6. Translation Flashcards
why is the 5’ cap important in eukaryotes?
allows 5’ and 3’ end to be close together –> for transcription initiation
how is the ribosome recruited to mRNA?
5’ cap is recognized by Eukaryotic Initiation Factor 4E, i.e. cap-binding protein
what does IRES stand for?
Internal Ribosome Entry Site
if the poliovirus genome has the VpG protein but no cap structure, how can translation be initiated?
by CAP-INDEPENDENT TRANSLATION
Describe cap-independent translation
the poliovirus 5’ UTR contains an Internal Ribosome Entry Site that allows internal initiation
how do ribosomes recognize IRES?
based on RNA secondary structure
can you predict IRES from primary RNA sequence?
technically, the ribosome recognizes specific secondary structures BUT if you see a long 5’ UTR that could form stem loops and other specific structures, can deduce that it involves IRES
what are the eIF requirements for 5’-end-dependent initiation?
all eIFs involved
what are the eIF requirements for type 1 or 2 IRES?
all eIFs involved except eIF4E
describe type 1/2 IRES
virus causes cleavage at eIF4G lets it shut down cellular replication so only viral replication can occur
what are the eIF requirements for hepatitis C virus IRES?
only requires eIF2 and eIF3
what are 6 mechanisms used by viruses to manipulate the translation?
- ribosome shunting
- methionine-independent initiation
- leaky scanning
- re-initiation
- suppression of termination
- ribosomal frameshifting
describe 1. RIBOSOME SHUNTING
- how does it work
- why is it helpful for the virus
ribosomes bypass/shunt over parts of the 5’ untranslated region to reach the start codon or bypass a stable secondary structure in the mRNA
helpful for the virus bc normally it would get stuck and have to unwind the secondary structure but this reduces the need for unwinding
describe 2. METHIONINE-INDEPENDENT INITIATION for the Cricket Paralysis Virus
the CRPV IRES mimics the Met-initiator tRNA (Met-tRNAi –> allowing the virus to recruit 80S ribosomes without any eIFs or Met-tRNAi
describe 2. METHIONINE-INDEPENDENT INITIATION for the Turnip Yellow Mosaic Virus
TYMV mimics tRNA and binds to valine on the P site of the ribosome
describe 3. LEAKY SCANNING
- which type of viruses
- how does it work
- why is it helpful for the virus
- used by PARAMYXOVIRUSES
- some ribosomes initiate translation at non-optimal codon via diff reading frams, diff start codons (ex. ACG 81, AUG 104 - bad) –> this tricks the ribosome to read the mRNA differently
- this is helpful for letting the virus pack lots of info in its mRNA and encode several proteins on the same mRNA
which method of translation manipulation is used with leaky scanning? why?
ribosome shunting –> allows for the other 2 open reading frames to be reached
describe 4. RE-INITIATION
- once ribosome reaches stop codon, the 40S subunit stays bound to the mRNA and the 60S subunit detaches then rejoins to allow RE-INITIATION for expression of a downstream ORF
describe 5. SUPPRESSION OF TERMINATION (READTHROUGH) in HIV
- in HIV, a UAG codon (stop codon) is suppressed 10% of the time to allow for synthesis of Gag-Pol fusion protein because the mRNA forms a pseudoknot –> ribosome pauses, allowing more time for a suppressor tRNA to be charged and forming Gag-Pol fusion protein
describe 6. RIBOSOMAL FRAMESHIFTING
- how does it work
- what is required for it to work
- why is it needed (2)
- ribosomes pauses, slips back and shifts into a different reading frame (+/- 1)
- requires a sequence that promotes ribosome slippage and the tRNA to move by 1 base
- needed bc it helps synthesize protein encoded in a different reading frame AND can bypass a stop codon
what is an example of ribosomal frameshifting being required?
In retroviruses, Pol may overlap with Gag so it requires diff reading frame via ribosomal framshifting
what is the main purpose of translation tricks?
to let viruses pack A LOT of info into the mRNA –> ex. 1 mRNA can make multiple proteins, fusion proteins, etc.
how do viruses affect host protein synthesis?
turn OFF host protein synthesis
why do viruses turn off host protein synthesis?
to prevent infected cells from mounting an antiviral response
explain this graph:
- uninfected cells increase their rate of protein synthesis at constant rate
- in infected cells: host protein synthesis decreases quickly
- then reaches a point where host protein synthesis is turned off
- then viral protein synthesis increases
explain this SDS-PAGE
cellular proteins are made at the beginning, then at 5h post infection, only viral proteins are made
what virus is the 2A protease from?
poliovirus
what are the 3 steps of the activity of poliovirus 2A protease?
- poliovirus 2A protease cleaves eIF4G
- this prevents host cap-dependent protein synthesis by bridging the cap-binding protein eIF4E to the translation initiation complex
- host protein synthesis is inhibited but viral protein synthesis can continue
why can virus protein synthesis continue after poliovirus 2A protease activity?
2A protease blocks cap-dependent protein synthesis but since poliovirus protein synthesis depends on IRES not a cap structure, the viral protein synthesis can continue
how do viruses attack machinery for host translation?
inhibit host translation factors by cleaving, (de)phosphorylating, etc.
