non-enveloped viruses enter host cells?

Receptor-mediated endocytosis (for the most part)

What is receptor-mediated endocytosis and how is it involved in virus entry?

Receptor-mediated endocytosis describes a process whereby cells internalize large particles after they bind specific receptors on the cell surface. During this process the particle becomes encased in a membrane bubble known as an endosome. Many viruses use receptor-mediated endocytosis to gain entry into host cells. After being internalized, however, the virus particle (virion) must still have a strategy to escape the endosome.

How are the enzymes reverse transcriptase and integrase involved in retrovirus replication in host cells?

Reverse transcriptase converts the single-stranded RNA genome of the retrovirus into double-stranded DNA. This double-stranded DNA genome then enters the nucleus of the host-cell where the viral integrase enzyme integrates the viral DNA into the host cell genome. The viral genome that is integrated into the host DNA is called a "provirus".

The Western blot is a common laboratory technique based upon which of the following fundamental biological interactions?

Specific binding between target proteins and antibodies.

How do bacteriophages infect a cell without the capsid entering the host cell?

Tail fibers facilitate attachment of bacteriophage to specific bacterial host cells; the virus injects its nucleic acid into the host cell and the viral genome enters the cytoplasm.

Packaging sequence

The assembly of icosahedral and helical virions differs slightly. Icosahedral capsomers spontaneously assemble into an empty capsid. The genome includes a ______ _____ which is bound by a protein that then "stuffs" the genome into the empty capsid.

How is the egress of new virus particles different for an enveloped virus versus a non-enveloped virus? Explain each process

The envelope of enveloped viruses is derived from the host cell membrane. Egress of these viruses requires a number of steps. First, viral proteins destined for the envelope must insert into the host cell membrane. These viral envelope proteins are usually transmembrane proteins that are delivered to the appropriate location by their signal sequence and transmembrane domains. Second the assembled nucleocapsid (genome/capsid complex) must recognize and associate with the envelope proteins. Third, the envelope and nucleocapsid must bud from the host cell to generate an enveloped virion. Non-enveloped viruses do not bud from the cell but instead escape directly from the cytoplasm after the host cell lyses.

What is membrane fusion and how is it involved in enveloped virus entry?

The enveloped virus and the host cell are both bounded by a lipid bilayer. In order for the viral genome to gain access to the host cell cytosol these two membranes must fuse into a single lipid bilayer. The fusion of two lipid bilayers does not occur spontaneously under normal conditions and must be facilitated by specific hydrophobic peptides called "fusion peptides". When the host cell and viral envelope bilayers fuse, the contents of the viral envelope

Class IV: Positive-sense single-stranded RNA viruses.

The genome can be recognized by the host ribosomes and thus functions directly as mRNA; it is referred to as positive-sense (same as mRNA). Genome replication usually occurs in the cytoplasm and requires a viral RNA-dependent RNA polymerase.

Nucleoside analog

Chemical mutagens that mimics the naturally occuring bases are called

How do enveloped viruses enter the host cell?

Endocytosis

CD4 function and virus?

Immune cell interactions; HIV

Receptor

Molecule on the surface of the host cell that are hijacked by the virus for cell attachment

The role of viral fusion peptides is to

mediate the fusion of viral membranes and host cell membranes during the entry phase of the viral replication cycle.

List the sequence of events in viral replication in the proper order 1. Uncoating viral particle to make genetic material accessible 2. Egress out of host cell 3. Bind receptor on host cell 4. Replication of viral genetic material 5. Assembly of mature viral particles 6. Viral particle enters host cell

3-6-1-4-5-2

Prophage

A phage genome that has been inserted into a specific site on the bacterial chromosome.

Provirus

A viral genome that is permanently inserted into a host genome.

Lysogen

A viral reproductive cycle in which the viral DNA is added to the host cell's DNA and is copied along with the host cell's DNA

Uncoating

AKA viral capsid disassembly; occurs to allow viral genome to interact with host cell mechanisms. Involves conformational changes or proteolytic processing

The drug AZT, used to treat HIV, inhibits viral DNA production. How does it do this?

