Viral Pathogens: Classification, Biology, Diseases I Flashcards
Describe a general transmission cycle of a virus
Reservoirs → vectors → Reservoirs and Dead-end hosts
vertical transmission happens between vectors as well
Describe the different viral genome structures
- ds circular DNA
- ds linear DNA
- ds linear RNA
- ss linear RNA
- ss linear DNA
- segmented RNA
What are the two types of virus?
RNA
DNA
What direction can a viral genome be encoded in?
either way
What is + sense RNA?
(+ sense) is when the RNA is coded in a way that can be read by the ribosome/reverse transcriptase = 5’ to 3’
What is - sense RNA?
(- sense) is when the RNA is encoded as 3’ to 5’ so it has to be converted to 5’ to 3’ before genome replication can take place
Why does some viral RNA get made into DNA when it could be read to make proteins needed by the virus as it is?
Because there is not much of the original genome - so the RNA must be made into DNA for the DNA to then be replicated and converted back into RNA to be packaged into protein shells.
However, some retroviruses will use RNA-dependent-RNA-polymerase to form - sense RNA and replicate genome by RNA replication
- LOOK AT THE NOTES BELOW ABOUT THE BALTIMORE CLASSIFICATION
Name all of the different types of virus (using the Baltimore classification)?
1: dsDNA
2: (+)DNA
3: dsRNA
4: (+)RNA → forms RNA (-) for genome replication
5: (-)RNA
6: (+)RNA → forms dsDNA for genome replication (uses reverse transcriptase)
7: dsDNA
Describe the different structures/forms of viruses and what this can dictate
The structure of the virus can dictate its tissue tropism and host range
- cylinder shaped (tobacco MV)
- adenoviruses (3D angular prism)
- spherical (flu)
- bacteriophages
Describe the structure of HIV - what characteristics does it have?
Has a lipid membrane covering the protein that covers the genetic material
- has glycoproteins called envelope proteins that stick out of the outer lipid bilayer, these glycoproteins can be called spikes made of heterotrimers of SU and TM subunits
- inside has protease, integrase and reverse transcriptase
Describe the genetic material/Baltimore classification of HIV
(+) Strand RNA (retrovirus)
What is Gag and what is it composed of?
Shells of Gag proteins are within the envelope
- Is made of 3 proteins: matrix (MA) capsid (CA) and nucelocapsid (NC)
- MA associates with the membrane
- CA forms the conical capsid
- NC coats the viral RNA genome
Describe the genetic component of HIV - how many strands?
- 2 RNA strands
- I think that these are the same and so they are like chromsosomes
Name the 3 polyproteins that retroviruses synthesise and what each will make
- Gag - antigen, viral core proteins, MA (matrix), CA (capsid), NC (nucleocapsid)
- Pol - viral enzymes, protease (PR), reverse transcriptase (RT), integrase (IN)
- Env - envelope glycoprotein = surface glycoprotein (SU) and transmembrane (TM)
Name the 2 membrane proteins that are needed for HIV binding and entry to a cell
CD4 and a chemokine receptor
Explain how HIV enters into a cell
HIV envelope proteins interact with receptors that allows for attachment and then fusion with the cytoplasm.
Describe the structure (arrangement) of the 2 subunits forming the protein that allows for HIV attachment to cells + the extra group
Envelope = Env = Spike proteins, consists of SU and TM subunits. TM and SU are arranged as a dimer of trimers (I think) so SUx3 TMx3.
- SU = gp120
- TM = gp40
- Covered in glycans
What are glycans?
Post-translational modification, in the envelope subunit they cover the SU3TM3
What is the function of the TM subunit of Env?
Mediates the fusion of the lipid bilayers
Fully describe the mechanism of HIV binding and entry into a CD4+ cell
- The gp120 subunit (SU) (this is shown in red below) is tucked into a ‘native’ conformation (the conformation that is found when normally circulating in the blood).
- There is a change in conformation when it engages with CD4 → this becomes an ‘open’ conformation instead of native.
- The open conformation uncovers the TM (transmembrane) subunit, TM mediates the fusion of the HIV and cellular lipid bilayers.
- The complex interacts with the co-receptor (shown in blue) during this process once in the open configuration.
What is meant by HIV being CD4 tropic?
That its tropism (tissues/cells that it can invade) is only for CD4 positive (and expressing the co-receptor) cells such as:
- helper T cells
- macrophages
The loss of these 2 can cause immunodeficiency = AIDS
Where does HIV have to travel to in the cell after entry?
A virus after entry into the cell will want to move to a place where replication of the genome is favoured, for HIV this is the nucleus as it can use the machinery etc.
What is the NPC?
The nuclear core capsid - this it the viral core that contains the viral genome surrounded by capsid within the target cell
Once the virus has fused, how does it get to the wanted destination?
