Quiz2 Flashcards
Which +stranded RNA viruses contain proteins, and thus are not naked?
Coronavirus, retrovirus
-stranded RNA viruses are ready to initiate ____ upon entry
RNA synthesis
Do -SSRNA viruses have proteins attached?
Yes.
Can DSRNA viruses be copied into mRNA by host cell?
Not unless they bring their own polymerase.
What are the two rules of RNA genome?
- They must be copied end to end with no loss of nucleotide sequence.
- Production of viral mRNAs that can be translated efficiently by host/cellular protein synthesis machinery
In de novo initiation of mRNA synthesis from RNA genome (no primer), what special mechanism is used?
slip-back mechanism
Poliovirus (Picornaviridiae) replication strategy
As it is a +SSRNA virus, it can directly be translated. After entry of the RNA, some of it is translated, some proteins are made. Those proteins (some vp proteins) act as protein primers, which is needed for the replication of the RNA. Some entered RNA pass using membrane vesicles, and are replicated in cytoplasm once the proteins are available.
+SSRNA virus examples
- Flavivirus (Dengue)
- Picornavirus (Poliovirus)
- Alphavirus
Alphavirus replication strategy
- Also ready to be translated upon entry.
- Right after entry, proteins necessary for viral replication (RNA pol, accessory proteins, proteases) are translated from the mRNA (nsp proteins)-> proteolytic cleavage.
- Using those proteins, + strand -> - strand replication, and some subgenomic mRNA is also synthesized from the -strand, which is translated to capsid proteins and envelope proteins (ribosomes with rough ER).
Need capped primer.
What kind of primers do polioviruses need?
5’ protein-primer
What kind of primers do alphaviruses need?
Capped primer
Vesicular stomatitis virus replication strategy
Since they are -SSRNA, they have other proteins attached to their genome, so they synthesize some subgenomic mRNAS, all of which get translated by separate cytoplasmic ribosomes (One by ER attached), some of these proteins help in replication; some of the ssRNA generated go back for mRNA synthesis.
Need capped primer.
Which RNA virus replicate in nucleus?
Influenza virus
Influenza virus replication strategy
Each segment produces mRNA inside nucleus. mRNA come out to cytoplasm to produce proteins. They go back to nucleus for replication.
Need capped primer.
Splicing to generate other proteins.
-SSRNA Examples
Unimolecular (Vesicular stomatitis virus)
Segmented (Influenza)
DSRNA virus examples
Reoviridae: Reovirus, rotavirus
Which viruses allow lysosomes to cut out their outer shell to generate ISVPs?
Reoviruses
What are some small DNA viruses that orchestrate the host?
polyomaviridae, papillomaviridae, parvoviridae
What are some large DNA viruses that encode most of their own replication systems?
adenoviridae, herpesviridae, poxviridae
Polyomavirus:
Size__
Type of genome__
Replication strategy + What kind of primer
5kbp
Circular, dsDNA
It is RNA primed, replication forks form an A-T rich region, bi-directional, leading: continuous, lagging: discontinuous
i.e., SV40
Parvovirus:
Size__
Type of genome__
Replication strategy + What kind of primer
4-6 kb
SSDNA, linear
Self-primed (hairpin loops {DNA}), strand displacement method
Adenovirus:
Size__
Type of genome__
Replication strategy + What kind of primer
36-48 kbp
DSDNA, linear
5’ terminal proteins as primer
Strand displacement
Semiconservative, origin at both ends
Herpes simplex virus:
Size__
Type of genome__
Replication strategy + What kind of primer
120-220 kbp
DSDNA, linear (coverts to a circle)
RNA Primed
Replication fork
Replicates as a rolling circle
2 OriS and a unique OriL
semiconservatie
Which host proteins help in circularization of HSV genome?
DNA ligase IV/XRCC4
Poxvirus:
Size__
Type of genome__
Replication strategy + What kind of primer
130-375 kbp
DSDNA, linear
Independent of cell proteins
Strand displacement; DNA Hairpin
Inverted terminal repeats
Which DNA virus replicate in the cytoplasm?
Poxvirus
In epstein-bar virus what origins are used when
oriP is used for low replication
oriL is used for exponential replication
What origins are used when in HPV?
Same origin both low and exponential replication
Of all the DNA viruses we studied, which one was single stranded?
Parvovirus (4-6 kbp)
Of all the DNA viruses we studied, which one was circular?
Polyomavirus
Most small DNA viruses follow which method of replication, and what’s the exception?
Replication fork
Exception: parvoviridae (strand-displacement)
Most large DNA viruses follow which method of replication, and what’s the exception?
Strand displacement
Exception: Herpes simplex virus (replication fork)
What is the poliovirus receptor?
PVR/CD155
Which was the first animal virus picture being taken and when?
