Exon Shuffling

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Exon Shuffling
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Module definition and identification
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A plot for the b chain of hemoglobin from humans.
The radius of the protein is 27Å.
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Module 1
Module 2
Module 3
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Module 2
Module 1
Module 3
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AP apple module EG epidermal growth-factor
F1 F2 fibronectin type-1 type-2 GA
g-carboxy-glutamate domain KR kringle
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Mosaic (or chimeric) protein a protein encoded
by a gene that contains regions also found in
other genes. The existence of such proteins is
evidence for exon shuffling.
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exon shuffling ? mosaic proteins
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3 types of exon shuffling exon duplication the
duplication of one or more exons within a gene
(internal duplication) exon insertion
exchange of domains between genes or insertions
into a gene exon deletion the removal of a
segment from a gene.
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Phases of introns and classes of exons
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Consequences of exon duplication deletion
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Consequences of exon insertion into introns
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Some module-coding exons are more prone to
participate in exon shuffling more than others.
One such module is the kringle.
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Exonization Pseudoexonization
Exonization is the process through which an
intronic sequence becomes an exon. Pseudoexonizat
ion is the process through which an exonic
sequence becomes an intron.
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Seneb Family (Dynasty IV) Seneb was Chief of
all the Dwarfs of the Clothing
Exonization leading to Laron Syndrome
Growth hormone receptor
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The aggrecan gene in rat contains 18 paralogous
exons 1 paralogous pseudoexon in intron 12.
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Pseudoexon
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For exonization and pseudoexonization to occur
without disruption of the reading frame, the
rules pertaining to exon insertion and exon
deletion must be respected.
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Principal biochemical reactions in the synthesis
of fatty acids from malonyl CoA in eukaryotes and
eubacteria _______________________________________
__________________________________________________
____________________________ Reaction
Enzyme __________________________________________
__________________________________________________
_________________________ 1. acetyl CoA
condensing-enzyme domain ? acetyl-condensing
enzyme acetyl transferase 2. malonyl
CoA acyl-carrier peptide ? malonyl-acyl-carrier
peptide malonyl transferase 3.
acetyl-condensing enzyme malonyl-acyl-carrier
peptide ? b-ketoacyl-carrier peptide
b-ketoacyl synthase 4. b-keto-acyl carrier
peptide NADPH H ? b-hydroxyacyl-carrier
peptide NADP
b-ketoacyl reuctase 5. b-hydroxyacyl-carrier
peptide ? 2-butenoyl-acyl-carrier peptide
H2O b-hydroxyacyl dehydratase 6.
2-butenoyl-acyl-carrier peptide NADPH H ?
butyryl-acyl-carrier peptide NADP enoyl
reductase 7. butyryl-acyl-carrier peptide
condensing-enzyme domain ? butyryl-condensing
enzyme acyl-carrier peptide
thioesterase _____________________________________
__________________________________________________
______________________________
7 enzymatic activities 1 acyl carrier protein
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Principal biochemical reactions in the synthesis
of fatty acids from malonyl CoA in eukaryotes and
eubacteria _______________________________________
__________________________________________________
____________________________ Reaction
Enzyme __________________________________________
__________________________________________________
_________________________ 1. acetyl CoA
condensing-enzyme domain ? acetyl-condensing
enzyme acetyl transferase 2. malonyl CoA
acyl-carrier peptide ? malonyl-acyl-carrier
peptide malonyl transferase 3.
acetyl-condensing enzyme malonyl-acyl-carrier
peptide ? b-ketoacyl-carrier peptide
b-ketoacyl synthase 4. b-keto-acyl carrier
peptide NADPH H ? b-hydroxyacyl-carrier
peptide NADP
b-ketoacyl reuctase 5. b-hydroxyacyl-carrier
peptide ? 2-butenoyl-acyl-carrier peptide
H2O b-hydroxyacyl dehydratase 6.
2-butenoyl-acyl-carrier peptide NADPH H ?
butyryl-acyl-carrier peptide NADP enoyl
reductase 7. butyryl-acyl-carrier peptide
condensing-enzyme domain ? butyryl-condensing
enzyme acyl-carrier peptide
thioesterase ____________________________________
__________________________________________________
_______________________________
In most bacteria, these functions are carried on
by discrete monofunctional proteins.
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Principal biochemical reactions in the synthesis
of fatty acids from malonyl CoA in eukaryotes and
eubacteria _______________________________________
__________________________________________________
____________________________ Reaction
Enzyme __________________________________________
__________________________________________________
_________________________ 1. acetyl CoA
condensing-enzyme domain ? acetyl-condensing
enzyme acetyl transferase 2. malonyl CoA
acyl-carrier peptide ? malonyl-acyl-carrier
peptide malonyl transferase 3.
acetyl-condensing enzyme malonyl-acyl-carrier
peptide ? b-ketoacyl-carrier peptide
b-ketoacyl synthase 4. b-keto-acyl carrier
peptide NADPH H ? b-hydroxyacyl-carrier
peptide NADP b-ketoacyl
reuctase 5. b-hydroxyacyl-carrier peptide ?
2-butenoyl-acyl-carrier peptide
H2O b-hydroxyacyl dehydratase 6.
2-butenoyl-acyl-carrier peptide NADPH H ?
butyryl-acyl-carrier peptide NADP enoyl
reductase 7. butyryl-acyl-carrier peptide
condensing-enzyme domain ? butyryl-condensing
enzyme acyl-carrier peptide
thioesterase ____________________________________
__________________________________________________
_______________________________
In fungi, the activities are distributed between
two proteins encoded by two unlinked intronless
genes, FAS1 and FAS2. FAS1 encodes 3 of the 8
activities (b-ketoacyl synthase, b-ketoacyl
reductase, and acyl-carrier protein). FAS2
encodes the rest of the five enzymatic
activities.
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In animals, all functions are performed by one
polypeptide, fatty-acid synthase. The gene
product has 8 modules, including one that
performs a dual function and another whose
function is unrelated to fatty-acid synthesis but
may determine the 3D structure of this protein.
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introns-early versus introns-late
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The introns-early hypothesis (the exon theory of
genes)
Ancient genes possessed self-splicing introns.
Most self-splicing introns were lost in
Bacteria and Archaea. In Eucarya, self-splicing
introns evolved into spliceosomal introns.
Walter Gilbert
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The introns-late hypothesis
Ancient genes had no introns. The addition of
introns occurred after the emergence of the
eukaryotic cell and the endosymbiotic process
that gave rise to the mitochondria.
Russell Doolittle
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The introns-late hypothesis
Nuclear spliceosomal introns were derived from
group II self-splicing introns, which in turn
were derived from transposable elements (e.g.,
retrons).
Russell Doolittle
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Molecular mechanisms for both intron gain and
intron loss are known.
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Models and examples of intron loss
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Models and examples of intron gain
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Roy and Gilbert. 2006. Nature Reviews Genetics
7, 211221
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Dollo estimate (maximum likelihood estimate)
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The introns-early hypothesis is supported by the
correspondence between exons and modules
(concordant positions). However, a huge number
of introns are found in positions not
corresponding with the borders of modules
(discordant positions).
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However, not all introns in discordant positions
can be taken as evidence against the
introns-early hypothesis.
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Intron sliding Introns liding
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35 early introns 65 late introns
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Carmel L, Wolf YI, Rogozin IB, Koonin EV. 2007.
Three distinct modes of intron dynamics in the
evolution of eukaryotes. Genome Res 171034-1044.
Intron gain and loss rates. Node sizes are
proportional to their (known or inferred) intron
density, and the branches are color-coded
(green) predominant intron gain (red)
predominant intron loss (blue) balanced gain and
loss (brown) extensive (significantly greater
than the mean over the tree) gains and losses.
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Genetic map of the single-stranded DNA phage FX174
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Causes of overlapping (a) Deletion of the stop
codon or deletion of a segment that includes the
stop codon.
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Causes of overlapping (b) Point mutation in stop
codon.
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Causes of overlapping (c) Frameshift by deletion
or insertion of segment that is not a multiple of
three nucleotides.
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Inferred causes of overlapping deduced from a
genomic comparison between Mycoplasma genitalium
Mycoplasma pneumoniae Deletion 65 Point
mutation 4 Frameshift 7 Unknown 24
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The rate of evolution in stretches of DNA
encoding overlapping genes is expected to be
lower than in stretches of DNA encoding single
genes.
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Eukaryotic genes (No alternative splicing)
RNA splicing removal of introns ligation of
adjacent exons
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Alternative splicing One gene, several proteins!
splice variant II
splice variant I
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2 types of exons Constitutive exons are
included within all the mRNAs transcribed from a
gene. Facultative exons are sometimes spliced
in and sometimes spliced out.
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Conditional Unconditional Alternative Splicing

