Viral Strategies of Translation and Modulation of Host Translation Flashcards
When and who discovered ribosomes?
In 1950 by George Palade
What is the abundance of ribosomes in E.coli cells?
15,000 ribosomes
What happened with ribosomes in 1960?
There was a reconstitution of bacterial subunits
What did Carl Woese do?
In 1970, sequencing of rRNAs
What does 16s rRNA do?
They play important roles in structure and functional parts of the ribosome
Who discovered the 16s rRNA role?
1981: Carl Woese and Harry Noller
When was the atomic structure of prokaryotic ribosomes discovered?
Began in 1980s and still ongoing
What makes up the 70S ribosome in prokaryotes?
The 50S subunit and the 30S subunit
It is 20 nm
How is the 50S subunit in prokaryotes made?
1) 31 ribosomal proteins
2) 5S rRNA
3) 23S rRNA
How is the 30S subunit in prokaryotes made?
1) 21 ribosomal proteins
2) 16S rRNA
What makes up the 80S ribosome in eukaryotes?
The 60S subunit and the 40S subunit
It is 24 nm
How is the 60S subunit in eukaryotes made?
1) 49 ribosomal proteins
2) 5S rRNA
3) 5.8S rRNA
4) 28S rRNA
How is the 40S subunit in eukaryotes made?
1) 33 ribosomal proteins
2) 18S rRNA
Why is translation important?
Translation is a key step in gene expression and regulation
What does eukaryotic translation require?
Translation requires coordinated action of:
1) mRNA
2) tRNAs
3) Ribosome
4) Translation factors
Why are mRNAs translated into polypeptides?
For various functions (structure, enzymes, gene regulation, signal transduction, trafficking)
What is the machinery needed for eukaryotic translation?
1) Anti-codon: mG-A-A–Y
2) Amino acid attachment side: 3’ –> A
3) 80S ribosome: 60S: 28S, 5.8S, 5S rRNAs
What is the start codon?
1) AUG
ORF: AUG to STOP codon
What are the two key findings when it comes to rRNAs?
1) rRNAs serve as both the structural backbone and the catalyst in translation
2) Proteins stabilize the structure of rRNAs and assist their function
What are the initiation factors in translation?
eIF1, eIF2,eIF3, eIF4F (4E, 4G, 4A)
What are the transcription elongation factors?
eEF1A, eEF1B, eEF2
What are the transcription termination factors?
eRF1, eRRF3
Where does translation in eukaryotic mRNA begin?
It starts from the binding of the 5’ m7G cap
What is EIF4F composed of?
4E, 4G, and 4A
Why is eIF4A important in translation?
eIF4A binds the cap structure
What is eIF4G?
It is the bridge between eIF4E and 43S pre-initiation complex
What is eIFA?
This is the helicase leading the way to AUG scanning
What does PABP do during translation of eukaryotes?
PABP binds polyA tail and eIF4G; which circuralizes the mRNA
mRNA needs to be circularized for translation
Why is initiation in translation so important?
Initiation of translation is the main step of translation regulation by both the host and viruses
In eukaryotes where does the initiation complex form?
It forms at the 5’ cap, and not at the Shine- Dalgarno/AUG site
How does the initiation complex work?
The complex scans mRNA for an AUG initiation codon, and translation usually begins at the first AUG
What is Kozak’s rule?
It describes the optimal sequence for efficient translation initiation in eukaryotes
What is Kozak’s sequence?
-3 position: A purine (A or G) \+4 position: G \+1: A \+2: U \+3: G
What is the function of the 5’ cap and 3’ PolyA tail?
1) Ensure that only intact mRNA are translated, whereas truncated mRNAs are quickly degraded
2) Required for the juxtaposition of the 5’ and 3’ termini of an mRNA for efficient and repeated translation
3) Both the cap and polyA tail are required for the assembly of the initiation complex for translation
What does it mean for viruses to bend the rules of translation?
Viruses take advantage of host translation, but they are good in modulating translation for their own benefit
How do viruses maximize the coding capacity of limited genomes? Give viral examples
Many RNA viruses and retroviruses encode replication related proteins as a polyprotein precursor, which is cleaved into multiple functional proteins by proteases
-> Picorna, Flavi, Corona, Timo, retro
What is suppression of stop codons during translation?
Common strategy to translate RdRP domains in RNA viruses and retroviruses;
It is one way to maximize the coding capacity of viral genomes
Explain translational read through?
In 10-20% of cases, the stop codon of the 1st ORF is misread, leading to continued translation into the 2nd ORF to produce a larger fusion protein (to ensure low levels of RdRP) As a result, sequences and the secondary structures downstream of the stop codon are important
In TMV, MMLV, and feline leukaemia what are the stop-codons misread as?
TMV: UAG is misread as a codon for Tyr
MMLV and feline leukaemia: UAG is misread as a CAG producing Gun
What are some viruses that use suppression of the stop codons?
1) Alphaviruses
2) Retroviruses (some)
3) TMV
4) Tombusviruses
What is ribosomal frame shifting?
In 10% of cases, ribosome slips to a different reading frame, producing a larger polypeptide
The tRNA slips forward (+1, jumps towards the 3’ end of the mRNA) or slips backward (-1, back toward the 5’ end)
The two translation products share their N-terminal region
What does ribosomal frame shifting require?
