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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.
Divergence
One copy dies
Identical copies
Isozyme (LDH)
Complete gene duplication
and different function
Human L-lactate dehydrogenase M4 (the isozyme found in skeletal muscle).
Isozyme
Isozymes are enzymes that catalyze the same biochemical
reaction but may differ from one another in tissue
specificity, developmental regulation or biochemical
properties.
Isozymes are encoded by different loci, usually duplicated
genes, as opposed to allozymes, which are different alleles
of an enzyme.
Isozymes are important for development. They allow
differentiation of cells.
Lactate dehydrogenase (LDH)
An enzyme that is composed of two types of subunits, M
and H (formally A and B), each encoded by a different
gene. “M” stands for “muscle” and “H” for heart.
•The M subunit is encoded by
LDHA, located on chromosome
11p15.4
•The H subunit is encoded by LDHB,
located on chromosome 12p12.2p12.1
(partial) LDH alignment
Lactate dehydrogenase (LDH)
The protein itself is tetrametric.
It can have one of the following isozymes:
•H4 (also called LDH1)
•H3M (also called LDH2)
•H2M2 (also called LDH3)
•HM3 (also called LDH4)
•M4 (also called LDH5)
Expressed mostly in the heart + blood cells
Expressed mostly in white blood cells
Expressed mostly in the lung
Expressed mostly in the kidney, placenta
Expressed mostly in the liver + muscles
LDH in starch gel
The H (B) monomer
is very negatively charged
Lactate dehydrogenase (LDH)
The enzyme catalyzes the following biochemical reaction:
Lactate dehydrogenase (LDH)
The enzyme catalyzes the following biochemical reaction:
Pyruvate + NADH
Lactate + NAD
How to color:
we give to the enzyme, a buffer sullution with lactic acid, NAD, NBT
(Nitro blue tetrazolium) and PMS (phenazine methosulfate).
LDH
Lactate + NAD
NADH + H+ + PMS
NBT + PMS[reduced]
Pyruvate + NADH
NAD+ + PMS[reduced]
NBT[reduced] + PMS
The NBT is dark blue
when it is reduced
Lactate dehydrogenase (LDH)
• The M form (LDH-A) is found
predominantly in white skeletal muscle
(fast twitch glycolytic fibers) and is best
suited for pyruvate reduction in anaerobic
conditions.
• the H form (LDH-B) is found in more
aerobic tissues such as heart and brain
and is most efficient for lactate oxidation.
Lactate dehydrogenase (LDH)
The reaction in context:
Glycolyses
Glucose + 2 ADP + 2 NAD+ + 2 Pi -----> 2 Pyruvate + 2 ATP + 2 NADH + 2 H+
Oxidative Phosphorylation (mitochondria)
NADH+ 3 ADP + 3 Pi -----> NAD+ ++H+ + 3ATP
Later
Pyruvate + ADP + NAD-----> CO2 + NADH + ATP
When we run for our lives, there’s not enough NAD here,
So LDH (M4 TYPE) in muscles does the following reaction
(when there’s lack of oxygen)
Pyruvate + NADH
Lactate + NAD
Lactate dehydrogenase (LDH)
The lactate diffuses to the blood, and from their to organs
where there’s no oxygen missing (the heart). There, not
much of glucose is needed, there’s enough NAD, and the
opposite reaction is catalyzed, by LDH type H4
Pyruvate + NADH
Lactate + NAD
Lactate dehydrogenase (LDH)
When a cell dies its LDH is released to the blood. LDH is
one of the main components in blood tests. High level of
LDH are indicative of heart attacks, cancer or anemia.
If LDH levels are high, another
test is performed to test the level
of the different isozymes, so that
the source of the problem can be
more accurately inferred.
Lactate dehydrogenase (LDH)
This is an example in which two duplicated genes have
become specialized to different tissues.
The isozymes are also differentially expressed in different
developmental stages. Before birth the heart is more
anaerobic compared with adulthood. Indeed, before
birth the main isozyme in the heart is the M4, and with
time it switches to HM3 (at birth), to H2M2 and HM3 at
1 year after birth, and to H3M AND H4 after 2 years.
My main LDH is HM3. Great!
My main LDH is HM3
LDH of mices
B4
AB3
A2B2
A3B
A4
-9
-5
-1
0
+12
+21
-9, -5, -1 days before birth as well as +12 and +21 days after birth and in adult mice
Lactate dehydrogenase (LDH)
4: Genome evolution
Vision. The Opsins stories
Complete gene duplication
and different function
The eye
Retina
Cones and Rods
There are two types of photoreceptor cells in the human
retina, rods and cones.
Cones and Rods
Rod cells are
responsible for vision
at low light levels
(scotopic vision).
They do not mediate
color vision, and have
a low spatial acuity
Cones and Rods
Cone cells are
active at higher
light levels
(photopic vision).
