Retroviruses: Structure and Function Flashcards
What are endogenous retroviruses?
remnants of historical infection, usually incomplete genomes which are transmitted in the germline
How much of the human genome do endogenous retroviruses make up?
8-12%
What is the common mechanism of replication of all retroviruses?
integrate into the host genome via reverse transcriptase
Give an example of insertional mutagenesis involving retroviruses?
in SCID gene therapy patients using retroviruses some patients got leukaemia as a result
How was retroviral taxonomy originally carried out?
based on morphology- size; shape of core; length of spikes, under electron microscopy
What are the gag proteins?
matrix; capsid; nucleocapsid
What are the structural components of a virion?
gag proteins; env proteins; lipid envelope
Where does the membrane envelope of a virion derive from?
host cell plasma membrane during virion production
What lines the membrane envelope?
gag-encoded matrix protein
What are the 2 env encoded glycoproteins?
transmembrane compoenet and surface component
What si the function of the TM env encoded glycoprotein?
contains peptide that promotes fusion of virion memrbane with target cell membrane
How is the SU glycoprotein attached to TM?
non-covalently
What is the virion core?
round or triangular structure somposed of gag-encoded capsid protein
What is found within the virion core?
2 copies of viral genomic RNA coated by gag-encoded nucleocapsid protein and pol-encoded enzymes
What are the 2 types of retroviral genome?
simple and complex
Rather than morphology, how are retroviruses now classified?
according to their genome organisation (simple/complex) and sequence analysis
Give an exmample of a virus with a simple genome?
murine leukaemia virus
What makes up a simple retrovirus genome?
LTRs at either end with gag, pol and env genes in between
What is a major determinant of virus phenotype?
virus envelope protein
What are the 6 additional genes that HIV possesses in addition to the simple genome?
Vpr; Rev; Vif; Tat; Vpu and Nef
Which of the 6 extra genes that HIV-1 has are absolutely essential for replication?
Tat and Rev
How are the simple genes encoded?
as polyproteins which have to then be cut down to size
What 4 proteins are encoded by HIV pol?
reverse transcriptase; protease; integrase and RNAase
What is the function of RNAase encoded by HIV?
eliminates RNA
What is the TM glycoprotein of HIV?
gp41
What si the SU glycoprotein of HIV?
gp120
What is the function of Tat?
transactivates transcription- produces protein which binds to LTR and activates viral transcription
What si the function of Rev?
regulates splicing- has a nuclear location signal and controls which RNA moves in and out of nucleus: without, all mRNA stays in nucleus
What is the function of Nef?
immune evasion- decreases MHC-I and Cd4 on surface of cell- without HIV grows very slowly
What is the function of Vif?
involvedi n viral assembly and increases viral infectivity- without decreased level of replication
What is the function of Vpu?
modulates CD4 and apoptosis
What is the function of Vpr?
allows nuclear import via importin interaction: most viruses need a cell to be rpelicating to access nucleus as in mitosis nuclear breaks down, this allows HIV to get in without replication
What is the most diverse part of the virus?
the envelope- in order to evade the immune system
What are the 2 types of retroviral phylogeny?
orthoretrovirinae and spumaretrovirinae
Where does reverse transcription happen in the host cell?
cytoplasm within a copmlex of viral proteins
What are the functions of the envelope protein?
determines viral tropism and viral diversity; repsonsible for cytopathic effect and is the target of humoral repsonse
Give an example of a cytopathic effect of retroviruses?
HIV infected T cells in vitro causes multinucleated syncytia
What are the 3 components of reverse transcription?
template; primer and revers transcription
What is the template for reverse transcription?
viral genomic RNA
What si the primer for reverse transcription?
a specific tRNA taken from the producer cell during viral assembly that anneals to homologous sequences- primer binding site of viral RNA
What are the functions of reverse transcriptase?
a viral DNA polymerase that utilises RNA or DNA as template, also posseses RNAase activity that degrades RNA when complexed with DNA
What are the steps of reverse transcription?
tRNA extended to form a negative strand; RNAase removes RNA hybridised to DNA; first jump: neg strand DNA hybridises with remaining R sequence; then neg strand DNA extended; majority of RNA removed; 3’ end of plus Dna strand extended as PBS attaches to tRNA; RNA and tRNA removed; second jump so that both PBS are joined together; both DNA strands completed
What makes up the LRRs?
