Mutation

Phenotypic Effects and Evolution

Mutations in the germ-line cells are heritable and provide the raw material upon which natural selection operates to produce evolution. Mutations in somatic cells, which are cells that are not germ line, are not heritable but may lead to disease in the organism possessing them.

Most mutations do not cause disease and are said to be "silent" mutations. This is for at least two reasons. First, most DNA does not code for genes, so changes in the sequence do not affect the types or amounts of protein made and there is no change in the phenotype of the organism. Second, most sexually reproducing organisms are diploid, meaning they possess two copies of every gene. Many types of mutation simply disable one copy, leaving the other intact and functional. Therefore these mutations display a recessive inheritance pattern, with no effect on phenotype unless an individual inherits two copies of the mutation. Diploid species can accumulate a large pool of such recessive mutations, which are mostly disadvantageous and thus contribute to the burden of genetic disease.

Some mutations lead to detrimental alterations of the normal pheno-type and are, therefore, selected against. Very occasionally, the mutant phenotype is superior and provides a selective advantage, which leads to an increase in the frequency of this mutant allele and, thus, to evolution of the population. Alternatively, a disadvantageous mutation in one environment may become advantageous in another, again leading to increased frequency of this allele.

Molecular Basis of Mutations

DNA is composed of a double helix, each side of which is a long string of four types of nucleotides. Each nucleotide possesses identical sugar-phosphate groups that contribute to the DNA backbone but differs in the structure of the base suspended between the two backbones. The bases are adenine, thymine, cytosine, and guanine (A, T, C, G). Because of their structure, A pairs only with T across the double helix, and C only with G.

Within genes, the sequence of DNA encodes a sequence of amino acids used to build a protein. The DNA is read in triplets of bases, with each triplet coding for an amino acid. With the recognition that the genetic information lies in the sequence of bases in the DNA, it became possible to understand the chemical nature of gene mutations and how these could be as stable as the original allele of the gene.

Consideration of the genetic code linking DNA and amino acids reveals how mutations can either alter a protein, have no effect, or prevent it from being produced entirely. Mutations fall into four broad categories (point mutations, structural chromosomal aberrations, numerical chromosomal aberrations, and transposon-induced mutations), each of which may be subdivided further.

Point Mutations

"Point mutations" are small changes in the sequence of DNAbases within a gene. These are what are most commonly meant by the word "mutation." Point mutations include substitutions, insertions, and deletions of one or more bases.

If one base is replaced by another, the mutation is called a base substitution. Because the DNA is double-stranded, a change on one strand is always accompanied by a change on the other (this change may occur spontaneously during DNA replication, or it can be created by errors during DNA repair. Consequently, it is often difficult to know which base of the pair was mutated and which was simply the result of repairing the mismatch at the mutation.

For example, the most common mutation in mammalian cells is the substitution of a G-C pair with an A-T pair. This could arise if G is replaced by A and subsequently the A is replicated to give T on the other strand. Alternatively, the C could be replaced by a T and the T could then be replicated to give an A on the complementary strand, the final result being the same. It is believed that the G-C to A-T conversion most commonly begins with a C-to-T mutation. This is because most of these mutations occur at DNA sequences in which C is methylated (i.e., chemically modified by the addition of a-CH₃ group). The methylated form of C can be converted to a base that resembles T (and thus pairs with A) by removal of an-NH₂ group (deamination)—a relatively common event.

Base substitution mutations are classified as transitions or transversions. Transitions are mutations in which one pyrimidine (C or T) is substituted by the other and one purine (G or A) is substituted on the complementary strand. The G-C to A-T conversion is a transition mutation, since C becomes T.

