5 - Mobile Introns and Inteins Flashcards
What are mobile genetic elements?
DNA elements that encode proteins that mediate the movement of the element within a genome and between genomes, can be found in all domains of life and viral genomes.
Parasitic genetic elements (proliferate within a genome and spread to other genomes)
Abundant and highly dynamic.
Over 50% of the human genome is composed of mobile genetic elements (aka Junk DNA)
What are alu sequences?
10% of the human genome. A primate specific mobile genetic element
300 bp sequence that is repetitive and able to jump around.
Some can still jump around and cause disease
What are mobile introns? List three types
Intervening sequences that are capable of self-splicing and moving themselves within and between genomes
- Group I introns (ribozyme)
- Group II introns (ribozyme)
- Inteins (proteins that carry out protein splicing and are also capable of moving the gene that encodes them to other locations - also mobile genetic elements)
How are inteins protein analogs of RNA splicing?
They are proteins embedded within a larger protein that have catalytic activity on themselves.
What are group I introns? Where are they found?
Mobile self splicing ribozymes that catalyze their own removal from RNA.
Found in rRNA (tetrahymena - first discovery)
Exist in proteins rRNA and tRNA genes in diverse eukaryotic nuclear, mitochondrial and plastid genomes, as well as in bacteria.
What do group I introns look like and how do they work?
- 200-500 nt in length
- COmplex secondary/tertiary structure
- Some (but not all) contain an ORF encoding a homing endonuclease (HE), which partially explains how parasitic mobile elements can spread throughout a genome
- Intron removed by two transesterification reactions (first initiated by OH group of exogenous guanosine)
Describe group I intron ‘homing’
Lateral (horizontal) transfer of an intervening sequence (eg. an intron) to an intron-lacking version of the gene
- The selfish mobile element self splices out of mRNA and is sometimes maturased by HE to fold into proper shape for splicing
- At the DNA level, the HE protein recognizes and cleaves 12-40 bp DNA sequence motifs (not as precise in homing as type II restriction endonucleases)
- The selfish mobile element is inserted into the recipient gene (in same or different genome - LGT)
- Intron is copied into recipient gene by DNA recombination/repair enzymes
Note: Recognition sequence is interrupted by the presence of the intron (HE protein does not cleave intron-containing genes)
Describe ectopic transposition of group I introns (3 types)
Transposition to a new spot by reverse splicing. Ectopic means it doesn’t have to the same gene that the intron came from (unlike homing)
- REverse splicing to another RNA by foruitous base-pairing between intron and RNA target (common)
- REverse transcription by an exogenous RT enzyme and recombination of cDNA into genome by recombination/repair enzymes (rare)
What are group II introns?
Like group I, but dependent on protein factors. Mobile genetic elements capable of self splicing out of precursor RNA.
Where are group II introns found?
- Protein genes in many bacteria, a few archaea and mitochondrial and plasmid genomes
- Progenitors of spliceosomal introns and retrotransposons
What do group II introns look like and how do they work?
More complex than group I introns
- 400-800 nt with complex secondary/tertiary structure
- Some contain ORF encoding multifunctional intron-encoding protein (IEP) that includes a reverse transcriptase domain
- Splicing occurs by transesterification reaction (first intiated by bulging A residue within the intron) forming a lariat
What are the four possible functional domains found in group II intron-encoded proteins (IEP)
- Reverse transcriptase
- RNA-binding domain (splicing)
- DNA binding domain (homing)
- Endonuclease domain (homing)
This is a big ORF, typically the same size as the rest of the molecule
- Helps the intron fold properly allowing splicing to occur (maturase)
- Mediates homing to intron-minus location
Describe group II intron homing
- ORF is expressed and makes multi domain intron-encoded protein with strong maturase activity. THE PROTEIN CAN COME FROM ANOTHER INTRON! (they can ‘help’ each other)
- Translated internal ORF aids in splicing
- Intron wrapped around IEP
- Homing site is recognized in DNA and cleaved
- Intron is inserted
- Recombination spreads intron to new locus (or by repair enzymes)
How can group II introns move to entirely new locations within the genome?
Just like group I introns, they can undergo ectopic transposition by reverse splicing into new RNA molecules and then undergoing reverse transcription.
What is a twintron?
An intron with another intron embedded into it (intron within an intron)
