Evolution by Gene Duplication Part I by sammyc2007

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									 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
                                     1790
                  influenzae
                  E. coli            5380


                  Yeast              6000

                  Nematode          19,700

                  Fruitfly          13,770

                  Ciona intestinalis 10,990
                   (Sea squirt)
                  Chicken           17,710


Eukaryotes        Human             22,200
    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
    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   Human
            (mammals)



Proteins       13         5380     ~22,200


18S rRNAs        1           7      ~300

tRNAs           22          85      ~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      Chemical
Smell                             Shape
         Name          Formula

         Ethyl-
Fruity                 C10H20O2
         octanoate



         Beta-
Minty                  C10H13O
         cyclocitral
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

								
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