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Mutation, Transposition, and Repair
A. Gene Mutation
1. Mutations are Classified in Different Ways:
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
- spontaneous – just a ‘mistake’ (typically in
replication)– assumed to be random
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
- spontaneous – just a ‘mistake’ (typically in
replication)– assumed to be random
- induced – caused by an external factor (mutagen);
usually identified by increased rates of mutation above spontaneous
levels in subpopulations exposed to the mutagen (radiation, chemicals)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
- autosomal vs. sex-linked
- somatic vs. germ-line (heritable)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
- substitution (“point mutation”)– the wrong base is inserted
transition: purine for purine, etc.
transversion: purine for pyrimidine, etc.
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
- substitution (“point mutation”)– the wrong base is inserted
transition: purine for purine, etc.
transversion: purine for pyrimidine, etc.
- substitutions may:
change the amino acid (new codon): missense
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
- substitution (“point mutation”)– the wrong base is inserted
transition: purine for purine, etc.
transversion: purine for pyrimidine, etc.
- substitutions may:
change the amino acid (new codon): missense
not change the AA (redundancy): silent
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
- substitution (“point mutation”)– the wrong base is inserted
transition: purine for purine, etc.
transversion: purine for pyrimidine, etc.
- substitutions may:
change the amino acid (new codon): missense
not change the AA (redundancy): silent
change to stop codon: nonsense
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
- substitution (“point mutation”)– the wrong base is inserted
- frameshift – bases are added or deleted, changing all codons
downstream.
Substitution mutation
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
d. By Effect on the Phenotype:
- loss-of-function (null)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
d. By Effect on the Phenotype:
- loss-of-function (null)
- gain-of-function (enhanced or new function)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
d. By Effect on the Phenotype:
- loss-of-function (null)
- gain-of-function
- neutral (change is not in a gene, or it is silent)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
d. By Effect on the Phenotype:
- loss-of-function (null)
- gain-of-function
- neutral (change is not in a gene, or it is silent)
- biochemical (physiological), morphological, behavioral
A. Gene Mutation
1. Mutations are Classified in Different Ways:
a. By Cause:
b. By Location:
c. By Type of Change:
d. By Effect on the Phenotype:
- loss-of-function (null)
- gain-of-function
- neutral (change is not in a gene, or it is silent)
- biochemical (physiological), morphological, behavioral
- lethal and conditional
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
a. Mutation rates are low – selection has favored organisms that can
replicate their DNA with few errors.
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
a. Mutation rates are low – selection has favored organisms that can
replicate their DNA with few errors.
b. But rates do vary by several orders of magnitude between different
types of organisms. In higher eukaryotes, mutation rates (10-5 – 10-6) are higher
than in bacteria and viruses (10-8).
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
Mismatched pairs will bind, but are less
stable (have lower “melting” temperatures)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift:
All bases can exist in different forms.
In the atypical form, they bind to different bases.
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift: (same base, but different pairing)
- deamination of A and C cause mispairings
deamination
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift: (same base, but different pairing)
- deamination of A and C cause mispairings
- depurination: loss of A or G base in ds-DNA, and random
replacement during replication.
G is lost; during replication, a base is placed in at random. In this
clase, it is “A”, leading to a change from a G-C pair to A-T pair
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift: (same base, but different pairing)
- deamination of A and C cause mispairings
- depurination: loss of A or G base in ds-DNA, and random
replacement during replication.
- oxidative damage to DNA due to normal metabolic production
of oxidants, or “reactive oxygen species” (ROS) such as
superoxides (O2.-), hydroxl radicals ( .OH), and hydrogen peroxide (H2O2)
The most common effect is oxidation of guanine to 7,8-dihydro-8-oxoguanine.
“8-oxoG” is used as an indicator of oxidative stress.
Can bind with both Cytosine and
Adenine
In E. coli and Archeans, there are two proteins that correct this error, either before
or after DNA replication. In eukaryotes, a related enzyme only cleaves the 8oxoG
before replication in the G-C conformation.
Guanine is more susceptible to oxidation as the terminal G in a string
of G’s (GGG) rather than as a single base in sequence. In this
context, “G-C rich repeats” outside of genes may act as ‘oxidation
pools’, soaking up the oxidative agents and protecting neighboring
gene sequences. (Faucher, Doublié and Jia , 2012)
http://www.mdpi.com/1422-0067/13/6/6711/htm
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift: (same base, but different pairing)
- deamination of A and C cause mispairings
- depurination: loss of A or G base in ds-DNA, and random
replacement during replication.
- oxidative damage
b. Frameshifts:
- replication slippage
Huntington’s Chorea – a trinucleotide repeat disorder’ – the more repeats, the
more severe the expression. CAG codes for glutamine, creating a poly-glutamine
region that eventually disrupts protein function.
Classification of the trinucleotide repeat, and resulting disease status, depends on the
number of CAG repeats
Repeat count
Classification
Disease status
<28
Normal
Unaffected
28–35
Intermediate
Unaffected
36–40
Reduced Penetrance
+/- Affected LATE IN LIFE
>40
Full Penetrance
Affected EARLY IN LIFE
Genetic anticipation – The onset and severity of the disorder occurs earlier and
earlier in life from one generation to the next. This occurs as repeats are added
during gametogenesis.
