Mutations and recombination

1
Mutations and recombination

• Level 3 Molecular Evolution and Bioinformatics
• Jim Provan

Patthy Chapter 3 Page and Holmes Sections
3.2.3/4
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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

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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

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Spontaneous substitution mutations

• Amino- and keto- groups can tautomerise
• Amino ? imino
• Keto ? enol
• Non-standard base pairing

• Cytosine can also spontaneously deaminate
• Forms uracil
• Uracil pairs with adenine
• Ultimately results in a GC to AT transition

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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

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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

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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

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Gap mutations (continued)

• Distinct mechanism can lead to triplet repeat
  expansion diseases
• Coincidence of disease manifestation with
  amplification of d(CAGCTG), d(CGGCCG) or
  d(GAATTC) repeats
• Huntingdons 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

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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

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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 mis-alignment between
  genes during meiosis
• Example is the Lepore mutation in haemoglobin

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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 TG-repeat hot spots
• g1 genes can convert part of the g2 gene

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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

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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

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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 P2s
• Advantageous mutations are not always fixed
• Even slightly deleterious mutations have a chance
  of fixation

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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

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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

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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

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Mutation data matrix

• Favoured interchanges between chemically similar
  amino acids
• Patterns imposed by natural selection against
  drastic changes
• Key properties include
• Size
• Shape
• Polarity
• Charge
• Ability to form bonds

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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

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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