4: Genome evolution

Types of Genomic Duplications Part of an exon or the entire exon is duplicated Complete gene duplication Partial chromosome duplication Complete chromosome duplication Polyploidy: full genome duplication

After a Gene is Duplicated Alternative fates: 1.It can die and become a pseudogene. 2.It can retain its original function, thus allowing the organism to produce double the amount of the derived protein. 3.The two copies can diverge and each one will specialize in a different function. Identical copiesOne copy diesDivergence

Duplication within a gene

The Ovomucoid Gene

Ovomucoid Is found in the albumin (egg white) of birds. It inhibits trypsin, the enzyme that catalyzes the digestion of proteins. The gene has 3 functional domains (Domain I, Domain II and Domain III).

Ovomucoid The two exons of each domain do not show any sequence similarity. Exon Intron Each Domain has two exons and a flanking intron.

Ovomucoid: amino acid identity Each domain is similar to the other two Exon Intron Exon Intron Exon Intron III I II 46% 33% 30%

Ovomucoid: nucleotide identity Each domain is similar to the other two Exon Intron Exon Intron Exon Intron III I II 66% 42% 50%

Ovomucoid: conclusion The basic Domain (containing the exon-intron-exon structure) had undergone two duplications. Since Domain I and II are more similar to each other than either of them to domain III, the first duplication probably included Domain III and the ancestor of Domains I + II.

4: Genome evolution

The antifreeze glycoprotein gene

The body fluids of teleosts (ray-finned fish) freeze at temperature ranging from -1.0°C to - 0.7°C Most fish cannot survive the freezing temperature (-1.9 ° C) of the Antarctic Ocean

The antifreeze glycoprotein gene Freezing resistance in Antarctic fish is conferred by different types of antifreeze proteins Antifreeze proteins prevent freezing of the body fluids by adsorbing to small ice crystals in the body and inhibiting their growth

Origin of antifreeze glycoprotein gene Derived from a gene encoding pancreatic trypsinogen Small sequence divergence (4-7%) between antifreeze glycoprotein and trypsinogen The transformation occurred quite recently, about 5-14 mya The estimated time of the freezing of the Antarctic Ocean is mya

Ancestral trypsinogen gene E1 E2E3E4E5 5’5’ E “ E6 ” GGG TGA Gly Stop ’3’ 3 5’5’ E1 ~1.7 kbp Antifreeze glycoprotein gene

Some part of the gene was deleted (in white). A new gene with only two exons was created. Ancestral trypsinogen gene E1 E2E3E4E5 5’5’ E6 E1 “ E6 ” 5’5’ 3’3’

E1 E2E3E4E5 5’5’ 3’3’ E6 acag CGG CAA g GGT GAC TCC … Arg Gln The deletion started at nucleotide 6 in the second exon ending one nucleotide before the start of exon 6 Gly Asp Ser Ancestral trypsinogen gene E1 “ E6 ” ACA GCG GCA GGG TGA … Thr Ala Ala Gly Stop 5’5’ 3’3’

E1 E2E3E4E5 5’5’ 3’3’ E6 acag CGG CAA g GGT GAC TCC … Arg Gln Exonization of 5 nucleotides: 4 nucleotide from the first intron and one from the fifth intron  frameshift of the reading frame encoded a tetrapeptide Thr Ala Ala Gly before reaching a new stop codon Gly Asp Ser Ancestral trypsinogen gene E1 “ E6 ” ACA GCG GCA GGG TGA … Thr Ala Ala Gly Stop 5’5’ 3’3’

E1 “ E6 ” ACA GCG GCA GGG TGA … Thr Ala Ala Gly Stop 5’5’ 3’3’ Fourfold duplication + Addition of a spacer sequence 3’3’ E1 “ E6 ” 5’5’ GGG TGA Gly Stop Internal duplication + Additional of an intron sequence “ E6 ” GGG TGA Gly Stop ’3’ 3 5’5’ E1 ~1.7 kbp

Some of the spacer sequences encode peptide motifs that serve as signals for the cleavage of the antifreeze glycoprotein polypeptide into the active proteins The sequence (approximately 1.7 Kb long) that was added to the intron probably had no functional consequences

Conclusions The evolution of antifreeze glycoprotein gene includes: recruitment of segments of an existing protein gene and amplification of a short DNA sequence Multiple mutational events in a very short time span The new gene must have been subjected to intense positive Darwinian selection, most probably due to an abrupt shift in environment conditions