Download Mutations

Mutations and
recombination
Level 3 Molecular Evolution and
Bioinformatics
Jim Provan
Patthy: Chapter 3 | Page and Holmes: Sections 3.2.3/4
Mutations
Mutations can occur due to errors during DNA
replication (replication-dependent mutations)
Mutations can also occur independently of DNA
replication (replication-independent mutations)
May occur in somatic or germ-line cells:
Somatic mutations are not inherited and thus play no major
role in evolution
In cases of antibody formation and malignant
transformation, somatic mutations are significant
Only germ-line mutations are inherited and thus are
important in evolution
Substitutions
Substitution mutations in
protein-coding regions can
be categorised by their
effect on the protein:
If they cause no change to
the amino acid sequence
they are synonymous
If they alter the amino acid
sequence then they are
non-synonymous
Synonymous substitutions
usually occur at third
codon position
Thr Phe Gly
ACA TTT GGA
ACA TTC GGA
Thr Phe Gly
Cys Gly Ile
TGT GGT ATA
TGT GTT ATA
Cys Val Ile
Spontaneous substitution mutations
Amino- and keto- groups
can tautomerise:
C
Amino  imino
Keto  enol
Non-standard base pairing
G
Cytosine can also
spontaneously deaminate:
Forms uracil
Uracil pairs with adenine
Ultimately results in a GC
to AT transition
iC
A
Induced mutations
Natural mutagens largely
act on DNA directly
Nitrous acid can covert
cytosine into uracil
Ultraviolet radiation is
another major natural
source of mutations:
Causes photochemical fusion
of adjacent pyrimidines
Defects in DNA photolyase
result in the condition
xeroderma pigmentosa
Correcting mutations
Most incorrect base-pairs do not ultimately become
incorporated into DNA:
DNA polymerase proofreads the polymerisation step before
proceeding to the next one
Incorrect bases are removed by the 3’5’ exonuclease
Some E. coli mutants with abnormally high mutation rates have
an altered DNA polymerase II with lowered 3’5’ exonuclease
activity
There may be an optimal mutation rate: balance
between proportion of non-viable progeny and diversity
Even incorrect pairings which escape proofreading may
be removed by mismatch repair
“Gap” mutations
In coding regions, deletions, duplications or insertions
involving a number of nucleotides not a multiple of
three will give rise to frameshift mutations:
Causes numerous amino acid changes
Likely to create a new stop codon
Polycyclic molecules may intercalate between bases
and cause “looping out” of DNA which leads to an
insertion or deletion event
Replication slippage or slipped-strand mispairing can
also give rise to deletions / duplications
“Gap” mutations (continued)
Distinct mechanism can lead to triplet repeat
expansion diseases:
Coincidence of disease manifestation with amplification of
d(CAG•CTG), d(CGG•CCG) or d(GAA•TTC) repeats:
– Huntingdon’s disease
– Fragile X syndrome
– Myotonic dystrophy
Caused by formation of stable hairpin structures which
interfere with movement of enzymes along DNA strand
Longer insertions, deletions or fusions occur mainly
by recombination and involve unequal crossing-over,
exon-shuffling or transposition
Recombination
Mutations can move between homologous
chromosomes or even to other chromosomes by
recombination
Recombination is an important aspect of sexual
reproduction since it means that by shuffling
mutations, progeny resemble neither of the parents
A
B
A
B
A
B
A
b
a
b
a
B
a
b
a
b
Recombination (continued)
Homologous recombination
occurs between regions
with similar sequences
Unequal crossing-over is a
major mechanism in the
evolution of multigene
families:
Occurs when there is a misalignment between genes
during meiosis
Example is the Lepore
mutation in haemoglobin
d
Anti-Lepore
b d
d
b
d
d b
Lepore
b
b
Gene conversion
Occurs when DNA sequence
of one gene is replaced
(“converted”) by sequence
from another
More similar sequences
have greater chance of
conversion
Primate g-globin genes:
Conversion occurs at TGrepeat “hot spots”
g1 genes can convert part of
the g2 gene
g1
g1
g1
g2
g2
g1
g2
g1
g2
TG “hot spot”
g1
g1
TG “hot spot”
g2
Factors affecting rates of mutation
Different sites are not equally susceptible to mutation:
sites that gain more mutations than expected are
called hotspots
Spontaneous deamination of 5-methylcytosine to thymine at
methylated 5’-CpG-3’ islands
Microsatellite length polymorphism
Enzymes for DNA replication etc. may have different
fidelity e.g. mitochondrial vs. nuclear genomes
High mutability in human and mammalian males:
Male/female ratio of substitution rate is ~6
Close to the ratio of the number of male/female germ-cell
divisions per generation
Natural selection and the fate of
mutations
The fate of a new mutation depends largely on
whether it is neutral, deleterious or advantageous
When competing genotypes differ markedly in fitness,
