Mutation, DNA repair, and Evolution
(with references to disease, including aging and cancer)
Objectives:
1. Define the nature of genetic variation
2. Provide a context for understanding mutation (disease and aging)
3.
Define evolutionary principles, such as natural selection, mutation rate,
molecular clocks
4.
Explain why rates of mutation/variation differ between genes, and
between different regions of the same gene
Reading:
Krane and Raymer, pp. 57-65
What is implied here?
1995 statement by the National
Association of Biology Teachers:
“Evolution is an unsupervised,
impersonal, unpredictable, and
natural process of temporal
descent with gradual modification”
How Do We Explain Adaptation?
• Divine creation; intelligent design
• Inheritance of acquired characteristics
(Lamarck)
• Natural selection (Darwin)
What is the keyboard upon which Natural Selection plays?
--- and ---
What is the ultimate source of genetic variation?
--- or ---
What is the pool of raw materials from which new variants
are selected?
Why is everyone different?
What are the three sources of genetic variation?
A human karyotype, or chromosome spread
2N = 4
So, is it possible that no genetic
information was inherited from
the paternal grandfather (F1)
and none from the maternal
grandmother (M2)?
1. Meiosis in humans creates tremendous variety:
223 combinations of 23 chromosomes via meiosis
= 8.4 million ways to assort 23 pairs of chromosomes
Then,…
8.4 million (sperm) x 8.4 million (egg) =
Every conception is one among 70 trillion unique possibilities
2. Crossing over between homologous chromosomes
during meiosis adds even more variation
Meiosis animation
showing random
assortment +
crossing over
3.
Mutation: a change in the sequence of DNA
“The Dwarf Francisco Lezcano”
Normal DNA sequence
5’…A G C T A C G G G G T G G G C…3’
5’…A G C T A C A G G G T G G G C…3’
Achondroplasia
painted by Diego Velazquez
c. 1642
How do gene mutations affect the structure of proteins?
Point mutations can affect protein structure and function
Type of point mutations:
- substitutions (missense and nonsense mutations)
- insertions and deletions (frameshift mutations)
Wild-type sequence
Categorize three different types of point mutations
1
GAA
… ATA TAC GTA CAT …
… ile tyr val his …
glu
2
3
TGC
TAG
… AAA GAA TGG GTT …
… lys glu trp val …
cys
… TCG CCA TGG CCA …
… ser pro trp pro…
X (stop)
Chemical
type:
Transversion
Transversion
Transition
Informational
type:
Missense
Missense
Nonsense
Functional
type:
Deleterious
Non-synonymous
Nondegenerate site
Deleterious
Non-synonymous
Nondegenerate site
Deleterious
Non-synonymous
Nondegenerate site
Categorize three more types of point mutations
4
5
GTC
… ATA TAC GTA CAT …
… ile tyr val his …
6
TGC
A
… AAA GAA TGT GTT …
… lys glu cys val …
val
cys
… TCG CCA TGG CCA …
… ser pro trp pro …
… TCG CAC ATG GCC A …
… ser his met gly
…
Chemical
type:
Transversion
Transition
Indel (insertion)
Informational
type:
Missense
Missense
Frameshift
Functional
type:
Neutral (silent)
Synonymous
(4-fold degenerate site)
Neutral
Synonymous
(2-fold degenerate site)
Deleterious
Non-synonymous
Is a 4-fold degenerate site ever functionally constrained?
What is natural selection?
“It may be said that natural selection is
daily and hourly scrutinising, throughout the
world, every variation, even the slightest;
rejecting that which is bad, preserving and
adding up all that is good; silently and
insensibly working, whenever and wherever
opportunity offers, at the improvement
of each organic being in relation to its
organic and inorganic conditions of life.”
-The Origin of Species
Charles Darwin
Darwin’s concept of Natural Selection provided a mechanism
by which species could adapt, become stronger, faster…..fitter
Ironically, natural selection alone did not explain
how species originate,
i.e.,
How Natural Selection can create a new species from a pre-existing one
For Natural Selection to work, a new mechanism was required
Enter Gregor Mendel
The monk,…and physicist,…and mathematician
7 pea traits, or characters, studied by Mendel
Gregor Mendel: 1866 - first described a set of mathematical rules by
which the appearance of an organism (its PHENOTYPE) could be
related to its inherited genetic makeup (GENOTYPE)
Dominant versus Recessive traits
How does natural selection occur?
• Variation exists within populations
• These variations are heritable
• More are born than can survive (“the struggle for
existence”)
• Some variations are “better adapted” to their environment
and, therefore, survive to produce more offspring than
those “less well adapted.”
• The frequency of these successful variations, therefore,
increases over time
• As the environment changes, different variations are
favored.
Light and dark morphs of the moth Biston betularia
dd = peppered (light colored)
Dd and DD = melanic (dark colored)
100
90
80
70
60
50
40
30
20
10
0
d allele
D allele
Soot on lichens due to industrialization
At the genetic level, evolution is simply a change in the
gene pool of a population over time.
