Mutations Involve Changes in the Base Sequence of DNA

III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
We now turn from DNA replication to DNA mutations and repair. Several types of mutations are known: (1) the
substitution of one base pair for another, (2) the deletion of one or more base pairs, and (3) the insertion of one or more
base pairs. The spontaneous mutation rate of T4 phage is about 10-7 per base per replication. E. coli and Drosophila
melanogaster have much lower mutation rates, of the order of 10-10.
The substitution of one base pair for another is the a common type of mutation. Two types of substitutions are possible.
A transition is the replacement of one purine by the other or that of one pyrimidine by the other. In contrast, a
transversion is the replacement of a purine by a pyrimidine or that of a pyrimidine by a purine.
Watson and Crick suggested a mechanism for the spontaneous occurrence of transitions in a classic paper on the DNA
double helix. They noted that some of the hydrogen atoms on each of the four bases can change their location to produce
a tautomer. An amino group (-NH2) can tautomerize to an imino form ( NH). Likewise, a keto group (
can tautomerizeto an enol form
. The fraction of each type of base in the formof these imino and enol tautomers is about10-4. These transient tautomers
can form nonstandard base pairs that fit into a double helix. For example, the imino tautomer of adenine can pair with
cytosine (Figure 27.41). This A*-C pairing (the asterisk denotes the imino tautomer) would allow C to become
incorporated into a growing DNA strand where T was expected, and it would lead to a mutation if left uncorrected. In the
next round of replication, A* will probably retautomerize to the standard form, which pairs as usual with thymine, but
the cytosine residue will pair with guanine. Hence, one of the daughter DNA molecules will contain a G-C base pair in
place of the normal A-T base pair.
Tautomerization
The interconversion of two isomers that differ only in the position of
protons (and, often, double bonds).
27.6.1. Some Chemical Mutagens Are Quite Specific
Base analogs such as 5-bromouracil and 2-aminopurine can be incorporated into DNA and are even more likely than
normal nucleic acid bases to form transient tautomers that lead to transition mutations. 5-Bromouracil, an analog of
thymine, normally pairs with adenine. However, the proportion of 5-bromouracil in the enol tautomer is higher than that
of thymine because the bromine atom is more electronegative than is a methyl group on the C-5 atom. Thus, the
incorporation of 5-bromouracil is especially likely to cause altered base-pairing in a subsequent round of DNA
replication (Figure 27.42).
Other mutagens act by chemically modifying the bases of DNA. For example, nitrous acid (HNO2) reacts with bases that
contain amino groups. Adenine is oxidatively deaminated to hypoxanthine, cytosine to uracil, and guanine to xanthine.
Hypoxanthine pairs with cytosine rather than with thymine (Figure 27.43). Uracil pairs with adenine rather than with
guanine. Xanthine, like guanine, pairs with cytosine. Consequently, nitrous acid causes A-T G-C transitions.
A different kind of mutation is produced by flat aromatic molecules such as the acridines (Figure 27.44). These
compounds intercalate in DNA that is, they slip in between adjacent base pairs in the DNA double helix.
Consequently, they lead to the insertion or deletion of one or more base pairs. The effect of such mutations is to alter the
reading frame in translation, unless an integral multiple of three base pairs is inserted or deleted. In fact, the analysis of
such mutants contributed greatly to the revelation of the triplet nature of the genetic code.
Some compounds are converted into highly active mutagens through the action of enzymes that normally play a role in
detoxification. A striking example is aflatoxin B1, a compound produced by molds that grows on peanuts and other
foods. A cytochrome P450 enzyme (Section 26.4.3) converts this compound into a highly reactive epoxide (Figure
27.45). This agent reacts with the N-7 atom of guanosine to form an adduct that frequently leads to a G-C-to-T-A
transversion.
27.6.2. Ultraviolet Light Produces Pyrimidine Dimers
The ultraviolet component of sunlight is a ubiquitous DNA-damaging agent. Its major effect is to covalently link
adjacent pyrimidine residues along a DNA strand (Figure 27.46). Such a pyrimidine dimer cannot fit into a double helix,
and so replication and gene expression are blocked until the lesion is removed.
27.6.3. A Variety of DNA-Repair Pathways Are Utilized
The maintenance of the integrity of the genetic message is key to life. Consequently, all cells possess mechanisms to
repair damaged DNA. Three types of repair pathways are direct repair, base-excision repair, and nucleotide-excision
repair (Figure 27.47).
An example of direct repair is the photochemical cleavage of pyrimidine dimers. Nearly all cells contain a
photoreactivating enzyme called DNA photolyase. The E. coli enzyme, a 35-kd protein that contains bound N 5,N 10methenyltetrahydrofolate and flavin adenine dinucleotide cofactors, binds to the distorted region of DNA. The enzyme
uses light energy specifically, the absorption of a photon by the N 5,N 10-methenyltetrahydrofolate coenzyme to
form an excited state that cleaves the dimer into its original bases.
