Module 10 - Viral Replication Strategies Flashcards
In order to replicate, what must all viruses do?
- Recognize host cells
- Make genome available to host cell machinery
- Replicate genome
- Make multiple copies of required proteins
- Assemble new viral particles
- Exit the cell
What is the consequence of viruses having a narrow host range?
They can only infect and replicate within specific cells
What determines the host range of a virus?
The interactions between viral and cellular proteins
What does the viral attachment protein do?
Interacts with the receptor on the host cell to allow entry
How come receptors cannot be eliminated to prevent infections?
These receptors are generally essential for the host cell
What is the cellular function of the CD4 receptor?
Immune cell interactions
What virus attaches to the CD4 receptor?
HIV (Retroviridae)
What is the cellular function of the ICAM-1 receptor?
Cell adhesion
Which virus attaches to the ICAM-1 receptor?
Rhinovirus (Picornaviridae)
What is the cellular function of the Bgp 1a receptor?
Cell adhesion
Which virus attaches to the Bgp 1a receptor?
MHV-A59 (Coronaviridae)
What is the cellular function of the CR2 receptor?
B-cell activation
Which virus attaches to the CR2 receptor?
Epstein-Barr virus (Herpesviridae)
What is the cellular function of the sialic acid receptor?
Various functions
Which viruses attaches to the sialic acid receptor?
Influenza virus (Orthomyxoviridae)
What is the cellular function of the OmpF receptor?
Transmembrane channel
Which virus attaches to the OmpF receptor?
T2 (Myoviridae)
What receptor does HIV (Retroviridae) bind to?
CD4
What receptor does Rhinovirus (Picornaviridae) bind to?
ICAM-1
What receptor does MHV-A59 (Coronaviridae) bind to?
Bgp 1a
What receptor does Epstein-Barr virus (Herpesviridae) bind to?
CR2
What receptor does Influenze virus (Orthomyxoviridae) bind to?
Sialic acid
What receptor does T2 (Myoviridae) bind to?
OmpF
What are bacteriophages?
Viruses that infect bacteria
What do most bacteriophages uses for attachment?
Tail fibers which recognize receptors present on the surface of bacterial cells
What 2 molecules does T2 recognize?
Lipopolysaccharide, and the outer membrane protein porin F precursor (OmpF)
What bacteria does T2 infect?
K-12 strain of E. coli
What strain of E. coli can T2 not infect?
O157:H7 (pathogenic strain)
What proteins are found at the tips of the T2 phage?
GP37 and GP38
How was it proven that T2 host range was due to strain specific differences in receptors?
The proteins on T2 tail fibers were replaced with proteins from a phage that could infect O157:H7 E. coli
What happened when the proteins on T2 tail fibers were replaced with proteins from a phage that could infect O157:H7 E. coli?
The T2 phage could not infect K-12 E. coli, but it could infect O157:H7 E. coli
How do enveloped viruses attach to host cells?
By a specific viral protein embedded within the envelope
What viral attachment protein is found in H1N1 influenza virus?
HA
What does HA stand for?
Hemagglutinin
How does adenovirus attach to a host cell?
With a viral attachment protein that extends from the capsid
How does poliovirus attach to a host cell?
With a protein that is part of the capsid itself
What do adenovirus and poliovirus have in common?
They are both non-enveloped viruses
What virus have scientists used to study strain specificity?
MHV
What does MHV stand for?
Mouse hepatitis virus
What viruses are related to MHV?
SARS coronavirus and MERS coronavirus
How come two strains of mice showed different susceptibility to MHV?
They had different protein receptors
Compare the Bgp 1a and Bgp 1b receptor.
The two proteins are structurally similar, but differ in amino acid sequences
What is the consequence of the amino acid differences in the Bgp 1 receptor?
It changes the conformation, so MHV interacts more strongly with Bgp 1a than Bgp 1b
What must happen after a virus binds to a host cell?
The virus or its genome must enter the cell
After an enveloped virus binds to a host cell, what separates the viral genome from the cell?
Two lipid bilayers (the viral envelope and the plasma membrane)
What interaction triggers receptor mediated endocytosis of influenza?
HA with sialic acid glycoprotein
What method does influenza use to enter the host cell?
Receptor mediated endocytosis
What causes the conformational change of HA?