They are capable
of color vision and
are responsible for
high spatial acuity
Colors
There are 3 types of pigments in cones. Their peaks of absorption
are at about 430, 530, and 560 nanometers.
Colors
The cones are “loosely” called "blue", "green", and "red“.
“loosely” because:
1. the names refer to peak sensitivities (which in turn are related to
the ability to absorb light) rather than to the way the pigments
would appear if we were to look at them.
Colors
The cones are “loosely” called "blue", "green", and "red“. “loosely”
because:
2. Monochromatic lights whose wavelengths are 430, 530, and
560 nanometers are not blue, green, and red but violet, blue-green,
and yellow-green
Terminology
Terminology is almost impossible to change.
Some call the cones just long, middle, and short.
An impossible elephant
Opsin and retinal
Each photopigment consists of two parts: a protein called opsin and a
lipid derivative called retinal.
The opsin is a
member of the
superfamily of Gprotein coupled
receptors.
The opsin’s sequence
determines the
absorbance
Opsin Genetics
The blue opsin is encoded by an autosomal gene.
The red and green opsins are encoded by X-linked genes.
There are cases in which the green opsin is duplicated on
the X chromosome.
Red and green are very similar in amino-acid sequence
(96%). Blue is more diverged (43%).
Blue diverged about 500 mya (million years ago).
Red and green diverged only 25-35 mya.
Opsin Genetics
Indeed new-world monkeys have only one X-linked
pigment, so the divergence of green and red occurred after
the divergence of new-world monkeys from old-world
monkeys.
Thus, old-world monkeys are trichromatic.
Opsin Genetics
New-world monkeys have only one X-linked locus
(except for the howler monkey from the Alouatta genus).
howler monkey
Opsin Genetics
But the X-linked locus in the new world monkeys, such as
for squirrel monkeys and tamarins, can be highly
polymorphic, with some alleles similar to the red opsion
and some to the green.
Thus, a female can be
trichromatic (if heterozygous)
but males are always
dichromatic.
Dichromatic monkeys cannot
distinguish between red and
green.
Squirrel
monkeys
Ishihara Plates: are you color blind?
The individual with normal color vision will
see the number 5 revealed in the dot
pattern.
An individual with Red/Green (the most
common) color blindness will see the
number 2 revealed in the dots
5 or 2?
Opsin: conclusion one
Old world monkeys achieved trichomatic vision by a
mechanism akin to isozymes (different proteins coded by
different loci).
Heterozygous female squirrel monkeys achieved
trichomatic vision by using two “allozymes” (distinct
proteins encoded by different allelic forms at a single
locus).
The polymorphism is probably a form of overdominant
selection.
Opsin: selective advantage?
The selective advantage of trichromatic vision is thought
to be the ability to detect ripe fruits against a background
of dense green foliage.
Pheromones
Old world monkeys, apes and humans have
trichromatic vision. Other placental mammals
don’t.
Hypothesis: The development of trichromatic
vision led to the eventual deterioration of
pheromones sensitivity.
This is explained by the superiority of
trichromatic vision over pheromones as a
means of communication.
Against this hypothesis: Howler monkeys
communicate via both channels.
4: Genome evolution
Carbamoyl-phosphate synthetase
Carbamoyl-phosphate synthetase
2MgATP + HCO3- + Glutamine + H2O
CPS
2MgADP + Pi + Glutamate + Carbamoyl-P
Carbamoyl-phosphate synthetase
The reaction is needed in a few places:
1. Pyrimidine biosynthesis.
2. Arginine biosynthesis.
3. Urea cycle (amino acid catabolism).
Carbamoyl-phosphate synthetase
In several organisms the CPS enzyme was
duplicated. In these organisms, the enzymes are
always specialized to one of these reactions.
When there’s no duplication – the enzyme does
all 3 functions (multifunctional).
From the specific example to the general
theory
Two theories of gene duplication:
1. After the gene was duplicated, there was a
period of random mutations, until the gene
obtained a new function, and from this point
onwards, selection is operating on it.
The orthodox model of gene duplication
The orthodox model for the evolution
of functionally novel proteins
(Ohno 1970 & Kimura 1983)
After gene duplication, one copy is rendered
redundant and can accumulate substitutions
at random.
By chance, some of these substitutions may
result in a new function.
Difficulties with the orthodox theory
One difficulty with this theory is that:
Unless the new function can be acquired through
one or a few nucleotide substitutions, it is more
than likely that the copy will become a
pseudogene rather than a new functional gene.
Difficulties with the orthodox theory
Another problem with this theory is that:
There are many evidences of positive selection
after gene duplication (rather than relaxation of
functional constraints).
From the specific example to the general
theory
The second theory is:
2. Genes that survive after duplication have had
more than one function before. After selection,
there’s a specialization of the two genes. This
gives a selective advantage for the duplication.
From the specific example to the general
theory
The CPS example, clearly supports the second
theory.