Translation Regulation Flashcards
Define no-go mRNA decay
Decay of mRNAs bound by stalled ribosomes due to extensive secondary structures
Why is mRNA decay important?
It protects the cell from accumulation and aggregation of abberant proteins and potentially toxic proteins.
Describe the mechanism of nonsense-mediated mRNA decay.
- ribosome reaches a stop codon during the pioneering (first) round of translation but eIF4A bound to UPF2 and UPF3 is sitting at the EJC, downstream of where ribosome is stalled
- SURF complex containing SMG proteins and UPF1 is bound to the ribosome, and the two complexes join to form the DECID complex, phosphorylating UPF1 and activating its ATPase
- UPF1 then inhibits the CBD and mRNA is degraded
What processes mediate nonsense mediated decay?
- translational repression
- dissociation of mRNA from ribosome
- targeted inhibition of splicing
- degradation of nascent polypeptide
When is eIF2 phosphorylated and inhibited?
- amino acid starvation
- heme deficiency
- ER stress
- double stranded RNA
Describe the mechanism of global translation regulation by eIF2 phosphorylation.
- guanine exchange factor eIF2b only acts on eIF2 when it is not phosphorylated
- when phosphorylated, eIF2 holds tightly to eIF2b so it cannot go on to remove GDP from other eIF2 molecules
What are three forms of global translation regulation?
- eIF2 hosphorylation
- mTOR and eIF4E
- EF-2 regulation
What is mTOR and what does it do in the cell?
Mechanistic Target of Rapamycin. Regulates cell growth by:
- controlling mRNA translation
- ribosome biogenesis
- autophagy
- metabolism
How is mTORc1 activated? Inhibited?
Activated by things that are good for the cell. Inhibited by things that are harmful to the cell.
Where are the factors found that act on mTOR?
Sitting on the lysosome.
How is eIF4E activity regulated by mTOR?
- mTOR phosphorylates 4E-BP which binds eIF4E and inhibits it. Phosphorylation allows eIF4E to be released and to interact with other factors such as eIF4G
- 4E-BP can be dephosphorylated by protein phosphatase 2A
Describe global translation regulation by EF-2.
- EF-2 is phosphorylated by the mTOR pathway (good)
- diptheria toxin or pseudomonas toxin causes ADP ribosylation of EF-2 (bad)
Describe cytoplasmic polyadenylation.
In order or an mRNA to be cytoplasmically polyadenylated it must have:
- cytoplasmic polyadenylation element (CPE) in 3’ UTR
- CPE-binding protein (CPEB)
- nucleation of proteins by CPEB to regulate polyadenylation and translation
In what processes is cytoplasmic polyadenylation invovled?
- germ-cell development
- cell division and senescence
- synaptic plasticity, learning, and memory
How is cyoplasmic polyadenylation regulated by CPEB?
- When CPEB is unphosphorylated, it binds CPE and forms complex with PARN and Gld2. Poly-A specific ribonuclease works faster than the Gld2 polymerase, and the polyA tail is degraded, keeping the mRNA static.
- a kinase phosphorylates CPEB so that PARN is released and Gldn2 adds A’s to the polyA tail, allowing it to be translated.
How is eIF4E affected by cytoplasmic polyadenylation?
When the mRNA is held static, PABP cannot bind, thus eIF4E cannot interact with eIF4G and translation cannot occur.
Why might mRNAs be localized to different parts of the cell for translation?
The protein product may be needed in that region of the cell.
Describe subcellular targeting of mRNAs.
- cis-acting elements specify RNA targeting
- trans-acting factors recognize cis-elements and bind them to form larger RNP particles
- molecular motors transport RNP particles to different parts of the cell.
- mRNAs are translationally dormant while en route
How is iron stored in cells and how does it enter cells?
In ferritin. It is brought to the cell by transferrin and enters through transferritin receptors.
How are proteins involved in iron storage and metabolism regulated?
- ferritin mRNA has IRE in 5’ UTR that are not bound by IRE-BP under high Fe, so the storage protein continues to be made.
- under low Fe, IRE-BP is active and binds IRE, blocking ribosomal scanning so no ferritin is made.
- TfR mRNA has IREs in 3’ UTR that have less stable AU regions, so no binding by IRE-BP under high Fe causes the transcript to be degraded
- when Fe is low, IRE-BP bind IRE and stabilize the transcript so that iron can be brought into the cell
How does eIF2 control translation through delayed re-initiation of specific mRNAs?
- under low stress, eIF2 has GTP and can reinitiate translation rather quickly after recycling, more chance to stay in same ORF and translate next start site.
- under high stress, eIF2 is phosphorylated and does not quickly reinitiate translation, so it may start in another ORF and translate mRNA for stress-related transcription factors
What is an IRES and how does it take place of a capping structure in viruses?
Internal ribosome entry site:
-secondary structure in 5’ UTR directly recruits eIF4G to 5’ end without eIF4E
Why might IRES be used by viruses?
So it can shut down translation of capped (host) mRNAs and only express its own proteins.
What is a common virus that uses IRES?
HepC
