32 - RNA editing, catalytic RNAs Flashcards
What five cis elements are needed for splicing in vertebrates?
- 5’ splice site (donor site)
- 3’ splice site (acceptor site)
- Branch point
- YYYY polypyrimidine track
- Exonic splicing enhancer/silencer (ESE/ESS) (only in vertebrates, silencer is obviously the opposite of being needed..)
Where is the exonic splicing enhancer found?
In exons upstream of introns. Only make sense in pre-mRNA
How is alternative splicing possible?
Exons with weak (suboptimal) splice sites are alternative, exons with strong splice site are constitutive.
Alternative splicing is determined and regulated by differences in the activities and/or amounts of general splicing factors and/or gene-specific splicing regulators during development or in different tissues
Splicing of regulated exons is modulated by trans and cis elements? (2)
- SR proteins (positive regulator) and hnRNPs (negative regulator) (trans)
- Splicing enhancers and silencers (cis)
What is negative control of alternative pre-mRNA splicing? What is an example of a negative regulator?
Where splicing occurs UNLESS there is a repressor present
hnRNP A1
What is positive control of alternative pre-mRNA splicing? What is an example of a positive regulator?
Where splicing does not occur UNLESS there is an activator present
SR protein
What is a ribozyme?
An RNA molecule possessing enzymatic properties
What is the difference between protein catalyzed and RNA catalyzed reaction?
None! Except RNA catalysis is slightly slower.
What is autocatalytic (intramolecular) endonucleolytic cleavage of RNA? What are two types of RNA that do this?
RNA molecules that can catalyze reactions on themselves. Eg:
- Self splicing introns
- Self cleaving transcripts
What are three types of RNA that have autocatalytic activity for self splicing their introns?
- Nuclear rRNA genes
- Mitochondrial rRNA and protein coding genes
- Chloroplast rRNA, tRNA and protein coding genes
What is true catalysis with RNA? What are some examples?
Ribozymes that catalyze reactions on molecules other than themselves.
- RNase P cleavage of pre-tRNAs to generate mature 5’ terminus
- Excised tetrahymena intron
- rRNA (in LSU)
- snRNA in spliceosome
What does Rnase P catalyze?
Processes 5’ end of primary tRNA transcript in all organisms
What are the two known classes of self-splicing introns?
Group I - Introns bind a free G nucleotide at a specific site to initiate splicing. Has a linear intermediate rather than a lariat like pre-mRNA splicing or group II introns
Group II - Introns use a reactive A nucleotide (branch point A) in the intron sequence itself for the same purpose
The mechanism used by group II intron sequences form a lariat and resembles the pathways catalyzed by the spliceosome
What four types of RNA have shown RNA editing?
- Nuclear gene transcripts (mRNA)
- Mitochondrial gene transcripts (mRNA, rRNA, tRNA)
- Chloroplast gene transcripts (mRNA)
- Viral RNA (hepatitis delta virus)
RNA editing has not been found in prokaryotes
What are four types of RNA edits?
- Insertion or deletion of U residues (mitochondria)
- Insertion of (Mostly) C residues (mitochondria)
- Conversion of C to U (deamination) (mammalian intestine and plant chloroplasts)
- Conversion of A to I (deamination)
What does ADAR do?
Adenosine Deaminase acting on RNA (ADAR) converts adenosine into inosine by deamination
How are glutamate channel activities facilitates in verves?
A deamination to I at a glutamine (CAG) codon in the mRNA of the glutamate receptor channel changes the codon into CIG, encoding arginine. This change alters the properties of the glutamate channel, improving nerve signal transmission.
What is an example of the function for U-insertion RNA editing?
Insertion of U residues can frameshift mRNA to create a correct reading frame
What do guide RNAs (gRNAs) do?
Specify where U residues should be added, sites on the transcript that do not bind to gRNA are places where U are added.
What is the function of the poly(U) tail of gRNA?
Helpts to stabilize the gRNA-mRNA pairing by binding to the unedited portion of the message
What is an editosome?
A complex of 16 proteins with TUTase, an RNA-editing terminal urydylyl-transferase.
It has nuclease, TUTase, exoribonuclease and ligase activity (can do things like insert U residues)
What is pan-editing in trypanosome mitochondria?
Editing of a cox3 mRNA in the organism that causes African sleeping sickness.
There is both U insertion and U deletion throughout more than 50% of the mRNA sequence
What is a heterogenous ribonucleoprotein particle (hnRNP)?
A negative regulator of splicing. Splicing occurs unless hnRNP is present.
What happens if both SR and hnRNP are present at an exonic splicing enhancer and exonic splicing silencer on an exon?
The SR with inhibit hnRNP and cause splicing to occur.
What are mobile/jumping cis elements?
Can jump into an intron/exon and affect RNA splicing.
