Mutation and Variation
In genetics, a mutation is a change of the nucleotide sequence of
the genome of an organism, virus, or extrachromosomal
genetic element.
Mutations result from unrepaired damage to DNA or to RNA
genomes (typically caused by radiation or chemical mutagens),
errors in the process of replication, or from the insertion or
deletion of segments of DNA by mobile genetic elements.
Mutations may or may not produce discernible changes in the
observable characteristics (phenotype) of an organism.
Mutations play a part in both normal and abnormal biological
processes including: evolution, cancer, and the development of
the immune system.
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Directed mutation in bacteria?
• Despite the apparently conclusive results of the fluctuation
test, there have been suggestions that something akin to
directed mutation can be observed in bacteria under
certain circumstances.
• This originated with work by Cairns and others which
showed that a strain of E. coli that was unable to ferment
lactose (Lac) reverted to Lac at a higher frequency when
supplied with lactose as the sole carbon source (i.e.
conditions under which the ability to ferment lactose was
advantageous) than when supplied with glucose (the
ability to ferment lactose therefore being of no advantage)
2
Types of mutations
 Point mutations
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base substitution : replacing one nucleotide by another
Silent mutations(synonymous codons)
nonsense mutation : are referred to as stop or termination codons (UAG : amber ,
UAA : ochre , UGA opal)
frameshift mutation : deletion or addition of a single nucleotide (or of any number
other than a multiple of three)
Polarity : If a point mutation results in premature termination of translation, it may
also affect the expression of other genes downstream in the same operon
Frameshift mutation and suppression.
(a) Initial (mRNA) sequence and translated product.
(b) Deletion of a single base alters the subsequent reading frame producing a
different amino acid sequence and encountering a stop codon.
(c) Addition of a base at a different position restores the original reading frame
and may suppress the mutation
Types of mutations
 Conditional mutants
There are many genes that do not affect resistance
to antibiotics or bacteriophages,
biosynthesis of essential metabolites or utilization
of carbon sources.
Some of these genes are indispensable and any
mutants defective in those activities would die (or
fail to grow).
Variation due to larger scale DNA alterations
 Deletions
 Insertion mutations
 Inversion (salmonella typhimurium)
Extra chromosomal agents and horizontal gene
transfer
Plasmids
 bacteriophages
Phenotypes
• There are strains that require an additional growth
supplement, such as a specific amino acid auxotrophs
and prototroph
• Mutants that are defective in their ability to use a
certain substrate (Lac‫)־‬
• The third type of commonly used mutation confers
antibiotic resistance (mutation in the gene coding for one
of the ribosomal proteins can make the cell resistant to
streptomycin)
• Unfortunately, observation of the phenotype does not
always tell us much about the genotype (Trp‫)־‬
Genetic nomenclature
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Ampʳ means the strain is resistant to ampicillin
His denotes a histidine auxotroph
Lac indicates inability to ferment lactose
hisA::Tn10., indicating that the mutation in the hisA gene is
due to insertion of the transposon Tn10
• hisA/FʹhisA has a mutation in the chromosomal
• hisA gene, but contains an Fʹ plasmid which carries a
functional hisA gene
• There are other genes with a trp designation that are not part of
the tryptophan operon and where mutation does not lead to
auxotrophy (trpT: tryptophan-specific tRNA , trpS : tryptophanyltRNA synthetase , TrpR protein is a repressor protein involved in
the regulation of the trp operon)
Restoration of phenotype
 A mutant strain with the UUU codon (phenylalanine) may
undergo a further mutation which restores the UUA codon (a true
back mutation)
 The effect of a mutation can also be negated by a second,
unrelated mutation; this effect is known as suppression. There are
two types of suppression that are of more general importance.
1. The first occurs with frameshift mutations
2. Another important type of suppression occurs with ‘nonsense’
mutations, where a stop codon has been created within the
coding sequence
• Permissive host : Phages carrying an amber mutation will show a
mutant phenotype (or fail to grow) on a normal bacterial host, but will show a
wild-type phenotype when an appropriate amber suppressor host is used
Suppression of a nonsense
mutation.
A base substitution changes
CAG to the stop codon
UAG, causing premature
termination of translation.
This can be suppressed by
a separate mutation in a
tRNA gene, giving rise to
a tRNA that can recognize
the UAG codon
Complementation
• Another way in which a mutant phenotype can be
converted back to the wild type is by acquisition
of a plasmid that carries a functional version of
the affected gene
Recombination
1. general or homologous recombination
2. site-specific recombinational mechanisms
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Recombination between two linear DNA molecules
Mechanisms of mutation
Spontaneous mutation
Spontaneous mutation
occurs through errors in
the replication of DNA
• The normal pairing of adenine
and thymine : adenine in the
amino form and the keto form
of thymine
• The imino form of adenine,
will base pair with cytosine
rather than thymine, while the
enol form of thymine will
hydrogen bond to guanine
Mechanisms of mutation
Chemical mutagens
Nitrous
acid
causes
oxidative deamination of
bases
Nitrous acid causes an
oxidative deamination in
which amino groups are
converted to keto groups
and thus cytosine
residues for example will be
converted to uracil
Mechanisms of mutation
Ultraviolet irradiation
Structure of thymine dimers
• The principal effect of UV
irradiation with which we are
concerned is the production of
pyrimidine dimers (commonly
referred to as thymine dimers)
• These pyrimidine dimers
cannot be replicated and are
therefore lethal to the cell
unless it is able to repair the
damage
Photoreactivation
The best defence that is mounted
against damage by UV irradiation
is known as photoreactivation.
This is catalysed by an enzyme
(photolyase) within the cells that
in the presence of visible light
can break the covalent bonds
linking the two pyrimidine
residues, thus re-establishing the
original nature of the base
sequence at that point
T^T dimers may be repaired by two mechanisms.
(a) In photoreactivation repair, the PRE enzyme activated by blue light breaks
the dimer, restoring the normal base pairing. Note that blue light is at the
same end of the spectrum as UV radiation.
(b) In excision repair, the uvr system excises the dimer, and the gap is filled in
by the proof-reading activity of DNAPol
Non-SOS repair is basically error-free, but SOS repair is error-prone. This is why UV is a
mutagen. May be due to RecA binding ssDNA in lesions, which could then bind to DNA Pol
III complex passing through this area of the DNA and inhibit 3'>5' exonuclease
(proofreading) ability. This makes replication faster but also results in more mutations.
This affect on proofreading seems to involve UmuD'-UmuC complex as well. RecA
facilitates proteolytic cleavage of UmuD to form UmuD'. The UmuD'-UmuC complex may
bind to the RecA-Pol III complex and promote error-prone replication