Acidification of the viral envelope
What happens when HA changes conformation?
It exposes a fusion peptide
What does the fusion peptide do in influenza virus?
It helps the fusion of the viral envelope and the endosomal membrane
What happens when the viral envelope fuses with the endosomal membrane?
The nucleocapsid is released into the cytoplasm
How does HIV anchor to a host cell?
The attachment protein gp120 binds to the CD4 receptor
What happens when gp120 binds to CD4?
There is a conformational change in gp120, allowing it to bind to the coreceptor
What happens when gp120 binds to the coreceptor?
This causes additional conformational changes, leading to the exposure of a fusion protein on gp41
What is the purpose of gp41 in HIV?
It has the fusion protein that helps the fusion between the viral envelope and the plasma membrane
What was the first antiretroviral drug approved by the FDA, and when?
Fuzeon in 2003
What does Fuzeon do?
It is designed to prevent entry of HIV by preventing fusion
How does Fuzeon work?
It binds to gp41, preventing conformational change and fusion
What does entry for non-enveloped viruses require?
Direct penetration of cellular membrane by virus particle or genome
Generally, how do non-enveloped viruses enter a cell?
Through receptor mediated endocytosis
How does receptor mediated endocytosis work?
Virus particles bind to the receptor on the cell surface, leading to endocytosis
What happens when a non-enveloped virus enters a cell through receptor mediated endocytosis?
The low pH of the endosome causes a conformational change in the capsid (similar to influenza HA protein)
What happens when the capsid undergoes a conformational change in the endosome?
It exposes a pore forming domain that leads to the formation of a hole in the membrane
What is the purpose of the pore forming domain in a non-enveloped virus?
It allows the viral capsid or genetic material to enter the cytoplasm of the host cell from the endosome
What type of virus is reovirus?
A non-enveloped virus
What part of a bacteriophage enters the host cell?
The genome (not the particle itself)
What happens when T4 binds to the receptor?
It leads to the contraction of the T4 tail
What is the result of the T4 tail contracion?
The tail core pushes through the cell wall, bringing the phage DNA in contact with the plasma membrane
How does the phage DNA in T4 enter the cell?
Through the help of a pilot protein
What does the pilot protein do?
It binds to the phage DNA, and helps it penetrate the plasma membrane
Where does the viral capsid go in a bacteriophage infection?
It remains outside the cell
True or false: plant viruses, like bacteriophages, inject their genome into host cells
False: they do not inject their genome
How do plant viruses enter cells?
They rely on the help of external forces, such as insects
How do insects help plant viruses?
- Insects feed on plants, damaging the cuticle and cell wall
- When feeding, insects may acquire viruses, and transmit the particles
How come plant viruses rely on external forces to enter cells?
Due to the tough cell wall
What is tomato yellow leaf virus?
A plant virus
For most mammalian viruses, what is needed to allow for the viral genome to interact with the required host cell machinery?
Some form of uncoating
What is the first step of poliovirus uncoating?
After binding, the particles undergo a conformational change, resulting in the loss of capsid protein VP4
What happens when poliovirus loses VP4?
VP1 can interact with the cell membrane
What does VP1 do?
It creates a pore through the cell membrane
How does the RNA in poliovirus get from the capsid to the cytoplasm?
It leaves the partially disassembled capsid through the VP1-induced channel
How many different replication groups are there?
7
How many DNA replication groups are there?
3 (dsDNA, ssDNA, dsDNA using RT)
How many RNA replication groups are there?
4 (dsRNA, + ssRNA, - ssRNA, ssRNA using RT)
What is Baltimore classification based on?
How the mRNA of different viruses is produced
What is a Class I virus?
dsDNA virus
How do Class I viruses make mRNA?
By using dsDNA genome as a template
Where does genome replication occur for Class I viruses?
Usually in the nucleus of host cells
What is an exception to the genome replication rule for Class I viruses?
Pox (replicates in cytoplasm using viral enzymes)
How do Class I viruses replicate the genome?
Through host cell DNA-dependent DNA polymerase
What is a Class II virus?
ssDNA virus
How do Class II viruses make mRNA?
By using a dsDNA intermediate
When does genome replication of Class II viruses occur?
As ssDNA gets converted into dsDNA, which serves as the template for more genomes
What is a Class III virus?
dsRNA virus
How do Class III viruses make mRNA?
