Mutants
The subject of mutations is a complicated one and here we shall simply present a summary of some key terms and
the main types of mutants, focusing largely, but not exclusively, on bacteria.

Some previous knowledge is required to understand this article fully. The required information can be found in the
articles on
ribosomes, the eukaryotic cell nucleus, and protein structure. This information is summarised where
relevant.

Recall that DNA is composed of a
sequence of bases (or nucleotides) and that the sequence is grouped into
sections called
genes. As DNA is almost always a double helix, in which two strands are wound around one-
another, we talk about
base pairs.

There are 4 bases universal to DNA: adenine (A), thymine (T), gunaine (G) and cytosine (C). The two strands of
DNA are hydrogen-bonded to one-another with each base on one strand hydrogen-bonded to its
complementary
base on the opposite complementary strand. A always pairs with T and G with C, so that the four possible pairings
are:

  A-T, T-A, G-C, C-G

Usually, each gene codes for the formation of a single polypeptide or protein, but some coding genes code for
DNA and others are control genes that regulate DNA function (such as by switching coding genes on or off).
Those that code for proteins have their series of bases divided into groups of three, called
codons, in which each
codon encodes one amino acid. Remember that DNA is first transcribed (copied) into single-stranded messenger
RNA (mRNA) before being translated by the ribosomes into protein. Usually 'codon' refers specifically to the three
bases on the mRNA. In mRNA the base T is replaced by uracil (U).

Mutation: an alteration of the genetic code.

Mutagen: a chemical or physical agent which is able to cause mutation.

Wild type: the study organism isolated from nature, which has not yet been exposed to mutagens in the laboratory.

Mutants: progeny of the wild type that express a mutation.

So, mutations are changes in the genome, consisting of some change in the sequence of DNA bases that make up
that
genetic code. These changes are often harmful, but by no means not always. One should not expect a
beneficial mutation to make an organism 'better' but rather to facilitate its survival in a certain niche differing from
the niche of the wild type. (Indeed, in what way can one organism be said to be 'better' than any other so long as
the organisms survive and reproduce). Many otherwise detrimental mutations can confer benefit in a particular
niche. One example in humans is the sickle-celled haemoglobin allele which although sometimes detrimental to
health is of benefit in areas where sickle-celled disease is endemic. That said, there are many documented
examples of genetic changes imparting sure benefits, such as hybrid vigour in plants and the acquisition of
antibiotic-resistance (and resistance to other stresses) in bacteria exposed to these stresses. Many mutations,
however, have very little or no effect on an organism - they may tweak the function of one protein or may be
completely neutral if they occur in the degenerate 3rd base of each
codon. As we shall see below, stable changes
often involve more than one successive mutation (e.g. suppressor-sensitive mutants) or changes to large sections
of DNA. For example, if a whole segment of DNA is duplicated, then one copy is free to mutate whilst the other
copy maintains any vital functions. The mutating section may become garbage or junk DNA or it may develop a
useful alternative to the original protein(s) or RNA encoded by the genes in the DNA.

Mutations may be
missense mutations, in which the mutated code represents a new amino acid sequence
resulting in a new protein being produced. In
nonsense mutations, the code is meaningless, perhaps because a
STOP codon has been introduced so that much of the code is never translated and is therefore redundant.

Different organisms mutate at different rates. Often this is controlled and dependent on the fidelity of the DNA-
replication system and the efficiency of DNA damage-repair systems. Organisms that reproduce faster can tolerate
higher levels of mutation being passed on to their progeny, since by lottery some will survive. In this way some
organisms benefit by having high mutation rates, since this enables them to rapidly change and adapt to changing
environmental conditions. Bacteria are, in this respect, amongst the most mutable and adaptable organisms.
Indeed, so rapidly can their genetic information change that one often talks about 'strains' rather than species
(indeed the definition of 'species' in bacteria is quite different to that in animals and plants).

Types of Mutant

Conditional mutants: do not function (grow and reproduce) under a restrictive set of conditions but do function
under a permissive set of conditions. Examples are:

  1. Temperature-sensitive mutants which operate well in one range of temperature, but not in another
    (whereas the wild type operated well in both temperature ranges) and is usually due to a change in the
    amino acid sequence of a protein (primary structure) affecting its folding (secondary, tertiary and quaternary
    structures -see proteins).
  2. Suppressor-sensitive mutants require a suppressor to function. The suppressor negates any negative
    effect of the mutation, usually partially but sometimes completely, and is often a secondary mutation itself. It
    may be intragenic mutation, that is occurring in the same gene as the original primary mutation, or it may
    be an extragenic mutation, occurring somewhere else on the genome. This mutation may partially or fully
    restore the function lost by the first mutation, producing a so-called pseudowild type. For example, an
    amber mutation involves a change in one base of one codon that formerly coded for an amino acid in a
    protein, but becomes mutated to the nonsense or STOP codon, UAG. A STOP codon codes for no amino
    acid, as there is no tRNA that can recognise it (tRNA, transfer RNA, see ribosomes) and so when the
    ribosome encounters it, translation stops and the final protein usually has little or no activity since it will
    probably be much shorter. A second mutation may then alter one of the tRNA molecules so that it now
    recognises the UAG codon and inserts an amino acid into the protein at this position. If this amino acid is the
    same one coded for before the mutation, then full functionality will be restored, otherwise a different amino
    acid will result, altering but most likely partially restoring, the activity of the affected protein. Similarly, opal
    mutations produce the nonsense codon UGA and ochre mutations UAA.
  3. Auxotrophic mutants are unable to synthesise one or more growth factors. In nature some bacteria can
    synthesise all the complex organic molecules that they need when growing on a single carbon/energy
    source (like glucose) in the presence of raw materials like inorganic salts. The bacterium Escherichia coli
    can do this. Some organisms, perhaps the majority, however, are unable to synthesise one or more organic
    molecules that they need and these molecules must then be provided in the organism's diet as essential
    growth factors. Growth factors are typically specific essential amino acids, nucleotides or vitamins. It is
    thought that many organisms acquired auxotrophic mutations during the course of evolution because the
    required molecule was already abundant in the environment and so loss of the ability to synthesise it was of
    no negative consequence (and may be advantageous since the organism saves resources which can be
    used to synthesise other materials). The wild type are often referred to as prototrophs. For example, a
    prototroph bacterium might be able to synthesise the amino acid histidine (designated His+), but an
    auxotrophic mutant might not (designated His-). The mutant will only grow if histidine is provided in its diet as
    an essential supplement or growth factor. Such a mutation often involves a defective enzyme somewhere in
    the biochemical pathway (a chain of biochemical reactions catalysed by enzymes) that synthesises
    histidine. However, sometimes a less obvious or cryptic mutation occurs, such as in the protein that
    imports one of the materials into the cell, from which the growth factor is synthesised.
  4. Forward, back and suppressor mutations. The loss of histidine synthetic ability in an usotrophic mutatnt
    (from His+ to His-) is a forward mutation. This may be a mutation in a gene encoding one of the enzymes
    needed for histidine synthesis. Less frequently, a secondary mutation, perhaps in the same codon, may
    restore histidine synthetic ability (His- to His+), such a mutation is a back mutation or reversion. Suppressor
    mutations, as already discussed, may restore the His+ characteristic (phenotype) even though they occur at
    a site remote from the mutated gene, perhaps producing a new enzyme with some ability to carry out teh
    function of the defective enzyme.

Spontaneous and Induced Mutations

Spontaneous mutations occur naturally in any population. They may result to exposure to a mutagen or from an
uncorrected error in DNA synthesis. In bacteria, the rate of spontaneous mutation is about 10^-4 (1 in 10 000) to
10^-10 (1 in 10 000 000 000) per generation for any given gene. The actual rate depends upon species, the
status of the cell, and on the gene in question. DNA replication itself, putting aside mutagens, has an intrinsic error
rate of about 10^-8 to 10^-11 per base (meaning that an error occurs on average once every 100 million to every
100 000 million bases).
Hot spots are hypermutable regions of DNA, that is DNA that mutates especially rapidly.
Hypermutable strains
of bacteria possess mutator genes which accelerate the normal rate of mutation. Such a
gene might be a mutated DNA polymerase gene which replicates DNA with low fidelity. It is not desirable for DNA
replication to have as a high fidelity as possible, since if it is too high then the organism will mutate and hence
evolve too slowly to environmental changes. Mutating too fast is also not desirable, since such organisms tend to
accumulate lethal mutations too often - there has to be a compromise, but this depends on the organisms, and
some naturally mutate faster than others. Some viruses, e.g. HIV, mutate very fast, enabling them to stay one step
ahead of the host's immune system.

In
Escherichia coli, some hot spots result from the chemical modification of the base cytosine by adding a methyl
(CH3-) group to it (to the 5th carbon atom of the base) to form 5-methylcytosine. This modified base sometimes
reverts into thymine (T) causing an G-C to A-T pair transition during the next round of DNA synthesis.

Point mutations: a mutation involving a change to a single base. Spontaneous mutations typically involve
changes to a single base. A point mutation in a control gene or an operon then several genes may be affected.
Such mutations and nonsense mutations, which can also be due to point mutations (generating a STOP codon)
can lead to
pseudogenes or dead genes - regions of the DNA that are no longer accessible to translation and so
are defunct (part of the so-called
junk DNA, a term for non-coding DNA of no known function, though some 'junk
DNA' probably has other functions, such as regulating transcription by changing the local shape of the DNA
molecule). Mutations in some coding areas are more influential than others - a mutation in the active site of an
enzyme, for example, might dramatically alter its function, whilst a mutation in a structural part of the enzyme
(remote from the active site) might have little or a negligible effect on enzyme function. Essential regions of a gene
which are less able to change without affecting gene function are
conserved, meaning that they change little
throughout time or evolution.

