evolution by gene duplication wen-hsiung li, ph.d. james watson professor ecology and evolution...
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Evolution by Gene Duplication
Wen-Hsiung Li, Ph.D.
James Watson Professor
Ecology and Evolution
University of Chicago
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Topics• Increase in gene number from simple
to complex organisms
• Evolutionary significance: Why gene duplication?
• Examples of duplicate genes
• Loss of duplicate genes
• Conclusions
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Fruitfly
Nematode
Ciona intestinalis
Yeast
Human
Chicken
Haemophilus influenzae
E. coli
# of genes
1790
5380
6000
19,700
13,770
10,990
17,710
22,200
(Sea squirt)
Prokaryotes
Eukaryotes
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Family size Yeast C. elegans 1 4,768 (78%) 12,858 (67%) 2 415 665 3 56 188 4 23 93 5 9 71
6~10 19 104 11~20 8 57 21~50 0 33 50~80 0 5 >80 0 3
# gene families 530 1,219 # unique gene types 5,298 14,077
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Why Gene Duplication?
• Producing more of the same
• Functional fine-tuning
• Functional diversity
• Creation of a new gene from a redundant duplicate
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Producing more of the same
The normal physiology of an organism may require many copies of a gene.
Example: The translational machinery of an
organism usually requires many transfer RNA (tRNA) genes and ribosomal RNA (rRNA) genes.
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No. of rRNA and tRNA genes in a genome
Genes Mitochondrion E. coli Human (mammals)
Proteins 13 5380 ~22,200
18S rRNAs 1 7 ~300
tRNAs 22 85 ~500
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Response to stress
Multi-drug resistance (P-glycoprotein) (mdr) genes
Amplification of mdr genes often occurs in cancer cells after a patient has been treated with drugs.
Insecticide resistance Multiple copies of esterase genes have been
found in mosquito populations treated with insecticide.
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Functional fine-tuning
Isozymes: Enzymes that catalyze the same biochemical reaction but may differ from one another in biochemical properties, tissue specificity, and developmental regulation
Are encoded by duplicate genes
Examples: Lactate dehydrogenase (LDH), aldolase, creatine kinase
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Lactate dehydrogenase (LDH)
Catalyzes the conversion between lactate and pyruvate
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LDH isozymes LDH: tetramer (consisting of 4 subunits)
A and B subunits are encoded by two separate genes
A4, A3B, A2B2, AB3, B4
B4, AB3: function better in aerobic
tissues such as heart
A4, A3B: function better in anaerobic
tissues such as skeletal muscle
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Developmental sequence of five LDH isozymes in rat heart
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Functional diversity
Immunoglobulins: Antibody diversity
Major Histocompatibility Complex (MHC) genes
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Immunoglobulins
Immunoglobulin: 2 light chains and 2 heavy chains 2 types of light chain: kappa & lambda 5 types of heavy chain: mu, delta, gamma
(4 subtypes), epsilon and alpha.
The type of heavy chain defines the class of immunoglobulin:
IgM, IgD, IgG, IgE and IgA
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Over 15,000,000 combinations of Variable, Diversity and Joining gene segments are possible. Imprecise recombination and mutation increase the variability into billions of possible combinations.
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Enhancing or expanding existing function
Color vision genes
Hemoglobin genes
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Pygmy chimp or bonobo
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Trichromatic color vision
from Backhaus, 1998
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400 500 600
Wavelength (nm)
A person with only a short-wave and a middle-wave photo-receptor
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Vision of most mammals (dichromats)
a. Short wave opsin (blue)
b. Long or middle wave opsin (red/green)
X-linked autosome
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Origin of routine trichromacy
New World Monkeys
Humans
Apes
Old World Monkeys
X chromosome Autosome
?
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Hemoglobin
In human and mammals: A tetramer consisting of two α
and two β globin chains
In jawless fish: A monomer and only 1 globin gene
Polymerization occurred probably after gene duplication
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Advantages of being a tetramer Allows hemoglobin to bind oxygen
in a cooperative fashion: The binding of the first oxygen molecule facilitates the binding of subsequent oxygen molecules.
Conversely, release of the first oxygen molecule facilitates the release of subsequent molecules.
As an oxygen carrier in blood it must load and unload oxygen molecules at the right partial oxygen pressure.
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Types of hemoglobin in humans
• In the embryo: ξ2ε2 and α2ε2
• In the fetus: Hemoglobin F (α2γ2)
• In adults:
Hemoglobin A (α2β2) - Most common type
Hemoglobin A2 (α2δ2) - δ chain synthesis begins late in the third trimester and in adults, it has a normal level of 2.5%
Hemoglobin F (α2γ2) - In adults it is restricted to a limited population of red cells
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Monomer
Monomer
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Creation of a new gene from a redundant duplicate gene
Myoglobin and hemoglobin
Trypsin and chymotrypsin
Olfactory receptors
Hox genes
Pax genes
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Hemoglobin: Oxygen carrier in blood.
Myoglobin: Oxygen carrier in tissues. It has a higher oxygen affinity than hemoglobin.
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Trypsin and chymotrypsin
Digestion of protein in the intestine is carried out by trypsin and chymotrypsin.
Trypsin attacks the peptide bond at the basic amino acids lysine and arginine, whereas chymotrypsin attacks the peptide bond at the carboxyl side of the aromatic amino acids phenylalanine and tyrosine.
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~1,500 million years ago
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Olfactory receptors
The detection of small molecules plays an important role in the survival of most animals, which use odor to identify and evaluate their food, predators, and territory.
The olfactory system is important for our quality of life. A unique odor can trigger distinct memories from our childhood or from emotional moments – positive or negative. When something tastes good it is mainly due to activation of the olfactory system.
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The vivid world of odors: A Nobel Prize (2004) was given to Richard Axel and Linda Buck for their discoveries of odorant receptors and the organization of the olfactory system.
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SmellMolecule Name
Chemical Formula
Shape
FruityEthyl-octanoate
C10H20O2
MintyBeta-cyclocitral
C10H13O
Examples of molecules in different odor classes
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Minty p-anisaldehyde C8H8O2
Nutty,Medicinal
2,6-dimethyl pyrazine
C6H8N2
Nutty,Medicinal
4-heptanolide C7H12O2
Nutty,Medicinal
p-cresol C7H8O
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Putative Binding cavity in Human OR1.04.06
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Binding cavity for retinal in Bovinerhodopsin 1HZX Chain A