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BIS477 World of RNA > Cytoplasmic mRNA quality control mechanisms > Flashcards

Cytoplasmic mRNA quality control mechanisms Flashcards

1
Q

What are the 3 main roles of ribonucleases in productive gene expression?

A
  • Processing functional RNAs from larger transcripts
  • Degradation in quality control pathways
  • Suppress accumulation of non-classical unstable RNAs
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2
Q

What are exoribonucleases? (3)

A
  • Either 5’ or 3’
  • Target free ends of RNA
  • Function in combination with other proteins that make the RNA ends accessible
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3
Q

Why is RNA surveillance important? (5)

A
  • Pervasive transcription generates unstable non-coding transcripts that are targeted to degradation to avoid accumulation
  • Accumulation would adversely affect gene expression and genome stability
  • RNA degradation is the default
  • Transcripts evade surveillance machinery by acquiring protective features
  • Surveillance allows evolution of new transcripts
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4
Q

What is pervasive transcription? (2)

A
  • Transcription of non-coding unstable RNAs from areas of chromatin with low nucleosome density
  • Generated by bidirectional transcription from promoter sites
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5
Q

What is the exosome? (2)

A
  • Multiprotein complex which is the main 3’ to 5’ exoribonuclease in eukaryotic cells
  • Involved in processing/quality control/degradation of unstable transcripts
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6
Q

What is the structure of the exosome? (4)

A
  • Ring structure with Rrp44 nuclease catalytic subunit at the bottom of the complex
  • RNA binding proteins at the top of the complex
  • Complete complex is a barrel structure
  • Structurally similar to the proteasome
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7
Q

What is the catalytic subunit of the exosome?

A

Rrp44

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8
Q

How does the exosome complex differ between organisms? (4)

A
  • Nuclear form in yeast contains additional RNase Rrp6 but cytoplasmic form doesn’t
  • Nucleolus form in humans has Rrp6 but not Rrp44, both domains in the nucleus, and both domains in the cytoplasm but a different form of Rrp44
  • Not one single complex, modular structure with diversity
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9
Q

What happens in the nucleolus?

A

Processing of rRNA

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10
Q

What is the major route for substrate degradation via the exosome? (4)

A
  • Substrate threaded through the channel from the top
  • 3’ end ends up at the active site of the catalytic subunit at the bottom of the structure
  • Some RNAs can be directly targeted to the catalytic subunits without threading through
  • Exosome has endonuclease subunits as well
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11
Q

What other factors is the exosome dependent on for RNA degradation? (3)

A
  • Many ribonucleases are unable to degrade structured RNAs
  • Terminal nucleotide transferases (TNTs) add oligo(A) or oligo(U) tails which provide a binding platform to engage the RNase
  • Associated RNA helicases can unfold RNA secondary structures to allow degradation
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12
Q

What are TNTs?

A

Enzymes which add oligo(A) or oligo(U) tails to RNAs for degradation

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13
Q

What RNA helicases does the exosome associate with? (2)

A
  • Mtr4 (yeast nuclear)
  • Ski2 (yeast cytoplasmic)
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14
Q

Why does the exosome associate with RNA helicase complexes?

A

Unfold substrates the thread through the central pore

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15
Q

How is Rrp6 associated with the exosome in yeast nuclear form? (2)

A
  • C-terminal end wraps around the exosome complex to tether
  • N-terminal end interacts with Mtr4 and the TRAMP complex
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16
Q

What is the TRAMP complex? (2)

A
  • Mtr4 doesn’t exist on its own in yeast it forms part of the TRAMP complex
  • Also contains Air1/2 RNA binding protein and Trf4/5 polyA polymerase so TRAMP complex has helicase and terminal nucleotide modification activity to aid degradation
17
Q

What does the cytoplasmic form of the exosome associate with instead of the TRAMP complex? (4)

A
  • No Rrp6
  • Ski complex consists of Ski2, 3 and 8 and is tethered to the exosome by Ski7
  • Ski7 N-terminal performs same function as C-terminal of Rrp6
  • Ski2 subunit is functionally homologous to Mtr4, also RNA helicase to feed RNA through
18
Q

How do the functions of the nuclear and cytoplasmic forms of the exosome differ? (2)

A
  • Cytoplasmic form involved in mRNA turnover
  • Nuclear form involved in RNA processing and surveillance
19
Q

What is the structure of Mtr4/Ski2? (3)

A
  • Helicase domain
  • Arch structure with RNA binding areas
  • Arch can also interact with other proteins bound to RNAs e.g. from other processing steps which facilitates targeting of the RNP complex to the exosome
20
Q

What is the NNS complex? (2)

A
  • Transcription termination of long RNA transcripts involves 3’ cleavage, polyA tail addition, polyA binding protein binds
  • Short transcript termination uses the NNS complex in yeast which doesn’t involve cleavage
21
Q

What are the components of the NNS complex? (3)

A
  • Nrd1 (RNA binding protein)
  • Nab3 (RNA binding protein)
  • Sen1 (RNA helicase)
22
Q

How is degradation/processing of short RNAs coupled to transcription termination in yeast? (5)

A
  • CTD phosphorylated at serine 5 early on in transcription
  • This allows Nrd1 to interact with the CTD via its CTD interacting domain (CID) therefore NNS is recruited to Pol II at the beginning of genes
  • Needs to be a number of binding sites on the RNA for Nrd1 and Nab3 for NNS to bind to RNA as it is being produced
  • This promotes helicase activity of Sen1 which releases the RNA from Pol II
  • CID of Nrd1 can then interact with Trf4 (TRAMP) which targets the RNA to processing/degradation depending on the nature of the RNA
23
Q

What are the major eukaryotic 5’ exoribonucleases? (3)

A
  • Xrn1
  • Xrn2
  • Only work on RNA with a 5’ monophosphate substrate so can’t work if there is a cap etc. meaning entry sites are generated by endonucleases or decapping enzymes
24
Q

What is the function of Xrn1? (2)

A
  • Cytoplasmic mRNA turnover
  • Degradation of mRNA so determines functional lifetime of mRNAs
25
Q

What is the function of Xrn2? (4)

A
  • In the nucleus
  • Important for coupled transcription termination and 3’ processing with pol II,
  • After 3’ cleavage Xrn2 attacks the 5’ end of the leftover RNA, degrades it and catches up with Pol II which is still transcribing to displace it from the template DNA (Torpedo model)
  • Also involved in RNA processing and surveillance
26
Q

What is Rai1? (3)

A
  • Xrn2 is associated with Rai1 which converts 5’ triphosphates to 5’ monophosphates (now Xrn2 sensitive transcript)
  • Also has decapping activity on non-methylated caps
  • May promote Xrn2-mediated surveillance of non-capped/incompletely capped RNAs, won’t act on a correctly methylated m7g cap
27
Q

What is the function of NAD caps?

A
  • Nicotinamide adenine dinucleotide (NAD) is found at 5’ end of some mRNAs
  • Promotes instability to direct the RNA to degradation
  • Dxo1 (Rai1 homologue in yeast with 5’ exonuclease activity) can remove this non-canonical cap and degrade the mRNA

BIS477 World of RNA (14 decks)

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