Gene Mutation, DNA Repair, and Transposition
We have a number of ways to classify mutations
Classes of gene mutations
 Based on location of the mutation
o
Somatic mutations and germ-line mutations can have very different
consequences
 Based on molecular changes
o
Obviously, if the insertion or deletion consists of a number of
nucleotides that is not a multiple of three, this will cause frameshift
mutations
o
Insertions or deletions consisting of nucleotides that are multiples
of three are called in-frame insertions or deletions
 Based on the type of nucleotide substitution
o
Frequency of spontaneous mutations
o
Insertions/Deletions > Transitions > Transversions
 Expanding trinucleotide repeats
o
First identified in fragile-X syndrome
o
Other genetic disorders have also been identified with this
mechanism
o
These have a tendency to expand from generation to generation
Classes of gene mutations
o Based on phenotypic effects
o
Neutral mutations lead to a different amino acid but do not affect
the protein function
o
There are loss-of-function mutations
 These are typically recessive
o
There are gain-of-function mutations
 These are usually dominant
o
Spontaneous vs. induced mutations
 Spontaneous refers to mistakes in DNA replication
 Induced mutations occur due to environmental factors
o
Although the DNA polymerase will rarely add an incorrect
nucleotide, in most instances, the proof-reading function will correct
this
 Occasionally, the mistake is missed
 Bases can sometimes take secondary forms
 Although these are usually transient, if the tautomeric shift is
in place during replication of the base, this can lead to an
incorrect base being added
o Spontaneous chemical changes can also occur
o
Depurination and deamination can lead to mutations
o Chemically-induced mutations
o
Base analogs can be incorporated into DNA molecules
o
Other chemicals can have other effects
o
Oxidative reactions can damage the DNA, causing chemical changes
to the bases and leading to mutations
o
Intercalating agents are ring-containing molecules that are about
the size of a base pair
 These produce frameshift mutations
o Radiation
o
UV radiation can cause the formation of pyrimidine dimers
o
Ionizing radiation causes damage to the DNA, increasing mutation
frequency
Human Diseases
o There have been many single-gene mutations that are responsible for human
diseases
DNA repair
o There are several mechanisms depending on the organism and the type of
mutation
o Photoreactivation is seen in many organisms, but not in humans
o Base excision repair corrects DNA with a damaged base
o Nucleotide excision repair can repair large segments of damaged DNA
o Extensive damage can lead to double-strand breaks
o
This requires DNA double-strand break repair
Identifying mutagens
o The Ames test is useful for identifying agents that increase the frequency of
mutation
o The vast majority of these also increase the frequency of cancer
Transposable Elements
o General characteristics
o Mobile DNA found in the genomes of all living organisms
o Does not require homologous sequences
o Can be responsible for many chromosomal mutations
Transposable elements in bacteria
o Insertion sequences (IS)
o
~800-2000 bp in length
o
Typically only contain the transposase gene
o Transposons
o
Genes are flanked by matching IS elements
o
Many of the genes on transposons code for antibiotic resistance
o
Many transposable elements have terminal inverted repeats
o
These are 9-40 bp in length
o Transposition generates direct repeats that flank the transposable element
o These are 3-12 bp in length
o The mechanism of transposition must involve the generation of staggered cuts
in the target DNA
Mutations due to transposition
o Since transposition is effectively insertion of a segment of DNA, all of the
associated effects are seen
o Transposition is known to be responsible for some forms of neurofibromatosis,
hemophilia, and muscular dystrophy
~50% of all spontaneous mutations in Drosophila are the result of transposition
events
Humans
o About 50% of the human genome can be accounted for by transposable
elements
o Alu sequences are the most common (~1 million/human genome)!