• Alternative splicing may be unconditional, i.e.,
  two or more mRNA variants are produced in all
  tissues expressing the gene.
• Alternative splicing may be conditional, i.e.,
  tissue specific, developmental-stage specific or
  physiological-state specific.

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Types of alternative splicing
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In the troponin-T gene, the presence of 5
cassette exons in conjunction with 2 mutually
exclusive exons, allows the production of 64
different proteins from a single gene.
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It is (apparently) very easy to create de novo
splicing sites!
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Trans splicing
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cob/box gene in yeast mitochondria codes for
cytochrome c apoprotein
765
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1240
417
alternative splicing
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304
14
840
maturase (423 aa)
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...
F8A
...
F8B
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i25
i24
i23
i22
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F8B
F8A
Coagulation factor VIII gene
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myoglobin Sulculus diversicolor
YEGVSDAPVTMIGGSAAQSSAMQLLDNLLGVTHSPDKQAFLDEISNYMIP
AHKQLL
YEGVWDTPKKFSGGSAGQSSIFQSLDVLLGVKHDV
GKGAFLQEIREYMPPAHKNFL
indoleamine 2,3-dioxygenase Mus musculus
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Perfection isnt evidence for evolution. Imperfec
tion is.
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RNA editing
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Substitutional editing
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Insertion/deletion editing
When RNA editing is extensive, so that the
resulting RNA bears little resemblance to the DNA
sequence, the DNA template is called a cryptogene.
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Organs of extreme perfection and complication
by Charles Darwin To suppose that the eye,
with all its inimitable contrivances... could
have been formed by natural selection, seems, I
freely confess, absurd to the highest possible
degree.
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There is nothing new in evolution. Omni gena
est gena.
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Bricolage moleculaire (Molecular tinkering)
François Jacob
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Lactalbumin was considered a mammalian novelty
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Lactalbumin
Lysozyme
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in mammals only
throughout the living world
Lactalbumin
Lysozyme
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no enzymatic activity
enzyme
Lactalbumin
Lysozyme
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Lactalbumin B chain of lactose synthetase
lactose synthetase heterodimer (A B)
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The A chain of lactose synthetase also serves as
N-acetyllactosamine synthetase.
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Molecular tinkering is the paradigm of molecular
evolution. Does tinkering drive morphological,
anatomical and physiological evolution?
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The best of all possible worlds!
available
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The evolution of imperfection and the
imperfection of evolution
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genome shuffling ? disruption of synteny
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Mouse-human synteny. Human chromosomes can be cut
into a small number of pieces, then reassembled
into a reasonable approximation of the mouse
genome.