Utilises the microtubule network of the cell to get the viral core (containing the genome) to the nucleus
- viral core has a number of different capsid modifications that allow for movement to the nucleus
Describe the 2 functions of reverse transcriptase in the viral capsid!
Once in the nucleus, reverse transcriptase synthesises more RNA from the RNA template so acts as a polymerase and then these RNA strands are converted by the same enzyme into double stranded DNA all inside the capsid
- this DNA can now be integrated into the host genome
Explain the function of the viral integrase enzyme
The virus wants to take advantage of the cell’s transcription mechanisms and so it integrates its genome into the cellular genome. The integrase enzyme recognises sequences at the terminals of the viral genome DNA and it cuts the cellular DNA and then sticks the viral DNA into the cut and repairs the cut.
What is the function of LEDGF?
This is a cellular protein that aids integrase in the integration of the viral DNA into the host DNA by forming a pre-integration complex, we think that this pre-integration complex is what recognises the DNA and guides it to integration.
Explain how the virus ensures that transcription of its genome is preferential to the other genes being transcribed in the host cell (name the protein involved)
Fist thing to be produced by the viral genome is the Tat protein which binds specifically to viral RNA and enhance the production of these RNAs via positive feedback
- all we need to know is that the virus produces Tat that allows for preferential transcription of viral genes
Describe the function of Rev and the mechanism involved
“The HIV-1 Rev protein mediates nuclear export of unspliced and singly spliced viral RNA”
Rev is transcribed then comes back into the nucleus and binds to the viral DNA to promote nuclear export of its mRNA - this is another way that the virus makes its RNA more preferable for production than the cellular
What are the stem loop structures in the viral genome and their function?
Are specific structures that the viral proteins (such as Rev) can recognise and binds to - allowing for preferential transcription
- one of these is the RRE (Rev responsive element) where Rev binds
- Rev also binds to Crm1 protein which interacts with nuclear pores - so there is more nuclear export than cellular RNA
What is meant by Gag-Pol vs Gag? So production of poly-proteins vs proteins by splicing?
A polyprotein is the normal synthesis of the RNA and the fusion of the proteins - so this would be the fusion of the proteins MA,CA,NC … (??)
“gag-pol protein is generated by -1ribosomal frameshifting induced by a ‘slippery’ sequence and an RNA hairpin structure”
Explain how the virus packages its 2 viral genomes in each virus
Genomic RNA (unspliced) will dimerise - this will promote its movement to the plasma membrane for incorporation into the capsids
Describe how the 2 genomes dimerise
The same mechanisms of Rev recognition of RRE and Tat recognition of the viral genome are used here - stem loop structures in the viral RNA (called kissing loop complexes) recognise each other and are brought together to dimerise
Explain and describe ribosomal frameshifting
This is one of 2 ways of producing the viral proteins
- aka ribosomal readthrough
This is when the ribosome comes to a particular site (that is ‘slippery’) on the mRNA and jumps to the next codon to form a second polyprotein - so at the bottom you can see that if there is ribosomal slippage below then the protein p6 is not produced and instead you get the polyprotein below
What is Myristoylation?
Post transcriptional modification to the polyproteins - is the addition of Myristic acid to glycine residues
What is the function of Myristoylation of the polyproteins produced?
Is a post-transcriptional modification that allows association of the polyprotein to the cell membrane for packaging (sticks it on)
How is the polyprotein trafficked to the plasma membrane?
Polyprotein is made → then myrisoylated → then is transferred to the cell membrane with the use of Tsg101 protein
How does the virus use the ESCRT machinery in the cell?
The virus hijacks the ESCRT machinery in the cell to cause abscission
What is abscission in this meaning?
abscission is the packaging of the viral RNA and proteins into a new capsid and being pushed out of the cell
- ESCRT complex pushes together the proteins for budding
What is the function of protease in this mechanism?
Protease releases the individual proteins form the Gag and Gag-Pol polyprotein
Fully explain the concept of a polyprotein and why it is important
You have one protein that gets cut up into multiple functional proteins - when cut up the proteins will reorganise and form the capsid which is pushed out of the cell, taking with it some of the envelope glycoproteins proteins sticking out of the plasma membrane
Describe the conversion of an immature capsid to a mature capsid
By cutting up the polyproteins, the proteins are liberated and can organise into a mature capsid as seen below
The HIV-1 promoter region contains binding sites for transcription factors that are present in T lymphocytes. What are these transcription factors
these TFs may be Lef or Nf-κB or GATA3 so these will increase transcription of the viral genome once integrated into the host genome
What does rev protein bind to?
Rev protein binds to RRE (rev responsive element) region, this promoted movement of viral RNA out of the nucleus
What process promotes the movement of HIV viral RNA to the cellular membrane?
Dimerisation of the 2 copies of HIV viral RNA promotes its movement (using cellular factors) to the cellular membrane. This is the same mechanism as used in Tat recognition of the viral genome and Rev recognition of RRE (stem loop structures recognise each other) .
