Evolution by Gene Duplication Part I

Evolution by Gene Duplication Wen-Hsiung Li, Ph.D. James Watson Professor Ecology and Evolution University of Chicago Topics • Increase in gene number from simple to complex organisms • Evolutionary significance: Why gene duplication? • Examples of duplicate genes • Loss of duplicate genes • Conclusions # of genes Prokaryotes Haemophilus influenzae 1790 5380 6000 19,700 13,770 E. coli Yeast Nematode Fruitfly Ciona intestinalis 10,990 (Sea squirt) Chicken 17,710 Eukaryotes Human 22,200 Family size Yeast 1 4,768 (78%) 2 415 3 56 4 23 5 9 6~10 19 11~20 8 21~50 0 50~80 0 >80 0 # gene families 530 # unique gene types 5,298 C. elegans 12,858 (67%) 665 188 93 71 104 57 33 5 3 1,219 14,077 Why Gene Duplication? • Producing more of the same • Functional fine-tuning • Functional diversity • Creation of a new gene from a redundant duplicate 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. No. of rRNA and tRNA genes in a genome Genes Mitochondrion E. coli (mammals) Human Proteins 18S rRNAs tRNAs 13 1 22 5380 7 85 ~22,200 ~300 ~500 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. 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 Lactate dehydrogenase (LDH) Catalyzes the conversion between lactate and pyruvate 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 Developmental sequence of five LDH isozymes in rat heart Functional diversity Immunoglobulins: Antibody diversity Major Histocompatibility Complex (MHC) genes 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 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. Enhancing or expanding existing function Color vision genes Hemoglobin genes Pygmy chimp or bonobo Trichromatic color vision from Backhaus, 1998 400 500 600 Wavelength (nm) A person with only a short-wave and a middle-wave photo-receptor Vision of most mammals (dichromats) a. Short wave opsin (blue) b. Long or middle wave opsin (red/green) X-linked autosome Origin of routine trichromacy X chromosome Autosome Humans Apes Old World Monkeys ? New World Monkeys 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 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. 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 Monomer Monomer Creation of a new gene from a redundant duplicate gene Myoglobin and hemoglobin Trypsin and chymotrypsin Olfactory receptors Hox genes Pax genes Hemoglobin: Oxygen carrier in blood. Myoglobin: Oxygen carrier in tissues. It has a higher oxygen affinity than hemoglobin. 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. ~1,500 million years ago 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. 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. Examples of molecules in different odor classes Molecule Name Ethyloctanoate Chemical Formula Smell Shape Fruity C10H20O2 Minty Betacyclocitral C10H13O Minty p-anisaldehyde C8H8O2 Nutty,Medicinal 2,6-dimethyl pyrazine C6H8N2 Nutty,Medicinal 4-heptanolide C7H12O2 Nutty,Medicinal p-cresol C7H8O Putative Binding cavity in Human OR1.04.06 Binding cavity for retinal in Bovine rhodopsin 1HZX Chain A