natural selection will operate:
Deleterious mutations will eventually be eliminated (purifying
or negative selection)
Mutations which confer a selective advantage will be
subjected to positive selection
Even a minor difference in fitness (s = 1%) may lead to
elimination of allele with lower fitness
In selectively neutral mutations, the fate of the new
genotype is determined by random genetic drift
Random genetic drift
The probability that a new mutation will become fixed
in a population also depends on the size of the
population
According to Kimura (1962), for a neutral allele the
fixation probability (P) equals its frequency in the
population:
Fixation occurs by random genetic drift
All alleles have equal probability of fixation
An advantageous mutation with selective advantage s
has a fixation probability of P=2s
Advantageous mutations are not always fixed
Even slightly deleterious mutations have a chance of fixation
The neutralist vs. selectionist debate
Selectionism considers selection as the only force that
drives the evolutionary process and that genetic drift
is of minor importance
The neutral theory of Kimura suggests that the
majority of evolutionary change is due to the random
fixation of neutral or nearly-neutral mutations
The neutralist / selectionist debate centres around the
frequency distribution and fitness of mutant alleles:
It is agreed that the majority of mutations are deleterious and
removed by purifying selection
Selectionists claim that very few mutations are neutral, whilst
neutralists maintain that most non-deleterious mutations are
neutral and very few are advantageous
Patterns of amino acid replacement
Since each codon can undergo nine types of
substitution (three positions x three substitutions),
point mutations in the 61 sense codons can lead to
549 types of substitution:
392 result in the replacement of one amino acid with
another (non-synonymous substitution)
134 result in “silent” (synonymous) mutations
Of non-synonymous substitutions, there are various
reasons why all do not occur with equal probability:
The genetic code - some interchanges require a single
substitution whilst others require two or three
Conservative changes are likely to be nearly neutral
Patterns of amino acid replacement
(continued)
Data collected by Dayhoff has shown striking
differences between the relative mutabilities of
different amino acids:
Asparagine, serine and alanine are the most mutable
Tryptophan, cysteine, tyrosine and phenylalanine are the
least mutable:
– Cysteine has several unique functions, most notably the ability
to form disulphide bonds
– Tryptophan, tyrosine and phenylalanine have bulky aromatic
side chains which are important in protein folding
20% of interchanges - far more than expected by
chance alone - involve changes of more than one
nucleotide - suggests the role of selection
Mutation data matrix
C
S
T
P
A
G
N
D
E
Q
H
R
K
M
I
L
V
F
Y
W
12
0
-2
-3
-2
-3
-4
-5
-5
-5
-3
-4
-5
-5
-2
-6
-2
-4
0
-8
2
1
1
1
1
1
0
0
-1
-1
0
0
-2
-1
-3
-1
-3
-3
-2
C S
3
0
1
0
0
0
0
-1
-1
-1
0
-1
0
-2
0
-3
-3
-5
6
1
-1
-1
-1
-1
0
0
0
-1
-2
-2
-3
-1
-5
-5
-6
2
1
0
0
0
0
-1
-2
-1
-1
-1
-2
0
-4
-3
-6
T P A
5
0
1
0
-1
-2
-3
-2
-3
-3
-4
-1
-5
-5
-7
2
2
1
1
2
0
1
-2
-2
-3
-2
-4
-2
-4
4
3
2
1
-1
0
-3
-2
-4
-2
-6
-4
-7
G N D
4
2
1
-1
0
-2
-2
-3
-2
-5
-4
-7
4
3
1
1
-1
-2
-2
-2
-5
-4
-6
6
2
0
-2
-2
-2
-2
-2
0
-3
6
3
0
-2
-3
-2
-4
-4
2
5
0
-2
-3
-2
-5
-4
-3
Favoured interchanges
between chemically
similar amino acids
Patterns imposed by
natural selection against
drastic changes
Key properties include:
6
2
4
2
0
-2
-4
E Q H R K M
5
2
4
1
-1
-5
6
2
2
-1
-2
4
-1 9
-2 7 10
-6 0 0 17
I L V
F Y W
Size
Shape
Polarity
Charge
Ability to form bonds
The molecular clock
Idea developed from observation that number of
amino acid or nucleotide substitutions separating
orthologous proteins is roughly proportional to the
time that has passed since divergence from a
common ancestor
Another important observation is that different types
of genes change at vastly different rates which are
inversely proportional to structural and functional
constraints:
Histones can accept and fix a smaller number of mutations
Disruptive mutations are rejected by natural selection
The molecular clock (continued)
“Ticks” of the clock do not occur regularly - mutations
happen at random time intervals:
Poisson distribution originally used but actual variation is
significantly greater
Suggests that variation in evolutionary rates is greater than
that observed by chance alone:
– Mutation rates vary greatly among different evolutionary lineages
– Changes in functional constraint and selection: accelerated rates
of evolution in insulin in some rodents due to adaptive changes
– Substitutions at different sites may not be independent
– Environment may alter mutation rate directly or may change
functional constraints