#6 Retrovirus I Flashcards
Infection consequences:
- no ill effects, tumors (rapid onset or long latency), wasting disease (neurodisorders), immune deficiences (HIV)
REtroviruses affects on host chromosomes or cell sequences
Aquire host cells sequences—oncogenes
Insert into host cells chromosomes—can actiate or inactivate genes > > cancer
Classification; based on
pathogenicity or shape but not relfect evolutionary relationships observed by sequence comparisons
MOre on classification system, how may groups
Either complex or simple and there is a total of 7 dif groups
based on genome structure and how many proteins they encode
retrovirus: Enveloped virus, env protein embedded in membrane, ________ under lipid bilayer
matrix protein
Capsid (core) made up of structual proteins called
(group of specific antigens or products of the ‘gag’ genes)
Gag genes
MA.CA.NC.PR
Matrix, Capsid, NucleoCapsid, Protease
what is unique about retrovirus genome
2 copies of (+) ssRNA genome.
Only virus is ‘diploid’ and accounts for recombiantion potential
TM and SU are made as GP______ or one protein that gets clipped
160
Retroviral genomic RNA is made by hosts Pol II so they are _______and _______ like other host Poll mRNAs
capped and polyadenylated
Capped Ends
a. R at start and end; it’s a ‘_____’ sequence and is at both ends
repeat
U5 is at the_____
U3 is at the_____
start
end
Gag gene: MA/CA/NC/PR are made as a
polyprotein that then gets clipped
-in HIV, the _____is in “pol” gene reading frame
PR
Pol Gene: polymerase gene has
RT
IN
RT-
IN-
together they =
reverse transcriptase
integrase
together = extended polyprotein
Envelope (env) gene: encodes env protein, made as precursor HIV, gp of 160→
to gp of 120 + 41
Complex Retrovirus organization
simular to simple (w/ gag-pol-env) but
more additional genes/proteins
Complex Retrovirus has mRNAs for
additional genes, the ‘accessory proteins’ are generated by complex splicing (simple retrovirus do a single splice to make env)
How does a complex retrovirus generate ‘accessory proteins’
using the mRNA for complex alternative splicing
Difference in splicing for simple vs complex retrovirus
simple splice once
complex splic multiple times
how many classes of RNA are derived form extensive splicing
3 classes
replication cycle sepearted into two phases by integration step:
1st phase steps A-E will ______ integration and 2nd phase (F-J) is_____ ingration
precede
post
1st step:
Absorption
- Virus binds cell via env protein and host cell receptor
- HIV receptor is CD4/CCR5 (specifics for T cells)
- other viruses use aa transporters, LDL- like receptor, many others
During absorption, the virus binds to the cell via the _____ protein
env
HIV receptor for absorption is ________
other retros us ______
CD4 or CCR5 (makes them T cell specific)
aa or LDL like receptors
2nd step: Penetration/uncoating
two main steps
viral envelope fuses with cell membrane at surface or in endosomes
genomic RNA is only PARTLY uncoated
RT, IN and some gag proteins remain associated with incoming ________
genomic RNA.
The proteins are needed to convert ssRNA→dsDNA via RT, nuclear import and integration
RT, IN and some gag proteins remain associated with incoming genomic RNA because:
reverse T and integrase are needed to convert ssRNA–>dsDNA as well as nuclear inport and integration
Do we start translation right after uncoating?
do NOT want to translate yet!!!! The protein particle prevents association of ribosomes… goal is to convert ssRNA→ dsDNA var RT
3rd step: Reverse Transcription: taking ssRNA→
dsDNA
During 3rd step: Integrated DNA (provirus) is longer then template RNA and has a U3 and U5 duplicated at the ends making the
Long Terminal Repeat or ‘LTR’
Reverse transcription accomplished in_______ via RT it brought along
cytoplasm
RT has 2 polymerase fnxs
a. RNA-dependent DNA polymerase (takes RNA→ DNA)
b. DNA-dependent DNA polymerase (copies 2nd strand of DNA from first strand)
DNA-dependent DNA polymerase
part of RT
(copies 2nd strand of DNA from first strand)
RNA-dependent DNA polymerase
part of RT
(takes RNA→ DNA)
is an ‘error prone’ polymerase~ see 5 errors made per genome, allowing for rapid evolution and drug resistance
Reverse transcriptase
What makes retrovises rapidly evolve and devo drug resistance
error prone polymerase (RT)
_____ is KEY as TARGET for antiviral therapies, numerous inhibitors available for HIV (AZT therapy)
RT
carried out bye integrase IN protein that enters cell w/ virus and stays associated w/ dsDNA
4th/5th step… Integration
INtegration is carried out by IN in the protein that enters the cell w/ virus and:
stays associated with the dsDNA
Integration requires dsDNA has access to ______;
host DNA
many retroviruses can’t cross nuclear membrane and need cell division to integrate but HIV»»
HIV CAN cross nuclear env which is key for infecting nondividing cells and for gene therapies
Integrase recognizes and is specific for sequences at the ends of dsDNA such as
U3 and U5
Integration rxn is NOT specific for host sequences thus insertion is essentially______
random
but prefers to be near actively replicating genes
_____alone performs insertion… makes it great therapeutic target
IN protein
After integration….virus is ________resident of host cells DNA
PERMANENT
6th step: Proviral Transcription: major role of LTR is to
direct synthesis of viral RNA
what directs synthesis of viral RNA
LTR
U3: has signal recognized by cell’s transcription machinery that directs transcription at beginning of ‘R’ region…but wait… they’re 2 U3 regions, how does it know????