Poliovirus, 1985.
Both X-ray crystallography and Electron cryomicroscopy
What is the resolution of electron microscopy?
50-75A
What is the resolution of electron cryomicroscopy?
3.3-20 A
What is the resolution of X-ray crystallography?
2-3A
First picture of what virus taken with X-ray crystallography?
Tomato Bushy Stunt Virus
What staining is used in electron microscopy? Who emits electrons?
The background is stained with electron-dense material phosphotungstate or uranyl acetate. Viruses scatter electrons (1959)
Who took the first picture of a virus using what and when?
Helmuth Ruska; Electron microscopy; 1940
What is genetic economy in the context of viruses and symmetry?
Particles were made with many copies of similar proteins. Their structure promote regular and repetitive interactions between them
What did Watson and Crick discover about viruses and when?
Viruses are either rod shaped or spherical shaped (1956); symmetry.
With what symmetry are identical protein subunits distributed in rod-shaped viruses?
Helical symmetry.
With what symmetry are identical protein subunits distributed in round viruses?
Platonic polyhedra symmetry
What are the symmetry rules which provide rules for self-assembly?
Rule 1: Each subunit has identical bonding contacts with its neighbors
(Repeated interactions between chemically complementary surfaces at the subunit interfaces naturally leads to a symmetric arrangement)
Rule 2: These bonding contacts are usually non-covalent
What are VLPs?
They lack the genetic material, but they are self-assembled into virus like particles; HPV and HBV vaccines are VLPs made in yeast
What are some examples of viruses with helical symmetry?
- Sendai virus -RNA
- Tobacco mosaic virus +RNA
- Vesicular stomatitis virus -RNA
Examples of -SSRNA enveloped viruses with helical symmetry
- Filoviridae (Ebola)
- Orthomyxoviridae (Influenza)
- Paramyxoviridae (Measles, mumps)
- Rhabdoviridae (Rabies)
How can you make a round capsid with proteins of irregular shapes?
- All round capsids have precise numbers of proteins (Multiple of 60)
- Despite being of various sizes themselves, their capsid proteins are 20-60kDa average.
Which process is used to acquire the lipid bilayer envelope from the host cell?
Budding
What kind of glycoproteins are the viral envelope glycoproteins?
Integral membrane glycoproteins
What are the parts of a viral envelope glycoprotein and what roles do they play?
Ectodomain: Fusion, antigenic sites, attachment
Internal domain: Assembly
Oligomeric: Spikes
What are the three parts of the influenza virus glycoprotein hemagglutinin?
Globular head, hinge, stem, perpendicular to the membrane
What kind of glycoproteins do flavivirus have?
E dimer; parallel to the membrane; B-sheets; class II fusion proteins
How many kinds of interactions can the viral proteins have with the viral envelope proteins and what are they?
3.
- Direct
- Via matrix proteins
- Via multiprotein layer
What kind of enzymes can virions contain?
Polymerase, poly(A) polymerase, capping enzymes, integrase and associated proteins, proteases, topoisomerases
What kind of components may virions contain?
Enzymes, activators of transcription, mRNA degrading proteins, mRNA, proteins required for efficient infection
What cellular components can virions contain?
histones, tRNAs, myristate, lipid, cyclophilin A, and many more
What is a subunit?
Single folded polypeptide chain
What is a structural unit?
Protomer, asymmetric; one or more subunits forming the capsid
How do virions move if they have no locomotory power of their own and are inanimate?
Brownian motion, laws of diffusion, electrostatistics
Which viruses do not need receptors/co-receptors?
Yeast and plant viruses
Until 1985, which was the sole virus receptor we knew?
Sialic acid for influenza
How do we know so many virus receptors now?
monoclonal antibodies, molecular cloning, DNA-mediated transformation
What are the receptors for HIV-1?
CD-4, and chemokine receptors CC and CXC
Which receptor does coxsackieB and adenovirus 2 and 5 share?
CAR
Another receptor for adenovirus 2 and 5 except CAR
Integrin avb3/5
Receptor for murine leukemia virus
Cationic amino acid transporter
Human coronavirus receptor
Amino-peptidase N
Measles virus receptor
CD46
Rhinovirus receptor
LDL-receptor
Which viruses share receptor with human poliovirus?
swine herpesvirus, pseudorabiesvirus (PVR/CD155)
Which viruses of the same family bind different receptors?
Rhinoviruses (3) and retroviruses (16)
What linkage is preferred by human strains of influenza virus between sialic acid and galactose?
a(2-6)
What linkage is preferred by avian strains of influenza virus between sialic acid and galactose?
a(2-3)
Steps of clathrin-mediated endocytosis
Virus particle binds to receptor -> Adapter protein binds to receptor proteins -> Clathrin would bind to adapter causing invagination -> Dynamin pinches off vesicle -> Clathrin coated vesicle in cytoplasm -> Clathrin falls off -> The naked vesicle moves with the help of microtubules and fuses with early endosome, at pH 6, it becomes late endosome -> Releases genome
To release genome: Enveloped virions; Fuses with endosomal membrane.