Let’s look at the following example of two genetic diseases
caused by mutations in the pathway for tyrosine metabolism,
Alkaptonuria (AKU) and Phenylketonuria (PKU)
Review of terms:
- Homozygous
- Heterozygous
- Recessive
- Dominant
- Allele
- Haplotype
- Pedigree
- Functional constraint
- Heterozygote advantage
Relationship between genes and proteins
Example of a monogenic, or single-gene disorder
What is wrong with the mouse on the right?
Alkaptonuria, aka Black Urine disease, in humans
Symptoms:
- urine and ear wax turns black as ink shortly after exposure to air
-ochronosis: musculoskeletal effects, including progressive
degenerative arthritis of the large joints, esp. hip and shoulder
- signs of ochronosis:
-black deposits in the sclerae (white of eye)
-blue colored auricles (ear lobes)
Inheritance pattern of Alkaptonuria,
i.e., genetic basis of the disease
A simple pedigree
Incidence: rare, ~1/150,000 births
Highly toxic: Phenylketonuria (PKU)
Mildly toxic: Alkaptonuria
Highly toxic: Type 1 tyrosinemia
What is the gene defect, or molecular genetic basis,
in alkaptonuria?
- four point mutations occur in the human HGO gene
- Blastp comparison of HGO gene from human and fungus
RVTLPDGPVRGYICELYQGHYQLPELGPIGSNGLANARDFQA
PVAAFDDEEGPTE 247
+ + +
RGYI E+Y H++LP+LGPIG+NGLAN RDFP+A ++D + P
SIDVFE-ETRGYILEVYGVHFELPDLGPIGANGLANPRDFLI
PIAWYEDRQVPGG 242
T196fs (frameshift)
P230S (missense)
KFNNHLFSARQDHTPFDIVAWHGNYYPYKYDLGRFNTMGSVSFDHPDPSIYT
VLT 307
K+
LF+A+QD +PF++VAWHGNY PYKY+L F + SV+FDHDPSI+
VLTT
KYQGKLFAAKQDVSPFNVVAWHGNYTPYKYNLKNFMVINSVAFDHADPSIFT
VLT 302
(missense) V300G
VGTAIADFVIFPP
RWLVAEKTFRPPWYHRNTMSEFMGLITGNYDAKTGGGFQPAG 367
G AIADFVIFPP
RW VA+KTFRPP+YHRN MSEFMGLI G+Y+AK GGF P G
PGVAIADFVIFPP
RWGVADKTFRPPYYHRNCMSEFMGLIRGHYEAKQ-GGFLPGG 361
R321X (nonsense)
Are any of the sites in these proteins functionally constrained?
Molecular basis of Alkaptonuria, 1898-1998
Mutations:
Proline230Serine and Valine300Glycine account
for most cases of the disorder
Haplotypes: each of these two mutant alleles constitutes a
haplotype, i.e., one haploid type. Progeny inherit
one haplotype from each parent.
But wait: are all mutations deleterious or neutral?
Can a mutation rarely be advantageous?
And,….can a “deleterious” mutation ever be advantageous?
Let’s examine the strange example of the PKU gene, defects in
which cause a deadly disease, phenylketonuria
Postnatal testing for a common inherited disorder
……phenylketonuria (PKU)
Phenylketonuria (PKU)
PKU is an inherited error of metabolism caused by a deficiency in the enzyme
phenylalanine hydroxylase (PAH).
Symptoms: Loss of the PAH enzyme results in mental retardation,
organ damage, unusual posture and can, in cases of maternal PKU,
severely compromise pregnancy.
Inheritance: autosomal recessive disorder, caused by mutations in both alleles
of the gene for phenylalanine hydroxylase (PAH), found on chromosome 12.
Biochemical basis of PKU: Mutations in both copies of the gene for
PAH means that the enzyme is inactive or is less efficient, and the
concentration of phenylalanine and phenylpyruvate in the body can
build up to toxic levels.
http:// willroberts .com/pku/
What is the incidence of Alkaptonuria and Phenylketonuria?
AKU: relatively mild, non-fatal & rare, ~1/100,000 to 1/200,000
PKU: severe and rapidly fatal* and common in some groups
Caucasians: 1/10,000
Turks:
1/2600
Irish:
1/4500
Japanese
1/143,000
How many caucasians carry the defective trait?
1.
1/10,000 live births x 1/4 chance of homozygous offspring with disease
when each parent is a carrier = 1/2500 marriages are between parents
who are both carriers; and…
2. Square root of 1/2500 = 1/50 caucasians is heterozygous, i.e., carries one
defective allele and one normal allele.
Gene Histories: PKU
A unique PKU
alle le originate d in
San’a and s pre ad
am ong Ye m e nite
Je w s .
