Translational termination, mRNA stability and modifications in eucaryotes (Moll)

What is abbreviated under RF1, RF2 and RF3?

Release Factors 1, 2 and 3

Which Stop-Codon does RF1 (Release Factor 1) recognize?

UAA and UAG

Which Stop-Codon does RF2 (Release Factor 2) recognize?

UAA and UGA

What is a unique feature of both RF1 and RF2 (Release Factors 1 and 2)?

They have a GGQ-motif

What is a GGQ-motif?

A universally conserved tripeptide sequence, found in release factors across all life domains

What is a tripeptide sequence of a GGQ-motif?

Glycine, glycine, glutamine

What is a function of a GGQ-motif in RF1 and RF2 (Release Factors 1 and 2)?

It facilitates the hydrolysis of the ester bond of the peptidyl-tRNA after translation

What is a function of RF3 (Release factor 3)?

RF3 promotes the release of peptidyl-tRNA from the ribosome and stimulates the activity of RF1 and RF2 during translation termination

What are non-stop mRNAs?

They don’t have a Stop-Codon

What is a stalled ribosomal complex?

A situation where the ribosome is unable to proceed with translation due to the absence of a stop codon, leading to the accumulation of ribosomes on mRNA

What is trans-transltion?

Mechanism of translation termination of non-stop mRNAs, facilitated by tmRNA

What is abbreviated under tmRNA?

Transfer-messenger RNA

What is a SmpB-factor?

Small protein that assists tmRNA during translation termination

When does trans-translation happen?

When the mRNA channel of the ribosome is half-empty

What is a unique feature of trans-translation in E. coli?

It’s a non-essential mechanism

What is a feature of tmRNA?

It has a Stop-Codon at the end, unlike non-stop mRNAs

What is alternative ribosome resque in E. coli?

Essential termination mechanism of non-stop mRNA, facilitated by factor AR-A and AR-B

What is abbreviated under AR-A and AR-B?

Alternative Rescue A and B

What is a feature of AR-A factor?

It mimics the Stop-Codon

Which factor recognizes AR-A in Alternative ribosomal rescue?

RF2 (Release Factor 2)

Where does AR-b bind to the ribosome?

To the A-site

What is a function of AR-B?

It has a GGQ-motif, which facilitates the hydrolysis of ester bonds between a peptide and tRNA

How are trans-translation and alternative ribosome rescue coupled?

Concentration of tmRNA influences expression of AR-A

What is a structure of ARF-A mRNA under normal conditions?

It has a hairpin loop prior to the Stop-Codon, which produces full-length mRNA with a hydrophobic region, which leads to immediate degradation

What happens to ARF-A mRNA under the uptake of tmRNA?

RNAse III cleaves the ARF-A mRNA, generating a non-stop mRNA, which stalls the ribosomes. As a result, tmRNA tags the ARF-A for degradation

What happens to ARF-A mRNA, when tmRNA is overworked?

The excess tmRNA leads to improper tagging of ARF-A, causing inefficient degradation and accumulation of faulty proteins

What is a chemical mRNA half-life?

50% decrease in the concentration of full-length transcripts after transcription had been blocked

What is a functional mRNA half-life?

50% decrease in the capacity of full-length transcripts to support protein synthesis after transcription had been blocked

How can mRNA half-lives be checked experimentally?

By using the antibiotic rifampicin, which inhibits RNA-Polymerase, researchers can measure decay rates of mRNA transcripts

What is a role of a PNPase in mRNA degradation?

It’s an exoribonuclease that degrades mRNA in a processive manner from the 3' to 5’, using an inorganic phosphate

What is a role of RNAse E in mRNA degradation?

It is an endoribonuclease that cleaves RNA molecules at 5’-monophosphate internally, usually in AU-rich single-stranded regions

What protects mRNA physically from degradation?

Active translation (protection by a ribosome) and RNA-binding proteins (protection by a protein)

Which mRNA features mak it more stable?

5’ Stem Loop and 3’ Stem Loop

What are non-canonical 5’ caps in mRNA?

Dephospho-CoA, NAD+ and NADH

What is a common feature of non-canonical mRNA caps?

All of them are added by the RNA-Polymerase and NOT post-transcriptionally, like in eucaryotes