U3(located at 3’ end); R and U5(located at 5’ end)
What was syncytial induction of CD4 T cells by HIV used for?
a quick assay to determine during efficacy against HIV
What is integration?
covalent linkage of the dsDNA copy of hte viral genome to host chromosomal DNA
What type of enzyme is integrase?
a nuclease
How does integration work?
integrase clips 2 nucleotides from the 3’ end of the 2 LTRs then makes a staggered cut in host chromosomal DNA in a random location and ligates the clipped 3’ ends of the viral DNA to host DNA; host enzymes then repair the 5’ ends of the viral DNA
What does retroviral genomic RNA incorporation in to virions require?
a cis-acting structure at the 5’ end of hte RNA called psi; a trans-acting factor, the zinc-fingers in the gag polyprotein
What is the function of the gag polyprotein in HIV-1 virion assembly?
directs virion budding and release- myristylated atthe amino-terminus and accumulates the cytoplasmic membrane where is multimerizes to form the virion macromolecular complex
Where are the zing-fingers which help incorporate viral genomic RNA into virions?
in the nucleocaspid domain of hte gag polyprotein
How is the envelope glycoprotein cleaved?
by a cellular protease in the golgi to produce TM and SU
What does the gag-pol polyprotein consist of?
gag polyprotein fused to the pol-encoded enzymes which in HIV-1 is produced by a ribosomal frameshift between the gag and pol reading frames
How is the gag-pol polyprotein integrated into nascent virions?
via interactions with the gag polyprotein
What needs to happen to create a mature virion?
when virions exit the cell, the gag and gag-pol polyproteins are intact, but once virion is released, protease is activated and the polyproteins cleaved–mature
What are the primate retroviruses in order of pathogenicity?
SIV–STLV–SRV–PFV
What subfamily do HIV and SIV belong to?
lentiviruses
What are the 2 families of complex retroviruses?
spumaretroviruses and deltaretroviruses
What family does SRV belong to?
betaretrovirus
What family does PFV belong to?
spumaretrovirus
What is the difference in morphology between SIV and HIV?
no difference
What is sooty mangaby SIV the originator of?
HIV2
What is chimpanzee SIV the origin of?
HIV-1
What are the serological similarities of HIV-1 patients to monkets with SIV?
share same antibodies to core proteins but not to envelope proteins
What happens when Asian macaques are given sooty mangaby SIV?
get SAIDs
What has SAIDs shown for humans?
given a parallel model to study; vaccine has been created for SAIDs using a fixed form of virion- shows that virus can be vaccinated against if the right immunogen is found
Which primates are infected with SRVs?
mainly macaques
Where can SRV be foudn in infected monkeys?
in all bodily fluids
What does SRV infection result in?
an immunodeficiency profile similar to AIDs and SAIDs- no genetic or morphological similarities however
What is the difference between different SRV serotypes?
different evelopes which causes variation in severity of disease; the macaques infected and the disease manifestations
What is a serotype?
a serologically distinguishable strain of a microbe
Why did SRV cause problems in HIV vaccine research?
it was possible to create a vaccine inducing neutralising antibodies which totally protected the monkeys whereas in HIV, even having lots of neutralising antibodies does not protect
Why are foamy viruses called such?
see lots of bubbles in cells infected
Why may foamy virus research be useful?
doesn’t cause disease; can be grown in pretty much every cell- good vector for gene therapy- no human disease and one of biggest retroviruses so could incorporate large genes into it
What is zoonosis?
emergence of novel viruses in humans as a result of interspecies transmission
What type of genome does SRV have?
simple
What family does HFV belong to?
spumaretrovirinae (only has one genus- SFV and HFV)
What are the first steps that should be taken in a new epidemic
case definition; facilitate suveillance and quarantine; safe body disposal; protect health services; facilitate collection of samples
What is the diference between plasma and serum?
plasma has been treated with anti-coagulatants; whereas serum is liquid part of blood after coagulation- devoid of clotting factors eg fibrinogen
What does identifying the tropism of hte virus allow you to do?
identify the cellular receptor it uses- inhibitor mechanism; virus neutralising target and possible inhibition of virus
What is a precipitin?
an antibody that can precipitate out of solution upon antigen binding
What is a precipitin line?
line formed by the binding of blood serum to antigen on a plate
What is the difference between direct/indirect ELISA and sandwich ELISA?
sandwich ELISA is measuring antigen detected by antibody bound to the plate wherease direct/indirect ELISA is looking at antibody which binds to the antigen coated well
What metals does reverse transcriptase need to work?
magnesium or zinc