From one strand (negative strand) of the ds genome
Where does genome replication of Class III viruses occur?
In the cytoplasm
How do Class III viruses replicate the genome?
Through viral RNA-dependent RNA polymerase
What is a Class IV virus?
ssRNA, positive sense
How do Class IV viruses make mRNA?
The genome can be recognized by host ribosomes, and functions directly as mRNA
Where does genome replication of Class IV viruses occur?
In the cytoplasm
How do Class IV viruses replicate the genome?
Through viral RNA-dependent RNA polymerase
What is a Class V virus?
ssRNA, negative sense
How do Class V viruses make mRNA?
By using viral RNA-dependent RNA polymerase on the genome (serves as template for mRNA)
How do Class V viruses replicate the genome?
Through viral RNA-dependent RNA polymerase
Where does genome replication of Class V viruses occur?
In the cytoplasm
What is a Class VI virus?
ssRNA, uses RT
What type of enzyme is RT?
RNA dependent DNA polymerase
How does a Class VI virus use RT?
It converts ssRNA genome into dsDNA, which becomes integrated into the host genome
How do Class VI viruses make mRNA?
From the integrated dsDNA in the host genome
How do Class VI viruses replicate the genome?
From the integrated dsDNA in the host genome (make more ssRNA)
What is a Class VII virus?
dsDNA, uses RT
How does a Class VII virus make mRNA?
From the dsDNA genome
How do Class VII viruses replicate the genome?
By using RT on the mRNA
How do Class VII viruses use RT?
By recreating genomic dsDNA from the mRNA
What does the genetic material of DNA viruses resemble?
The genetic material of host cells
Generally, where does replication of DNA viruses occur?
In the nucleus
What do DNA viruses use to replicate the genome?
Host cell DNA polymerase
What do DNA viruses use to produce mRNA molecules?
Host cell RNA polymerase
What is an example of a typical DNA virus (that replicates in the nucleus)?
Papillomaviruses
What are certain strains of papillomaviruses strongly associated with?
Cervical cancers
What is an example of an atypical DNA virus?
Poxviruses
Why is a poxvirus an atypical DNA virus?
It replicates in the cytoplasm, not the nucleus (like most DNA viruses)
What type of virus is poxvirus?
Class I (dsDNA genome)
What proteins do poxviruses bring with them when infecting a cell?
Viral RNA polymerase and several transcription factors
How is poxvirus mRNA made?
From using the viral RNA polymerase in the cytoplasm
What happens to the poxvirus mRNA?
It gets translated in the cytoplasm
What is one key enzyme produced by poxvirus mRNA?
A viral DNA polymerase to replicate the genome
How does poxvirus replicate its genome in the cytoplasm?
One gene it encodes for is a viral DNA polymerase, which replicates the genome
What do early genes in poxvirus code for?
DNA polymerase and other proteins necessary for genome replication
What do late genes in poxvirus code for?
Structural proteins needed for capsid and envelope formation
In terms of the central dogma, what do cells usually do?
Make RNA from DNA
In terms of the central dogma, what do cells not usually do?
Make RNA from RNA
Which protein produces RNA from an RNA template?
RNA dependent RNA polymerase
For RNA viruses, what does RNA dependent RNA polymerase do?
Makes genomic RNA, and mRNA that can be recognized and translated by host ribosomes
Where does replication of RNA viruses usually occur?
In the cytoplasm
What is a retrovirus?
A virus that uses RT (Class VI and Class VII)
What class of virus is poliovirus?
Class IV (+ ssRNA)
Where do Class IV viruses get RNA polymerase?
It is translated directly from the ssRNA genome
True or false: Class IV viruses need to bring RNA polymerase into the cell
False: it can be transcribed directly from the + sense ssRNA genome
What happens if the poliovirus genome is artificially injected into the host cell?
It will still cause the same infection
How come injecting the poliovirus genome directly into a host cell will cause the same infection?
It is a + sense ssRNA genome, so it can be used directly by the cell
What is another name for viral + sense ssRNA?
Infectious RNA
What is - sense ssRNA used for?
A template for the complementary + sense ssRNA (which can be read by the host cell ribosomes)
Where do Class V viruses get RNA polymerase?
