Exon Shuffling (Isalan L6)
Common type of shuffling in early eukaryotes
0-0
Reason for 1-1 shuffling
1-1 introns usually interrupt glycine codons (which will still be formed) which are ideal for linkages between protein domains
Mechanism of LINE exon shuffling
Additional RNA is reverse transcribed and inserted back into the DNA at a new location. Over time the line may degenerate and disappear, leaving behind the inserted DNA
What proteins are required for multicellular structures
Adhesion proteins are required for cell adhesion
What are amyloid plaques associated with?
Alzheimers
Ideal intron for α2 Type 1 Collagen tripeptide
As a tripeptide with lots of glycine repeats, the 1-1 family is ideal
Advantage of exons corresponding to domains
Can generate novel genes and proteins with diverse functional modules and functions
How do DNA transposons shuffle exons?
Carry exons/introns between their flanking inverted repeats. Moved by transposase
Example of sequences carried by transposons
Could carry termination exons would would trunkate proteins
Homodimeric proteins
Dimer proteins composed of two identical polypeptides
What does exons corresponding to domains allow?
Duplication, permutation and rearrangement
Exon 1-1 shuffling emergence
Emerged with the start of the metazoa
How can phenotypic diversity be achieved from fewer genes?
Exon shuffling
x-x shuffling
Exon shuffling is classified by the phase of their flanking introns
Expansion of protein-protein interaction networks
Exon shuffling promotes self-interaction domains which produce homodimeric proteins. Not always specific, some are more promiscious
KPI domain DNA structure (shuffling)
Flanked by introns, so was potentially gained through shuffling
Splice frame rule
Following a successful shuffling event a newly acquired exon will be flanked by 2 introns of the same phase otherwise it will produce a frameshift in the resulting sequence
Outcome of β-secretase followed by λ-secretase
Forms soluable APP as well as β-amyloid protein which forms beta-sheet structures resulting in gel-like plaques
Potential results of illegitimate non-homologous recombination
Gene fusion, domain deletion/insertion and unequal crossing over
α2 Type 1 Collagen tripeptide
Gly, X, Y where X is often proline and Y is often hydroxyproline
α2 Type 1 Collagen
Has a highly repetitive sequence made up to a tripeptide
Exon shuffling mechanisms
Illegitimate non-homologous recombination, LINEs and DNA transposons
Benefit of duplicating domains
Increases interactions between proteins - v useful if they are part of a cascade
How can increasing complexity occur?
Increasing gene number, protein number and function
How do indels affect the phase
Insertions and deletions can affect the reading frame, disrupting it for all downstream exons
What type of insertion doesn't affect phase?
Insertions in multiples of 3
What determines APP processing
KPI (Kunitz protease inhibitor) domain which inhibits α-secretase, making plaque formation more likely
KPI domain
Kunitz protease inhibitor domain
Exon shuffling in adhesion proteins
Shuffling essential for formation of multicellular organisms. New adhesion proteins allow the formation of new and complex structures
Alternative theory for alzheimers
Some claim plaques are protective structures that tackle toxic intermediates
Exon shuffling with expression patterns
Splicing allows combinatorial variety and therefore new expression patterns
What is 1-1 exons shuffling associated with
The emergence of features necessary for multi-cellularity
How large are protein domains
40-100 AA
How do LINEs shuffle exons?
When they move, they can carry a piece of nearby DNA along with it, usually from its 3' end
amyloid precursor protein
a membrane protein found mainly in neurons that gives rise to the material in amyloid plaques. Has several isoforms
Hydroxyproline
a neutral heterocyclic protein amino acid
APP
amyloid precursor protein
Proteins in cascades are often...
coded by co-evolved genes
Outcome of α-secretase
forms soluable APP - a good cellular outcome
Folding in small and flexible domains
independent
Intron phase: Phase one
introns lie between 2 codons, referred to as the universal phase
Intron phase: Phase two
introns located after first nucleotide
Intron phase: Phase three
introns located after second nucleotide
Some examples of protein domain functions
stabilisation, binding and catalysis
Most exons are...
symmetric (less likely to frameshift)
TPA
tissue plasminogen activator
What % of human genes produce homodimeric proteins?
24.6%
What domain in present in APP isoforms?
A protease inhibitor domain (Kunitz-type)
What is required for illegitimate non-homologous recombination
A tiny overlap
APP outcomes
APP has different outcomes depending on how it is processed by proteases
What is responsible for domain shuffling?
Likely to be retrotransposition as rates of domain shuffling is higher in certain organisms compared to others
Structure of TPA
Made up of 4 exons - a hybrid of three other proteins min the cascade, exons 'copied' from these proteins
Why does protein structure allow exon shuffling
Many eukaryotic protein are mosaics of domains so exons can be shuffled to create new combinations
Primary mechanism of illegitimate non-homologous recombination
Non-homologous end joining
Adhesion proteins
Often modular
Tissue plasminogen activator
Part of the vertebrate blood clotting protein cascade
Illegitimate non-homologous recombination
Process by which two unrelated double stranded segments of DNA are joined.
Amyloids
Proteins that polymerise to form a cross-beta structure, in vivo or in vitro, inside or outside cells
Benefit of repeated domains
Repeated domains in the same gene can increase stability and catalysis as well as modify its function
two ways illegitimate non-homologous recombination can occur
Replication slippage or mediated by enzymes such as topoisomerase
Self-interacting vs non-interacting domains in exon shuffling
Self-interacting domains show more exon shuffling. Must be subject to positive selection
Domain shuffling
Structural domains from different genes are joined together
What limitations prevent protein domain acquisition
Structural limitations
Which species is APP present in?
Vertebrates
Bad outcome pathway
β-secretase followed by λ-secretase