Fragile-X syndrome – a CGG trinucleotide repeat disorder’. Over 200 repeats
in the promoter region of the gene and the gene is methylated - no protein is
produced. The protein is important in neural development. Absence results in
mental retardation/ intellectual disability. Most common genetic correlate with
autism (5%), and 15-60% of fragile X individuals are classified with ASD (autism
spectrum disorder). The most common genetic cause of intellectual disability in
males (X linked).
Classification of the trinucleotide repeat, and resulting disease status, depends on the
number of CGG repeats
Repeat count
Classification
Disease status
<54
Normal
Unaffected
50-200
‘premutation allele’
Mild* or Unaffected
>200
mutation
Fragile X Syndrome
Also exhibits genetic anticipation
* = fragile x associated tremor/ataxia syndrome (FXATAS) and primary ovarian
insufficiency (POI)
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift: (same base, but different pairing)
- deamination of A and C cause mispairings
- depurination: loss of A or G base in ds-DNA, and random
replacement during replication.
- oxidative damage
b. Frameshifts:
- replication slippage
- most common where there are repeat sequences (like ‘tandem
repeats’ of CGCGCGCGCGCGCGC…).
- because errors are common, these are ‘hypermutable’ regions,
and we differ at an individual level in the lengths of these sequences… often
used for ‘DNA fingerprinting’
Variable Number Tandem Repeats (VNTR): (tandem = adjacent)
- microsatellites - < 5 base repeat: CAG CAG CAG CAG
- minisatellites - > 5 base repeat: CCCAGC CCCAGC CCCAGC
C
D
Variable Number Tandem Repeats (VNTR):
- microsatellites - < 5 base repeat: CAG CAG CAG CAG
- minisatellites - > 5 base repeat: CCCAGC CCCAGC CCCAGC
Restriction Sites or ‘Flanking Regions’
Chop these up with a different restriction
enzyme… creating “restriction fragment
length polymorphisms”
A. Gene Mutation
1. Mutations are Classified in Different Ways:
2. The Rates of Spontaneous Mutations:
3. How Spontaneous Mutations Occur:
a. Substitutions:
- truly random error in replication
- tautomeric shift: (same base, but different pairing)
- deamination of A and C cause mispairings
- depurination: loss of A or G base in ds-DNA, and random
replacement during replication.
- oxidative damage
b. Frameshifts:
- replication slippage
- transposons – “jumping genes”
can jump into an exon and turn a gene off
jump into introns and affect splicing pattern – new gene
“carry” a gene and multiply it through the genome
Bacterial transposons:
Insertion Sequences: encode a transposase that cuts the sequence out and
inserts it elsewhere at the same restriction site:
Inverted terminal
repeat
Bacterial transposons:
Insertion Sequences: encode a transposase that cuts the sequence out and
inserts it elsewhere at the same restriction site.
Tn elements: Have a structural gene associated with the transposase.
Barbara McClintock,
Nobel Prize 1983
Ds = dissociator – it is a transposable
element, like a bacterial IS, but the
transposase gene has a loss of function
mutation – so it has the cleavage sites, but
can’t make the transposase itself.
W = a phenotypic trait – like kernel color
(though the actual relationships are more
complex)
Ac = activator. Also an IS-like sequence that produces a transposase,
which recognizes and moves Ds. Ac can move autonomously; Ds can’t.
The effects of Ds depend where it jumps – it may cause ds-DNA breakage
(the cytological effect McClintock associated with a change in
phenotype).
Or it can disrupt other genes; turning them on and off.
P elements in Drosophila
Found in 1970’s when lab stocks cultured since the early 1900’s were mated
with wild flies from nature.
Dysgenic Hybrids:
- sterile
- many mutations
- chromosomal anomalies
P elements in Drosophila
Found in 1970’s when lab stocks cultured since the early 1900’s were mated
with wild flies from nature.
P-elements are transposable elements that
may have infected Drosophila as a virus.
Subsequent selection favored stabilization of
these elements, by an iRNA silencing
mechanism (RISC formation, etc.)
Lab strains isolated from viral infection in nature
never received P-elements, nor evolved the
specific piRNA silencing pathway.
When genes from males WITH P-elements are
placed in an egg that LACKS piRNA (because
the mother was a lab fly), the P-elements
transpose, creating mutations.
Reciprocal crosses simply add male genomes
without P-elements to eggs that have and
repress them with maternal pi-RNAs.
Humans:
Long and Short Interspersed Elements (LINES and SINES) – 50% of
the genome
Other families of transposable elements = 11%
Most are not mobile – their movement is repressed
Diseases:
- cases of hemophilia, Duchenne’s muscular dystrophy, and breast
cancer have been identified that resulted from an insertion of a
transposable element into a functional gene.
Evolutionary Effects:
- may cause a significant fraction of new mutations – up to 50% of
mutations in Drosophila.
- Telomeres in Drosophila are transposable elements that copy
themselves and add sections, maintaining the length of their
telomeres. Tn transposons in bacteria transfer antibiotic genes.
- Transposons create homologous regions that increase the
liklihood of recombination - and the unequal cross-over events
that create gene duplication and exon shuffling.
OR