Transversions are mutations in which a purine is replaced by a pyrimidine or vice versa. Sickle cell anemia is caused by a transversion: T is substituted for A in the gene for a hemoglobin subunit. This mutation has arisen numerous times in human evolution. It causes a single amino acid change, from glutamic acid to valine, in the β subunit of hemoglobin. Sickle cell anemia was the first genetic condition for which the change in the protein was demonstrated in 1954 by Linus Pauling (a Nobel laureate from the California Institute of Technology) and subsequently shown to be a single amino acid difference by Vernon Ingram (a Nobel laureate from the Massachusetts Institute of Technology).

Base substitutions are sometimes silent mutations—mutations that do not change the amino acid sequence in the protein encoded by the gene. Silent mutations are possible because the original and mutated sequences can code for the same amino acid, given the redundancy of the genetic code. In the divergence between sea urchins and humans, for example, one of the histone proteins has only two amino acid substitutions, although the gene has many base pair substitutions. Histones are proteins around which DNA is wrapped in chromosomes. The very close similarity in sequence between such distantly related organisms is an indication of how critical the structure is for the function: Most mutations that change it are very disadvantageous.

One type of substitution mutation that almost always inactivates the gene is mutation to a stop codon. A stop codon ends the assembly of the protein, and a truncated protein is usually not active biochemically. Many recessive genetic diseases occur when a mutation converts a coding triplet to a stop codon.

Other mutations involve the insertion or deletion of one or more base pairs in the DNA. When they occur in genes, such mutations typically inactivate the encoded protein, because they change the "reading frame" of the gene. The DNA sequence is translated in groups of three nucleotides. Insertion or deletion of a nucleotide changes the sets of triplets, and thus every subsequent amino acid is altered, changing the protein completely, as shown in Figure 2. Stop codons also frequently arise from insertions or deletions.

Naturally occurring trinucleotide repeat sequences (e.g., CAGCAG CAGCAG) are hot spots for certain important human mutations that involve the insertion of more copies of the repeated sequence. For example at the locus for Huntington's disease, a sequence of 10-29 copies of CAG is normal and stable, but if there are 30-38, there is a high rate of mutation to increased numbers of copies, and if there are 39 or more copies, middle-age dementia called Huntington's disease results.

Functional Consequences and Inheritance Patterns.

Mutations can be classified by their functional consequences. Mutations that inactivate the resulting protein, or prevent it from being made at all, are called loss-of-function mutations. These are usually recessive, since the organism still retains one functional copy on the other chromosome. Loss-of-function mutations may be dominant if the organism cannot compensate for the loss by using the other gene copy. Gain-of-function mutations are those in which the protein takes on a new function, or loses the ability to be regulated by other proteins. These mutations are typically dominant, since the new function may be deleterious even in the presence of a normal protein, encoded by the other gene copy.

Chromosomal Aberrations and Transposons

"Structural chromosomal aberrations," the second category of mutations, arise when DNA in chromosomes is broken. The broken ends may remain unrepaired or may be joined with those of another break, to form new combinations of genes, such as translocations. A translocation between chromosomes 8 and 21 in humans causes acute myeloid leukemia by increasing the activity of c-myc, a gene involved in cell replication.

Translocations often cause human infertility, because they interfere with the normal distribution of chromosomes during meiosis. Chromosomes pair up before separating, as eggs or sperm are formed, and the correct pairing depends on matching sequences between them. Structural aberrations also include inversions and duplications of pieces of chromosomes.

Most chromosomal aberrations lead to the formation of chromosomal fragments without centromeres. Centromeres are crucial for proper chromosomal division, during both mitosis and meiosis. Therefore a chromosomal fragment is likely to be lost from one of the daughter cells formed after cell division.

Structural aberrations are nonetheless common in evolutionary history. As a result, although the chromosomes of mouse and man are quite different in appearance, most genes have the same neighbors in the two species, representing the ancestral mammalian arrangement, even if they have been moved to another chromosome as shown in Figure 3.