AZT is structurally similar to thymidine (it is a thymidine analog) that lacks the 3' hydroxyl group necessary for DNA elongation. This group is instead replaced by an azide (N3) group. The reverse transcriptase of HIV has approximately 100-fold more affinity for AZT than human DNA polymerase and therefore this drug is capable of disrupting viral replication at concentrations that have minimal effect on the host.

Reverse Transcriptase (RT)

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.

RNA-dependent RNA polymerase

An enzyme that produces an RNA complementary to a template RNA strand.

Integrase

An enzyme used by retroviruses to splice itself to a genome.

In addition to the replication of the viral genome, what are some additional steps in the viral replication cycle that could be targeted by antiviral drugs?

Drugs have been developed to target many steps of the viral lifecycle. Protease inhibitors have been used to disrupt viral assembly. Other drugs could target viral binding and entry, viral uncoating, viral movement from the cytoplasm to the nucleus, viral assembly, and viral escape.

In plant virus infections, viral nucleic acids are free to interact with the host cell's _____ in to begin genome replication immediately.

Enzymes; machinery

T/F: All DNA viruses replicate in the nucleus, using host cell polymerases and all RNA viruses replicate in the cytoplasm of the host cell, using virally-encoded polymerases.

False

T/F: If a virus encounters a cell without the correct surface receptor, the virus will be able to infect the cell.

False

T/F: Viruses that infect cells with cell walls (either plants and bacteria) rely on the help of outside forces to damage the host walls to allow entry of the viral genetic material.

False

T/F: Viruses that infect eukaryotic cells typically recognize and bind with common cell membrane proteins such as integrins and adhesins, thus ensuring as wide a cell host range for the virus as possible.

False

T/F:A major difference between enveloped and non-enveloped viruses is that enveloped viruses display attachment proteins on their surface while non-enveloped viruses do not.

False

What are the 7 classes of viruses (Baltimore classification scheme)?

I: Double-stranded DNA virus II: Single-stranded DNA virus III: Double-stranded RNA virus IV: Positive-sense single-stranded RNA virus V: Negative-sense single-stranded RNA virus VI: Single-stranded RNA viruses that utilize reverse transcriptase VII: Double-stranded RNA viruses that utilize reverse transcriptase

How and where do many DNA viruses such as SV40 replicate in the host cell?

Many DNA viruses utilize the host cell DNA polymerase to replicate their genomes, which requires that the viral genome enter the host cell nucleus. Such viruses often encode factors, like the large T antigen of the SV40 virus, that drive the host cell towards DNA replication.

Class II: Single-stranded DNA virus

Messenger RNA forms from a double-stranded DNA intermediate. Genome replication occurs as the single-stranded genome becomes converted to double-stranded DNA, which then serves as a template for the production of more genomes

Class III: Double-stranded RNA viruses.

Messenger RNA is generated from one strand of the double-stranded genome. Genome replication generally occurs in the cytoplasm and requires a viral RNA-dependent RNA polymerase.

Explain why viruses of mammals generally undergo some form of uncoating, but viruses of bacteria usually do not

Most viruses of animals enter the host cell cytoplasm as an intact particle containing the viral genome surrounded in a protein shell. In order for the viral genome to replicate and direct the synthesis of viral proteins the genome must be released from the associated proteins. Unlike animal viruses, most bacteriophages inject their genomes directly into the host cell cytoplasm, leaving the protein shell on the outside of the bacterial cell. Therefore phage entry and "uncoating" occur simultaneously.

What are nucleoside analogs and how do they function as antiviral drugs?

Nucleoside analogs are structurally similar to the building blocks of RNA and DNA. Effective analogs have higher affinity for the viral RNA or DNA polymerases than for the host enzymes and are incorporated into the viral RNA or DNA as it is being synthesized. This blocks synthesis of the viral nucleic acid to prevent new viruses from being formed.

Temperate Phages

Phages that are capable of using either the lytic or lysogenic cycle.