They bring it with them
True or false: Class V viruses need to bring RNA polymerase into the cell
True: they need it to create the + sense ssRNA from the - sense ssRNA genome
What does the ssRNA genome of retroviruses produce?
RT
What does RT do once an RNA retroviruses enters the cell?
It uses the RNA as a template to make a DNA-RNA heteroduplex
What happens after RT makes the DNA-RNA heteroduplex?
It degrades the original RNA molecule with endonuclease activity, and converts the ssDNA into dsDNA
What is the endonuclease activity of RT?
RNAse H
What happens after RT makes dsDNA?
The dsDNA moves to the nucleus, where it is integrated into the genome
How is dsDNA integrated into the genome (for retroviruses)?
Through the viral enzyme integrase
What does integrase do?
Integrates viral dsDNA into the host cell genome
What is the integrated viral DNA known as?
Provirus or proviral DNA
What happens once the dsDNA is integrated into the genome?
The host cell RNA polymerase transcribes the integrated viral genome, producing mRNA
What happens when the full length genomic RNA molecules leave the nucleus (in Class VI viruses)?
The viral mRNA is translated in the cytoplasm to produce viral proteins and new viral RNA genomes
What can the genome of a bacteriophage be?
DNA or RNA
How do DNA bacteriophages make new genomic copies?
Through the host cell DNA polymerase
How do RNA bacteriophages make new genomic copies?
By using viral RNA polymerase
What type of genome do most RNA bacteriophages have?
+ sense RNA genome
What do lytic phages do?
They replicate and lyse the host cell
What is another name for lytic phages?
Virulent phages
What do temperate phages do?
They either insert their genome into host cells, or enter the lytic phase
How does the genome of P1 of E. coli exist?
As a plasmid in the cytoplasm
What type of virus is P1?
A temperate phage
What does the cell do when it has an integrated viral genome?
It continues to replicate the viral genome without production of viral particles
What can lambda phage do in E. coli to replicate?
It can either lyse the cell, or integrate the genome into the genome of the host cell, and replicate with the host DNA
What is a prophage?
The quiescent viral genome that exists as either a plasmid or integrated into the host genome
What is a lysogen?
A cell containing a prophage
What happens when linear lambda phage DNA enters the cell?
It becomes circular
What does circular lambda phage DNA do?
It integrates into the viral genome (via integrase enzyme)
What is c1 and what does it do?
Viral repressor protein that represses cro genes
What is cro and what does it do?
Repressive protein required for lytic replication
What happens if there are high amounts of c1?
cro is repressed, and lysogenic phase is maintained
How can c1 levels drop in a cell?
In response to damage causes by UV light or chemical mutagens
What happens when c1 levels drop?
The cro protein represses the c1 protein needed to maintain the lysogenic phase
What happens if there are high amounts of cro?
The proteins for lytic replication are produced, maintaining lytic replication
How can lambda phage switch between lytic and lysogenic replication?
Based on the relative ratio of the two repressor proteins c1 and cro
How do cro and c1 levels change in the cell?
In response to the overall health of the cell
What does c1 bind to?
The cro promoter
What does cro bind to?
The c1 promoter
What happens after a virus makes copies of the viral genome and proteins?
New viral particles must assemble and leave the infected cell
For assembly, what are many viral components?
Self assembling
What is the advantage of self assembly?
From an energetic perspective, it is fast and cheap
How do viral proteins assemble?
Around the viral nucleic acid, or inserted into an empty capsid
How does TMV assemble?
The viral proteins assemble around the viral nucleic acid
What must a viral genome have to allow viral proteins to assemble around it?
A sequence specific assembly motif
What is another name for the sequence specific assembly motif?
The packaging sequence
How does poliovirus assemble?
An empty capsid is partially assembled, and the genome is inserted
What does the mechanism of egress depend on?
The virus type and host cell type
What are the steps for egress of enveloped viruses?
- Viral proteins are inserted into the host cell membrane
- Nucleocapsid migrates to membrane with viral proteins
- Budding of nucleocapsid
What does budding of the nucleocapsid result in?
A lipid bilayer containing enveloped proteins
What does the envelope of HIV contain?
gp120 and gp41 proteins
How do non-enveloped viruses egress?
Through lysis of the cell
How do bacteriophages egress?
They produce specific enzymes to destroy the cell membrane and cell wall
How do non-enveloped mammalian viruses egress?