What process mediates association of glycines with the plasma membrane?
Myristoylation of glycines in the MA domain of Gag mediates association with the plasma membrane
What does association of the cellular protein Tsg101 with the HIV polyprotein allow for?
Association of the cellular protein Tsg101 with the HIV polyprotein allows it to be transported to the cell surface for budding.
How does Rev perform its function in HIV?
As well as binding RRE, Rev also binds Crm1 - Crm1 interacts with the nuclear pore which allows for export of the viral RNA
Why is some of the viral RNA (HIV) made in a cell spliced and some is unspliced?
Unspliced is packaged into capsids to leave the cell and spliced is used to make proteins needed for replication inside the cell
Name the 2 ways that spliced HIV RNA in a cell can produced proteins
- Normal ribosome translation, will produce one long protein strand (polyprotein) of all the HIV proteins
- Readthrough/ribosome frameshifting, is when the ribosome comes to a particular ‘slippery’ sequence and jumps to the next codon, this produces a different polyprotein
What are the four structures of viral genomes?
- SsRNA
- DsRNA
- SsDNA
- DsDNA
What are the structure of RNA genomes?
Linear and segmented
What are the structure of DNA genomes?
Linear or circular
What is the central dogma?
- DNA polymerase facilitates replication
- RNA polymerase facilitates transcription
- Ribosomes facilitate translation
How do viruses use the central dogma?
- Reverse transcriptase reverses RNA polymerase
- RNA dependant RNA polymerase reverses RNA replication
What is the baltimore classification?
Classes of genetic material present in the virion
What are group I viruses made up of?
DNA +/-
What are group II viruses made up of?
DNA+
What are group III viruses made up of?
RNA +/-
What are group IV viruses made up of?
RNA+
What are group V viruses made up of?
RNA -
What are group VI viruses made up of?
RNA+
What are group VII viruses made up of?
DNA+/-
What does the HIV-1 outer envelope consist of?
Lipid bilayer with protruding Env spikes
What lies inside the HIV-1 envelope?
Shells of Gag proteins
What does the capsid form?
Conical capsid
What does the viral RNA genome form?
Nucleocapsid
What does the envelope consist of and covered by?
- A trimer of gp41 and gp120 peptide subunits
- Covered with glycans
What are the two membrane proteins necessary for HIV-1?
CD4 and a chemokine receptor
What is HIV-1 tropic for?
CD4 expressing cells
What are the early phases of HIV-1 infection?
- Fusion
- Uncoating and reverse transcription
- Intracellular trafficking
- Nuclear entry
What is reverse transcriptase a heterodimer of?
P66 and p51 subunits
What are the three enzymatic properties of reverse transcriptase?
- RNA dependant DNA polymerase
- RNAse H
- DNA dependant DNA polymerase
What is reverse transcription mediated by?
Reverse transcriptase
What does reverse transcriptase act as?
Polymerase to make the RNA template from the RNA genome
How does the HIV DNA insert itself into the host chromosome?
- Ends of viral DNA have specific sequences that are recognised by integrase enzymes
- Sticks and pastes the viral DNA into cellular DNA
How does the integrase enzyme Stick and paste the viral DNA into cellular DNA?
Bending the viral DNA round into very close contact with the cellular DNA
What binds HIV-1 integrase and facilitates chromatin targeting?
LEDGF/P75
What does the HIV-1 promoter contain?
Binding sites for transcription factors that are present in T-lymphocytes
What does the HIV-1 promoter do?
Recruits cellular proteins to the viral genome that are required for mRNA transcription
What is the first thing that gets produced by the genome and what does it do?
- Tat protein
- Specifically binds to the RNA and enhances RNA replication
What does the HIV-1 rev protein mediate?
Nuclear export of a spliced viral RNA
What does HIV-1 rev protein form?
A feedback loop wherein it comes back into the nucleus and promotes the nuclear export of the RNA viral genome over cellular RNA
What does REV protein interact with to promote viral genome replication?
Crm 1 and RRE RNA
What does dimerisation of the un spliced viral RNA allow?
Packing of two genomes in the virus
What is the kissing loop complex?
Two of the same sequence brought together
What is gag-pol protein generated by?
7 ribosomal frameshifting induced by a slippery sequence on RNA hairpin structure
What is myristoylation?
Post-translational modification of glycines in the MA domain of Gag
What does myristoylation mediate?
Association with the plasma membrane
What causes the polyprotein to be made, myristoylated and transferred to the cell surface?
Tsg 101
What is hijacked by HIV to perform membrane abscission during viral release?
ESCRT
What is abscission?
Combining proteins and RNAs into a capsid, which essentially pushes the new capsid into the extracellular space
What does Gag processing generate?
Mature viruses
What is - sense RNA?
(- sense) is when the RNA is encoded as 3’ to 5’ so it has to be converted to 5’ to 3’ before genome replication can take place
