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)!