"Numerical chromosomal aberrations," the third category of mutations, are changes in the number of chromosomes. In some cases, the whole genome has been duplicated (called polyploidy) and the mutant has, for example, four of each chromosome (and is thus tetraploid) rather than the usual two (diploid, as in humans). These are much more common in the evolution of plants than animals. In other cases, only one or a few of the chromosomes are involved, which is referred to as aneuploidy. Down syndrome, in which a person has an extra chromosome 21, is an example of such a mutation. Aneuploidy may also involve the loss of a chromosome. The absence of one of the sex chromosomes, X or Y, is a mutation in humans that results in Turner's syndrome, in which there is only one X.

"Transposon-induced mutations" are the fourth category of mutations. Transposable genetic elements (transposons) are pieces of DNA that can copy themselves and insert into a new location in the genome. They were first discovered by Barbara McClintock, a U.S. geneticist and Nobel laureate in 1950. When transposons jump into a new position, the insertion may disrupt a gene and thus mutate it, usually inactivating it. Sometimes the transposon jumps again, and the activity of the gene it leaves is restored. Often, however, the transposon stays in the original position, permanently disrupting the gene. Some forms of hemophilia are due to transposon insertion. Transposon mutations have been extremely common in human evolution, and such mutations are still occurring.

Mutations in Research and Medicine

Early geneticists treasured mutations in the organisms they studied, since no characteristic can be studied genetically unless heritable variants exist. If, for example, everyone had brown eyes, nothing could be learned about the inheritance of eye color, as all generations would have the same color of eyes. For this reason, geneticists collected and propagated all the mutants they could find, and methods were developed to deliberately induce mutations, a process called mutagenesis. Such techniques include exposing their experimental organisms to X rays and chemicals.

Transposons can also be deliberately used to introduce mutations in model organisms. In the plant Arabidopsis thaliana and in the fruit fly Drosophila melanogaster, transposon mutagenesis is often used to induce mutations, as the mutation can be very rapidly cloned and mapped with the transposon's DNA sequence as starting point.

Comparing existing mutations can help determine the evolutionary relatedness of two organisms. During evolution, there has been a relatively constant rate of accumulation of mutations in genes for a number of proteins, so the number of changes can be used to estimate the time since two species had a common ancestor. This is called the molecular clock and is illustrated in Figure 1. Each gene has evolved at a characteristic rate—the result of mutation rates, selection, and chance changes in the gene pool.

Advances in genetics have only intensified the search for mutations, especially in complex traits such as behavior and cancer, as the key to finding the genes involved and then unraveling the underlying mechanisms. This involves mapping the mutations, cloning the genes, and studying the mutants to discover what biochemical processes are changed in the mutants.

Mutations are believed to underlie most, if not all cancers. Cancer-causing mutations found so far include genes involved in communication between cells (signal transduction) and in the control of cell division. Many of these genes have been categorized into two broad classes: oncogenes and tumor suppressor genes. The mutation that has been found most often, in a tumor suppressor gene called p53, usually arises as a somatic mutation but can also be inherited as Li Fraumeni syndrome.

Xeroderma pigmentosum is an autosomal recessive condition in which the ability to repair DNA damage induced by UV light is defective. Many mutations are produced, and the affected people have large numbers of skin cancers.

SEE ALSO CARCINOGENS; CHROMOSOMAL ABERRATIONS; DNA REPAIR; GENE; HEMOGLOBINOPATHIES; MUTAGENESIS; MUTATION RATE; POLYPLOIDY; TRANSPOSABLE GENETIC ELEMENTS.

John Heddle

Bibliography

Drake, John W. "Spontaneous Mutation." Annual Review of Genetics 25 (1991): 125-46.

Hartwell, Leland H., et al. Genetics: From Genes to Genomes. Boston: McGraw-Hill,2000.

Lewis, Ricki. Human Genetics: Concepts and Applications, 4th ed. Boston: McGraw-Hill,2001.

Pauling, Linus, et al. "Sickle Cell Anemia, a Molecular Disease." Science 110 (1949):543-548.

Internet Resource

International Agency for Research on Cancer. <http://www.iarc.fr/>.