a. while U3 is repeated at both ends, only 5’ LTR is transcriptionally active
signal recognized by cell’s transcription machinery that directs transcription at beginning of ‘R’ region
U3
.HIV LTR requires transcription factor of _____ that is only expressed in activated T cells…
NFkB
reason why HIV RNA is not transcribed in infected memory T cells bc
memory cells do not express NFkB and HIV LRT requires it ot be activated
7th step: RNA processing
as pol II transcripts, all viral RNAs are ______ and some must be sliced to generate
_______ while a large part aren’t because
polyadenylated,
env mRNA,
serve as a gag-pol mRNA and as genome for progeny virions
Three fates of viral RNA
full length–>
full length–>
RNA splicing–>
Full length RNA → genomic RNA
Full length RNA → gag-pol mRNA
RNA splicing → all retroviruses make env mRNA (and others) by splicing: splicing is incomplete to preserve full-length RNA for genomic RNA and gag-pol mRNA
gag-pol region is spliced our by
host splicesome
Translation
1. Most abundant protein is _____and ____made as polyproteins form full length mRNA
gag and gag-pol,
gag initiates____ start codon, ends at a stop codon,
AUG
gag-pol made from same AUG start as gag, but ribosomes…..
‘ignore’ or circumvent the gag stop codon and continue to the end of pol.
How often do ribosomes ignore gag stop codon
What does this result in
only happens about 5% of the time
RT and IN proteins are less abundant than gag
Both gag and gag-pol proteins are eventually cleaved by________, releaseing ind proteins
protease PR domain
Env protein made from spliced mRNA on ER-bound ribosomes, move through ER-golgi and
inserted into plasma membrane
env gp160 precursor proteins is cleaved to
gp120 + gp41 by cellular protease
Cleavage of gp160 MUST happen bc
gp 160 can’t support membrane fusion thus virus wouln’t be able o fuse with target cell`
Virion assembly and budding involves what three steps
Packaging
Budding
Maturation
Ky for Packaging;requires a signal, _____contained in unspliced but not spliced RNA
Psi
What removes the psi signal
splicing
Where is the psi signal contained
in the unspliced rna
Budding—viral gag and gag-pol polyproteins recruit_____ and assemble______ cell surface
RNA
under
During budding,
Gag proteins interact with env, and budding occurs as ______
particle forms
Maturation:
causes protein rearrangements and the core to become _______
more dense
proteolysis of gag and gag-pol by PR occurs
after budding
During buddin: viral particles still form and bud if proteolysis is inhibited, but
viruses are not infectious
Blocking thi step is the basis of HIV PR inhibitors
Maturation or budding
Retroviruses discovered as agents isolated from naturally occuring tumors in animals– There wer inocculated to naïve animals→ see
they again cause tumors
Non-transforming retroviruses: ‘non-acute’ or ‘slow’ tumor viruses
take _______ to appear
6 moths to a year
Non-transforming retroviruses
do NOT transform cells in culture (low frequency and no ‘cancer’ phenotype’)
viruses do not contain oncogenes
tumors caused by activation or inactivation of host genes
tumors caused by activation or inactivation of host genes (2 reasons)
a. promoter insertion: viral promoter used and see expression of unregulated protein or at wrong time
b. enhancer insertion: cell promoter inappropriately turned on→ correct protein made at wrong time
Transforming retrovirus: or ‘acute’ virus
- infections case tumors w/in weeks
2. efficiently cause tissue culture cells to become ‘transformed’ or cancer-like
- infections case tumors w/in weeks
2. efficiently cause tissue culture cells to become ‘transformed’ or cancer-like
transformning retrovirus or ‘acute’virus
What did the transforming ‘acute’ retrovirus have to induce tumor onset
mutated copy of cellular gene involved in growth control, an ‘oncogene’
a. infection indroduce cancer causing gene, so see rapid tumor onset
most oncogene containing viruses are defective bc
oncogene replaces one or more viral genomes
Viruse have impact on cancer biology—d/t large number of oncogene identified
first oncogene idendified is____in the Rous sarcoma virus
(Src)