Contrast the replication strategy of positive-sense RNA viruses with that of negative-sense RNA viruses

Positive-sense RNA viruses have genomes that can be translated directly by host-cell ribosomes to generate viral proteins (their genomes "look" like an mRNA molecule). Therefore these viruses do not need to bring along their own proteins to establish an infection. Negative-sense RNA viruses have to first make a complementary (positive) copy of their genome before any viral proteins can be produced. For this to occur the negative sense RNA viruses must bring a copy of their RNA-dependent RNA polymerase that enters the cell at the same time as the viral genome

How can protease inhibitor drugs specifically disrupt viral assembly?

Protease inhibitor drugs can prevent the proteolytic processing (cleavage) of viral precursor proteins into mature (processed) forms that are required for the virus to assemble or to make a virion that is able to infect neighboring cells.

Viral Attachment Protein

Proteins that allow host cell recognition & binding to host cell upon infection

Describe the lytic and lysogenic replication cycles of bacteriophages

The lytic replication cycle of a bacteriophage occurs when the phage uses a host-cell or phage-encoded DNA polymerase to make multiple copies of the phage genome. Each of these newly replicated genomes is packaged into a phage particle (protein coat) prior to lysis of the host cell. Lysogenic replication, in contrast, occurs when the phage integrates its genome into that of its host. The phage genome is copied at the same time as the host-genome - no phage particles are produced and host-cell lysis does not occur. Phages that are lysogens can be triggered to enter lytic replication if the host-cell becomes damaged.

What is meant by the term "host range"?

The term "host range" is used to describe the types of animals (or bacterial cells, in the case of bacteriophages) that can be infected by a virus - also referred to as "host specificity". HIV, which can only successfully infect humans and a few primate species has a fairly small host range. Some strains of influenza can infect a larger number of species (several species of birds and mammals, for example) and therefore these viruses stains have a larger host range than does HIV. A major factor that determines host range is whether the viral attachment protein can bind to a receptor on the surface of the host cells.

Class VI: Single-stranded RNA viruses that utilize reverse transcriptase.

The viral enzyme reverse transcriptase, an RNA-dependent DNA polymerase, converts the ssRNA genome into dsDNA, which then becomes integrated into the host genome. Messenger RNA and new genomic RNA is generated from this integrated DNA.

Please answer the following questions regarding this scenario. A virus recognizes surface protein B on the surface of an epithelial cell. Normally this virus does not infect endothelial cells. What is the most likely reason this virus does not infect endothelial cells?

The virus cannot infect endothelial cells because endothelial cells do not express protein B on their surface.

A mutation occurs that renders a bacteriophage's enzyme used for degrading the cell wall useless. What might occur in the infection process?

The virus will not be able to continue the infection process and will not be able to replicate in the host.

How do non-enveloped viruses attack host cells?

They much make their genome accessible to the replication/transcription/translation mechanisms

OmpF function and virus?

Transmembrane channel; T2

T/F: Bacteriophages can inject their DNA into a host cell.

True

T/F: Nonenveloped animal viruses are released from their host cells by host autolysis.

True

T/F: Positive-sense RNA viruses are referred to as infectious RNA because the RNA can lead to the production of new viral particles

True

T/F: Protease inhibitors block the action of enzymes responsible for modifying precursor virons into mature viral particles.

True

T/F: Protein synthesis is not a viable target for antiviral drugs because viruses use host cell ribosomes to make viral proteins.

True

T/F: Signal sequences identify viral proteins to be transported and inserted into the cellular membrane.

True

T/F: The type of nucleic acid determines a virus' ability to replicate in a host cell.

True

T/F: Viral polymerases are common targets for antiviral drug therapy because they are less specific than host cell polymerases and are more likely to incorporate modified nucleic acids.

True

Nucleoside analogs such as AZT are drugs that

are structurally similar to normal nucleosides and interfere with nucleic acid replication

RNA-dependent DNA polymerase

converts the single-stranded RNA retrovirus genome into double-stranded DNA