Requires a slippery sequence, which is a homo-polymeric twin and a pseudo knot structure several nucleotides downstream of shifting sites
Which viruses use ribosomal frame shifting?
Retroviruses: -1 frameshift
Coronaviruses: -1 frameshift
Closteroviruses and other plant RNA viruses: + 1 frameshift
What is leaky scanning?
Efficiency of translation initiation at a start codon is affected by the context sequence surrounding AUG
What are some viral examples of leaky scanning?
1) Influenza B, RNA 6
2) HIV-1 Env/Vpu
3) SV40 (VP2, VP3)
4) Human T-lymphotropic virus (Tax, Rex)
5) HPV 16 (E6, E7)
6) Alphaflexiviridae, Betaflexiviridae
How does re-initiation of translation occur after leaky scanning?
Using Influenza B virus, RNA segment 7 as the example.
1) Stop codon of M1 ORF overlaps with the start codon of BM2 ORF: the 60S ribosomal unit falls off, as termination occurs at UGA
2) Termination upstream ribosome binding site ‘UGGG’ located 45 nucleotides upstream of BM2 ORF start codon
3) UGGG base pairs with a loop in the 18s rRNA, tethering the 40S subunit onto mRNA to initiate re-initation of translation
What is ribosome shunting in translation?
1) The 5’ cap is required for binding of the pre-initiation complex to mRNA but no AUG scanning is followed
2) The small subunit jumps over several “hills” and lands at the initiation codon
3) The large subunit joins in, starts translation at the AUG immediately downstream
The mechanism is not known yet
What are some viruses that use ribosome shunting?
1) CaMV 35S RNA
2) Adenovirus: Major late mRNAs
3) Reoviruses
4) Paramyoxoviruses
5) Hepandaviruses
What happens when viruses lack a 5’ cap?
Undergo 5’ cap independent translation
Explain the Poliovirus
5’ end: VpG (22-24 aa residues), and a 5’ UTR which is extremely long, there is a clover leaf at the 5’ end and IRES of this 5’ UTR
Middle: Single ORF, co and post translational cleavage by viral proteases to produce 11-12 functional protein products
3’ end: polyA tail
What are the common features of an IRES?
Extensive SL in 5’ UTR
Pseudo-knot
Conserved element: GNRA
Pyrimidine rich region
What are the two mechanisms used for IRES translation?
1) Translation initiation using type I and type II IRES do not require the C-terminal domain of eIF4G
2) For other types of IRES, the 40S subunit binds directly at IRES to initiate translation
What did Pelletier & Sonenberg do?
In infected polio cells, 40S did not bind when there was a 5’ cap, but did bind to an IRES
What dud Chen and Sarnow do?
Used circular mRNA, and when there was an IRES, a protein was produced, but without IRES, no protein was produced.
What do the insect viruses of picornavirales do?
They use one to two IRES to translate all viral proteins
Why is the 3’ terminal sequence important in cap-independent translation initiation?
3’ CITE: Cap-independent translation elements
Long distance interaction between this 3’ CITE and the 5’ step loop, which initiations translation. When these two sites interact, the mRNA forms a loop and translation can begin
Why are viruses special?
They use a plethora of strategies to modulate translation of cellular mRNAs
When will viruses take over translation of host cells?
Mostly at the initiation stage
A wide range of strategies are used to achieve this purpose, depending on the virus
How does poliovirus inhibit the pre-initiation complex at the cap of cellular mRNAs?
1) Protease cleaves eIF4G from eIF4E(PV)
2) De phosphorylates 4E-BP1, sequestering eIF-4E since eIF-4E cannot do anything with out 4E–BP1’s phosphorylation (encephalomyocarditis)
How is translation inhibited by the phosphorylation of eIF2a?
Several kinases phosphorylate eIF2a, blocking translation initiation in response to viral infection, stress, and starvation
PKR: induced by INFs in response to viral infections (dsRNA)
PERK: component of unfolded protein response
How is PKR activities regulated?
PKR is a serine/threonine kinase
1) dsRNA is generated due to infection by RNA and DNA viruses
2) dsRNA binding to PKR causes PKR to dimerize
3) Autophosphorylation of this PKR dimer renders PKR active, leading to phosphorylation of eIF2a
4) Phosphorylated eIF2a can no longer bind to GTP, blocking ternary complex formation
5) Inhibition of translation initiation
6) Pact activates PKR in the absence of dsRNA
How do viruses reverse eIF2a phosphorylation?
1) Small non coding RNAs competitively bind PKR, prevents binding by dsRNA
2) dsRNA binding proteins sequester dsRNA
3) Inhibition of kinase activity (Vaccinia K3L and HSV-1 US11 binds PKR and sequester it from binding to eIF2a) (HSV-1 gB binds ER liminal domain of PERK, blocking its association with ER)
4) Reversal of phosphorylation of eIF2a (HSV-1 ICP34.5 recruits phosphatase, dephosphorylates eIF2a)
How do viruses regulate polyA binding protein activity?
1) Circularization of mRNA via binding of PABP with eIF44G is required for efficient translation
2) Viruses deploy various strategies to block the juxtaposition of mRNA ends:
- -> cleavage of PABP by viral protease: enteroviruses and caliciviruses
- -> Sequesteration of PABP: rubella virus CP
- -> Block PABP binding at eIF4G: rotavirus and reoviruses
- -> Redistribution of PABP to the nucleus