The cell becomes unstable due to viral replication (no specific enzymes required)
True or false: plant viruses lyse the host cell
False: they do not lyse the host cell
How do plant viruses egress?
They travel from one cell to another through cytoplasmic connections
How can plant viruses spread from one plant to another?
Through disruption of the cell wall structures by outside forces (insects)
How do viruses move towards cells?
Via simple diffusion
What is E. coli strain O157:H7 associated with?
Severe intestinal disorders in humans
What is T2ppD1?
The altered T2 phage with different tail fiber proteins (to test host range)
What did scientists use to study strain susceptibility to MHV?
SDS page of the two different receptors
How do antibodies block viral infections?
They bind to viruses to block the interaction between virus and host cell to prevent attachment
What is Maraviroc used to treat?
HIV
What is another name for Maraviroc?
Selzentry
How does Maraviroc work?
It blocks the interaction between the viral attachment protein and the CCR5 co-receptor by binding to CCR5
What types of patients is Maraviroc used for?
People already with the virus (to slow down progression) (not for prevention)
What type of HIV is Maraviroc ineffective against?
Strains of HIV that use CXCR4 co-receptor
How does HIV enter the cell?
It fuses directly with the envelope (no endosome)
What is the structure of the fusion peptide?
A short string of hydrophobic amino acids
What is meant by a virus being pH-dependent?
It relies of the low pH of the endosome to function
What is a cuticle?
A thick waxy cover to protect the plants
What are plasmodesmata?
Cytoplasmic connections between plant cells
Which types of viruses generally require uncoating?
Mammalian viruses
Which types of viruses do not require uncoating?
Bacteriophages
What does PVR stand for?
Poliovirus receptor
What receptor does poliovirus bind to?
PVR
What happens when poliovirus binds to PVR?
The 160S particle becomes a 135S particle
What happens when poliovirus becomes a 135S particle?
Lipophilic portions of VP1 and VP4 are exposed
Which factors do not inhibit poliovirus replication?
Blocking endocytosis, and blocking endosome acidification
How does poliovirus RNA likely enter the cell?
Through either the plasma membrane or the endosomal membrane
What is the result of measuring the kinetics of viral replication?
A one-step multiplication curve
What can be determined from a one-step multiplication curve?
The burst size (average number of progeny viruses released from one cell)
What family is SV40 a part of?
Polyomaviridae family
What is the genome is SV40?
Small circular DNA genome
What viral proteins unwinds the viral genome for SV40?
Large T antigen
What happens after the viral genome of SV40 is unwound?
Host cell primases and DNA polymerases replicate the genome
How does large T antigen facilitate viral replication?
By priming the cell towards DNA synthesis
How does large T antigen prime the cell towards DNA synthesis?
By interacting with cell cycle regulatory proteins
What can viruses facilitating DNA synthesis lead to?
Immortal cell lines
Besides SV40, what other virus can drive the cell towards DNA synthesis?
HPVs (Human Papillomaviruses)
For polyomaviruses and papillomaviruses, what is responsible for transcription of the viral genes?
The host cell RNA polymerase II
What happens if + sense RNA is converted into a DNA plasmid?
The plasmid becomes infectious
What is the purpose of making an infectious plasmid from + sense RNA?
Researchers can mutate the plasmid (representing the viral genome), and observe the effect on cells
What does HIV cause?
AIDS
Why were retroviruses initially studied?
Their ability to form tumors
Who studied the first retrovirus?
Peyton Rous in 1911
What is the most famous retrovirus?
HIV
How does HIV assemble?
It forms a non-infectious precursor, which is then proteolytically processed to a mature, infectious particle
How do protease inhibitor drugs work as antivirals?
They block proteolytic processing for proper HIV assembly
What is the initial precursor capsid of poliovirus made out of?
VP1, VP3, and VP0
How is poliovirus processed to become a mature virion?
VP0 is cleaved into VP2 and VP4
What is the advantage of a segmented genome?
It allows for genetic variability
What virus has a segmented genome?
Influenza (8 - ssRNA)
How is the nucleocapsid brought in contact with the membrane for egress?
Interactions with amino acids of the tail region with the nucleocapsid
What enzyme does T4 make for egress?
Lysozyme (break down cell wall)