The genetic code is also
degenerate, so a change in a single base might have no actual effect. For example,
UUU codes for phenylalanine (Phe) and if the third U changes to a C, giving UUC, then the codon still codes for
phenylalanine: the genetic code is degenerate, meaning that several different codons code for the same amino
acid. (Methionine is an exception, coded by AUG only). It is the third base in the codon which is allowed ti vary, we
say that the third base has
wobble. Thus, mutations in the third base of a codon are less likely to have a
significant affect.

Pseudogenes are also more free to mutate, and may undergo many mutations and may eventually become active
again, but with a very different gene product. Since such freely mutable regions of DNA can accumulate mutations
largely unrestricted (without harming the organism and being selected against) they act as
genetic clocks. Two
identical pseudogenes, each in a separate daughter cell with the same parental origin, will mutate differently and
as the generations pass they will differ more and more. This allows the relatedness of different organisms in
evolutionary terms to be assessed - more closely related organisms, which evolved apart relatively recently, will be
more similar genetically, not only in the functional genes which give them their similar characteristics, but also in
their pseudogenes.

Spontaneous base pair substitution involves the spontaneous change of one base into another, resulting in
an abnormal or
forbidden base-pair, such as A-C or G-T. These occur occasionally because bases have
isomeric forms into which they occasionally and reversibly change. These isomers are called
tautomers, in a
phenomenon called tautomerism. In an A-C forbidden base-pair, the adenine has switched to its rare chemical
state (tautomer) in which it hydrogen-bonds to C instead of T. Although rare, such abnormal pairings are bound to
occur.

Induced base pair substitution is induced by a mutagen, such as nitrous acid (HNO2). Nitrous acid chemically
alters bases. For example, it converts adenine, A, into hypoxanthine which pairs with C. It can also change C into
uracil, which pairs with A. A charcteristic of nitrous acid is its ability to induce the following base-pair change in
either direction:

  •        A-T to G-C
  •        G-C to A-T.

Deletions and insertions are mutations in which an extra base is either deleted or inserted. Since the ribosome
reads the mRNA transcript three codons at a time, this causes it to read different codons, for example, take the
following mRNA sequence:

  -UUU-AAG-CGU-AAA-UUC-GCG-

which, if you look at the
genetic code table,  codes for the amino acids: Phe-Lys-Arg-Lys-Phe-Ala-. Now imagine
that a deletion occurs, let's say the third U is deleted, a deletion point mutation, and then we have:

  -UUA-AGC-GUA-AAU-UCG-CG

which codes for: -Leu-Ser-Val-Asn-Ser- ... which is a very different polypeptide! Such a 'random' polypeptide may
or may not have some sort of functionality. A frameshift has occurred and this is an example of a
frameshift
mutation
. If one of the new codons was a STOP codon then a much shorter polypeptide would result.

Ultraviolet (UV) Light

This is a very commonly encountered mutagen in sunlight! UV radiation can damage DNA by inducing the
formation of base dimers, such as
thymine dimers (T-T). These slow DNA synthesis and are removed by the
DNA repair systems of the cell. However, these repair systems are not infallible and the repair may introduce an
error or point mutation. Many viruses hide in the DNA of cells and become reactivated by many stimuli, including
UV light. The chicken pox virus will integrate its DNA into the host chromosome, where it will remain even after
infection when the host has acquired immunity to the virus. Certain factors, including UV light, can reactivate the
virus in peripheral nerve cells, resulting in shingles. Possibly, the UV light damages the cell and the virus senses
this and seeks to escape from the damaged DNA of its host cell. Many mutagens are implicated in causing tumours
and
cancers. Cancer cells have damaged communication systems, meaning that they are unable to communicate
properly with neighbouring cells and their cell cycle becomes unregulated - they multiply and keep multiplying.
Mutagens possibly damage genes that form part of the cell's communication system, or they may be reactivating
latent viruses which hijack the cells for their own purposes. Research is increasingly turning up more connections
between infectious agents, whose DNA integrates into the host cell, and cancers.

Mobile Genetic Elements

In addition to viruses, there are a number of different types of mobile genetic element. These are segments of
DNA that can integrate into DNA and then trigger their removal from the DNA at a later stage and perhaps
integrate into another region of DNA or another DNA molecule. Whatever their evolutionary origin, some of these
elements are beneficial and perform functions normal to the cell, whilst others are detrimental and others
apparently neutral, doing little except hopping around and replicating themselves (like parasites). Sometimes these
elements derive from viruses and sometimes they infect viruses to be passed on to other cells using the virus as a
vector, usually to the detriment of the virus (by displacing part of its DNA). (Even the 'fleas' have 'fleas'!).
Transposons and insertion sequences are types of mobile genetic element. Such mobile elements may be the
main cause of spontaneous mutations - if they insert into the middle of a gene then they disrupt the normal
function of that gene.
Above: a selection of bacteria. Bacteria are useful organisms for the study of genetics.