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