Non-enveloped virions; lysis or permeabilization
What are caveolae?
Lipid raft forming flask-shaped invaginations of the plasma memrabne
Caveolae mediated endocytosis
Same as that of clathrin, but here invagination is caused by the lipid raft, and the caveolae coated virus directly fuses with endosome.
Macropinocytosis for viruses
Virus attach to the cell surface -> Acts as a signal for plasma membrane protrusion through actin filaments -> Closure of the vesicle captures attached virions -> Macropinosome -> Late macropinosome -> early endosome -> Late endosome
How was the diffusion constant calculated for the rates of transport of viral particles by diffusion?
Taking into consideration the radius of the virus and the viscosity of the water at RT. It was assumed that the diffusion constant at cytoplasm would be 500 times lower than that of water.
Poliovirus capsid time to travel in water and in cytoplasm
3.85s; 0.5h
Herpes simplex virus nucleocapsid time to travel in water and in cytoplasm
14.6s; 2.0 hours
Vaccinia virus intracellular mature virion time to travel in water and in cytoplasm
35s; 4.9 hours
How do enveloped viruses penetrate?
They penetrate by fusion with either the plasma membrane or that of the membranes of the intracellular vesicles
How do non-enveloped viruses enter cytosol?
By forming transmembrane channels through which the nucleocapsid or genome can pass; or inducing lysis of the endocytic vesicles
Measles (Paramyxoviridae) Fusion (Enveloped)
2 Proteins (Attachment HN + Fusion F)
Initially the fusion protein is folded towards the membrane of the virus.
HN protein fuses with its receptor on the host cell membrane; Causes a conformational change in the fusion protein ; fusion peptide now exposed, N terminal cleaved by a protease, and can insert into the cell membrane
HIV Fusion
2 Subunits (TM [Has fusion peptide] and SU non-covalently linked).
SU binds CD4-> Conformational change in SU-> SU in turns binds a second chemokine receptor CCR -> Bumps fusion peptide in the right position so it enters the cell.
Influenza endosomal pathway
There are proton pumps on the endosomal membrane; they pump protons into the interior and lower the pH; as it is acidified; HA undergoes conformational change -> globular heads come away-> exposes a fusion peptide -> can fuse with endosomal membrane
What are class III fusion proteins?
Perpendicular to the membrane
Mixture of a helices and b sheets
Form trimers
Which viruses have class III fusion proteins?
Rhabdoviridae and herpesviridae
Which viruses have class I fusion proteins?
Influenza, measles
Which viruses have class II fusion proteins?
Flavivirus (Dengue)
A specific characteristic of class II fusion proteins
Cleavage of a second protein required for activation
A specific characteristic of class I fusion proteins
Proteolytic cleavage activates the fusion protein
How does non-enveloped adenovirus release its genome?
Docking on the nuclear pore
+
Some proteins disassemble the endosomal membrane at low pH
How does non-enveloped poliovirus release its genome?
The receptor for the virus itself catalyzes a conformational change in the virus particle that leads to the formation of a pore in the virus particle from which the genome comes out
Co-receptors in coxsackievirus B
DAF; its receptor CAR is not accessible in the apical surface; its a part of tight junctions; binding to DAF initiates a cascade of signaling events; loosen up cytoskeleton, open up gaps between cells, and then virus move up to CAR and then enters.
What is special about reovirus genome delivery?
dsRNA genome; (segmented) icosahedral; taken up by endocytosis; endosomes acidify; fuse with lysosomes; delivers proteolytic enzymes to lysosomes, enzymes strip off the outer shell; to end up with only the inner shell particle (ISVP-> core). As it is hydrophobic, it can easily penetrate the endosome. RNA is not released but mRNA is produced easily inside the core.
Which proteins are made from direct translation of mRNA in alphaviruses?
Some nsp proteins that form polymerase and other accessory proteins following proteolytic processing
What does a single amino acid change in poliovirus Rdrp cause?
Increased fidelity; reduces viral fitness and virulence under selective pressure
What is rate of error frequencies by RDRP?
1 in 10^3-10^4 NT incorporated
What are the sources of viral diversity?
- Mutation
- RNA editing (Non-templated RNA synthesis)
- Recombination
For polyomavirus, what is the origin of replication like?
A-T rich
What is the adenovirus origin of replication like?
Origin at both ends
What is the HSV origin of replication like?
It has 2 OriS in the short region, and 1 oriL in the long region
