RR13: Post-transcriptional/translational regulation of gene expression Flashcards
When mRNAs get exported from the nucleus to the cytoplasm to get translated, there’s a RNA helicase that’s waiting for them on the outside of the nucleus to get rid of all the proteins on the mRNA. Is RNA helicase 100% efficient to get rid of all the proteins?
No. Sometimes, the RNA helicase doesn’t get all the proteins on the mRNA. That’s why eIF4A is an RNA helicase that works in the pre-initiation complex to get rid of all secondary structures that might be on the mRNA before the translation.
OR (check the answer in the discussion board)
The first round of translation is used to get rid of all the proteins that were not successfully taken out by RNA helicase.
What happens when there’s a mistake in an mRNA and we find a stop codon in the middle?
It can give rise to a truncated protein.
What does a truncated protein do?
70% of the time, a truncated protein doesn’t cause a problem, but it could cause grief for the cell.
It can disrupt the homeostasis of the cell. Like a protein without an activation domain will bind to DNA but it can’t do anything, so we have less functioning DNA segments.
What does the cell do when it recognizes a truncated protein?
nonsense-mediated decay NMD
What are the proteins that could be found on mRNA that need to be removed otherwise it would give rise to a truncated protein?
SR proteins that define the exons.
Polyadenylation of the pre-mRNA
Export factors on the mRNA.
They all need to go after the first round of translation.
How does nonsense-mediated decay wok?
It brings in devoted exoribonucleases that will eliminate that mRNA.
Why is nonsense-mediated decay so important?
Because it makes sure that we don’t find truncated variants of the protein interfering with normal cellular homeostasis.
It’s an important quality control mechanism.
Is the degradation of mRNAs with mistakes in them highly regulated?
Yes. The stability of the mRNA is critical for efficient translation.
Are mRNAs more stable in the nucleus or in the cytoplasm?
mRNAs are more stable in the nucleus because that’s where they’re made. When they get to the cytoplasm, their stability can vary between different organisms.
What are some factors that can influence the stability of the mRNAs in the cytoplasm of the cell?
The temperature is stable.
Constant flow of nutrients
Ensure cellular homeostasis is stable.
Why do some mRNAs need to be purposely destabilized in the cell?
They’re only present for a short amount of time.
Might be mRNAs linked to the cell cycle:
- genes that activate the cell cycle are important, but they can’t be there for too long, we want them to stop at one point or we could get tumours, so they get destabilized.
Or cytokines involved in immune response need to be activated quickly and destabilized quickly.
What’s something that can be used to destabilize mRNAs?
A sequence motif. By adding a specific sequence, we can reduce the half-life of a gene. The sequence will be recognized by proteins that will recruit exoribonucleases to destroy the mRNA.
Can RNA decay occur at both ends of the strand?
Yes.
5’ to 3’ decay
3’ to 5’ decay
How does the 3’ to 5’ decay work?
The deadenylase complex.
It’s deadenylation-dependent.
The deadenylase complex will chew up the Poly A tail with a specific enzyme.
Then, the exosome will come in and chew up the RNA.
How does the 5’ to 3’ decay work?
It’s deadenylation-independent.
Decapping enzymes will take off the cap on the 5’ end. They remove the 7-methylguanine cap and that exposes the 5’ end.
Then, XRN1 will degrade the RNA.
During destabilization of RNA, where does the decapping of the 5’ end occur?
It happens in P-bodies (liquid-liquid condensate) where they bring all the enzymes necessary to destabilize the mRNA in the cell.
What is the exosome?
It’s a complex of similar polypeptides that is designated to chewing up mRNAs from the 3’ to 5’. It sucks the mRNA inside all the different subunits and at the end of the tube, there are 2 ribonucleases: exoribonuclease and endoribonuclease.
What’s the job of the exoribonuclease in the exosome?
It chews up the RNA as it comes close to it at the end of the tube (exosome).
What is the job of the endonuclease in the exosome?
It chews up the bits of RNA that the exoribonuclease might have missed.
Is the exosome efficient to destroy mRNA?
Yes. Because it first has the exoribonuclease, then the endoribonuclease makes sure every part of the mRNA is destroyed.
What is the kiss of death for an mRNA?
It’s when an endonuclease cuts the mRNA in half, so it activates 5’ to 3’ decay and 3’ to 5’ decay at the same time on the 2 different fragments.
It destroys the mRNA very rapidly.
Is the stability of mRNAs random?
No. mRNAs are regulated by proteins to make sure they’re stable.
Why would we need to regulate the stability of the mammalian transferrin receptor?
TfR (tranferrin receptor) is needed for the import of iron into the cell.
We need to regulate it in response to iron concentration in the cell.
Iron is required for some enzymatic reactions, but it can also be very toxic, so the cell needs to regulate the levels of iron.
What is the job of the Transferrin receptor?
It brings iron into the cell when the levels are starting to drop.
What’s the secondary structures found in the Transferrin receptor?
IREs. Iron Response Elements.
They’re secondary structure in the 3’ UTR of Transferrin receptor. They have AU-rich elements.
What’s the job of the secondary structures, IREs, found in the transferrin receptor?
The Iron Response Elements have AU-rich elements and they’re the ones doing the important job.