Mutations in the PAH
gene have occurred
independently in many
human populations and
spread due to evolutionary
forces
nsm1.utdallas.edu/bio/Yasbin/H umanGenetics/ Population2W.ppt
A deleterious mutation should be eliminated from
the gene pool, but the deadly PKU allele has instead
survived and spread widely…..WHY?
pku frequency
+/pku
Parents
1/4
Progeny
+/+
x
+/pku
1/2
+/pku
50%
1/4
+/pku
X
pku/pku
dies
33%
Why is PKU, a devastating disease, common?
And why is AKU, a milder disease, rare?
- the answer is probably rooted in evolution (ultimate causes):
- two fungi, Aspergillus ochraceus and Penicillium viridicatum
Ochratoxin A
Gene dosage determines how much phenylalanine
will be present in the body
PKU genotype:
Phenylalanine levels:
+/+
+/pku
pku/pku
PHE
PHE
PHE
TYR
TYR
TYR
“The dose makes the poison”
Does evolution explain the high incidence of
PKU in humans?
1. Carriers of PKU (+/pku heterozygotes) have elevated phenylalanine levels
--- BUT they do not develop PKU symptoms
2. Women who are PKU carriers have a much lower-than-average
incidence of miscarriage
3. Ochratoxin A is a fungal poison known to cause spontaneous abortion.
The fungi that produce this toxin grow on grains (wheat, barley, rye, etc.).
Hypothesis: Excess phenylalanine inactivates the fungal poison
Rationale: If PKU carriers were more likely to have children than
non-carriers because of the protective effects of the PKU gene, then
over time, the disease-causing allele would increase and spread through
the population.
Genes are selected for their reproductive fitness, even if the
consequences for some individuals is disastrous
pku frequency
+/pku
Parents
x
1/4
Progeny
X
+/+
+/pku
1/2
+/pku
50%
1/4
+/pku
X
pku/pku
dies
Susceptibility to
miscarriage reduces
reproductive success
“Natural Selection, the blind, unconscious, automatic
process which Darwin discovered, and which we now
know is the explanation for the existence and
apparently purposeful form of all life, has no purpose…
….It is the blind watchmaker”
---Richard Dawkins, The Blind Watchmaker
Arms
Race
without
End
The Red Queen hypothesis
explains how antibiotic
resistant bacteria, and
new diseases, emerge
"...in our country," said Alice, still panting a little, "you'd
generally get to somewhere else -- if you ran very fast for a long
time as we've been doing."
"A slow sort of country!" said the Queen. "Now here, you see, it
takes all the running you can do to keep in the same place. If you
want to get somewhere else, you must run at least twice as fast as
that."
Antibiotics
Antibiotics on
filter disc
Emergence of antibiotic-resistance coincides with
the appearance of antibiotics
http://www.sumanasinc.com/scienceinfocus/sif_antibiotics.html
http://www.fda.gov/cvm/Documents/01_Selection_Pressure.wmv
http://www.pbs.org/wgbh/evolution/educators/lessons/lesson6/act1notes.html
“Nothing in biology can be understood
except in the light of evolution”
-- Theodosius Dobzhansky
Where can you find resources for the basics of heredity and genetics?
1. http://www.mun.ca/biology/desmid/brian/BIOL2250/Ghome01.html:
-- a brief online genetics primer, taken from the following text:
2. Introduction to Genetic Analysis, 8th ed. 2005.
-- this is the text for Bio 211 - Genetics
Assignment for Monday, 10/11:
1.
2.
Online reading: read Introduction + Part One “Patterns of Inheritance”
Online problems: “Homework Assignment 1” and “HA2” in Pt. One above
3.
Analyze the following two pedigrees, and do the following:
A
B
a. Deduce the pattern of inheritance, i.e., dominant or recessive
b.
Deduce the genotype for each progeny individual, and write it out for each one,
e.g., AA, Aa, or aa
Assignment: Compare the homogentisic acid oxidase genes between
Aspergillus nidulans (aka Emericella nidulans), flies, and human
1.
Find the A. nidulans, Drosophila melanogaster, human genes, and make a
MSWord file showing the protein sequences of each. Terms to search:
Homogentisate 1,2-dioxygenase, hmgA, HGO, homogentisic acid oxidase, AKU
2.
Using the fly protein as a query sequence, perform a Blastp search.
Copy the alignments for fly - fungus and fly - human into a MSWord file.
Use Courier 10 or 11 font, and make sure you preserve the properly formatted
alignments. Record the following information in a separate table:
a.
b.
3.
% identity and % similarity for each alignment.
Gene regions that are excluded from the alignment. If absent, these will
be at the N- or C-terminus, and at exon-intron boundaries.
Identify regions or blocks of sequence that are functionally constrained in all
three of the genes. This may be an approximate, rather than precise, undertaking.
Identify these regions by using a color highlighter. What is the evolutionary
significance of these functionally constrained regions.