The excision of modified bases such as 3-methyladenine by the E. coli enzyme AlkA is an example of base-excision
repair. The binding of this enzyme to damaged DNA flips the affected base out of the DNA double helix and into the
active site of the enzyme (Figure 27.48). Base flipping also occurs in the enzymatic addition of methyl groups to DNA
bases (Section 24.2.7). The enzyme then acts as a glycosylase, cleaving the glycosidic bond to release the damaged base.
At this stage, the DNA backbone is intact, but a base is missing. This hole is called an AP site because it is apurinic
(devoid of A or G) or apyrimidinic (devoid of C or T). An AP endonuclease recognizes this defect and nicks the
backbone adjacent to the missing base. Deoxyribose phosphodiesterase excises the residual deoxyribose phosphate unit,
and DNA polymerase I inserts an undamaged nucleotide, as dictated by the base on the undamaged complementary
strand. Finally, the repaired strand is sealed by DNA ligase.
One of the best-understood examples of nucleotide-excision repair is the excision of a pyrimidine dimer. Three
enzymatic activities are essential for this repair process in E. coli (Figure 27.49). First, an enzyme complex consisting of
the proteins encoded by the uvrABC genes detects the distortion produced by the pyrimidine dimer. A specific uvrABC
enzyme then cuts the damaged DNA strand at two sites, 8 nucleotides away from the dimer on the 5 side and 4
nucleotides away on the 3 side. The 12-residue oligonucleotide excised by this highly specific excinuclease (from the
Latin exci,"to cut out") then diffuses away. DNA polymerase I enters the gap to carry out repair synthesis. The 3 end of
the nicked strand is the primer, and the intact complementary strand is the template. Finally, the 3 end of the newly
synthesized stretch of DNA and the original part of the DNA chain are joined by DNA ligase.
27.6.4. The Presence of Thymine Instead of Uracil in DNA Permits the Repair of
Deaminated Cytosine
The presence in DNA of thymine rather than uracil was an enigma for many years. Both bases pair with adenine. The
only difference between them is a methyl group in thymine in place of the C-5 hydrogen atom in uracil. Why is a
methylated base employed in DNA and not in RNA? The existence of an active repair system to correct the deamination
of cytosine provides a convincing solution to this puzzle.
Cytosine in DNA spontaneously deaminates at a perceptible rate to form uracil. The deamination of cytosine is
potentially mutagenic because uracil pairs with adenine, and so one of the daughter strands will contain an U-A base pair
rather than the original C-G base pair (Figure 27.50). This mutation is prevented by a repair system that recognizes uracil
to be foreign to DNA. This enzyme, uracil DNA glycosylase, is homologous to AlkA. The enzyme hydrolyzes the
glycosidic bond between the uracil and deoxyribose moieties but does not attack thymine-containing nucleotides. The
AP site generated is repaired to reinsert cytosine. Thus, the methyl group on thymine is a tag that distinguishes thymine
from deaminated cytosine. If thymine were not used in DNA, uracil correctly in place would be indistinguishable from
uracil formed by deamination. The defect would persist unnoticed, and so a C-G base pair would necessarily be mutated
to U-A in one of the daughter DNA molecules. This mutation is prevented by a repair system that searches for uracil and
leaves thymine alone. Thymine is used instead of uracil in DNA to enhance the fidelity of the genetic message. In
contrast, RNA is not repaired, and so uracil is used in RNA because it is a less-expensive building block.
27.6.5. Many Cancers Are Caused by Defective Repair of DNA
As discussed in Chapter 15, cancers are caused by mutations in genes associated with growth control. Defects in
DNA-repair systems are expected to increase the overall frequency of mutations and, hence, the likelihood of a
cancer-causing mutation. Xeroderma pigmentosum, a rare human skin disease, is genetically transmitted as an autosomal
recessive trait. The skin in an affected homozygote is extremely sensitive to sunlight or ultraviolet light. In infancy,
severe changes in the skin become evident and worsen with time. The skin becomes dry, and there is a marked atrophy
of the dermis. Keratoses appear, the eyelids become scarred, and the cornea ulcerates. Skin cancer usually develops at
several sites. Many patients die before age 30 from metastases of these malignant skin tumors.
Ultraviolet light produces pyrimidine dimers in human DNA, as it does in E. coli DNA. Furthermore, the repair
mechanisms are similar. Studies of skin fibroblasts from patients with xeroderma pigmentosum have revealed a
biochemical defect in one form of this disease. In normal fibro-blasts, half the pyrimidine dimers produced by ultraviolet
radiation are excised in less than 24 hours. In contrast, almost no dimers are excised in this time interval in fibroblasts
derived from patients with xeroderma pigmentosum. The results of these studies show that xeroderma pigmentosum can
be produced by a defect in the excinuclease that hydrolyzes the DNA backbone near a pyrimidine dimer. The drastic
clinical consequences of this enzymatic defect emphasize the critical importance of DNA-repair processes. The disease
can also be caused by mutations in eight other genes for DNA repair, which attests to the complexity of repair processes.
Defects in other repair systems can increase the frequency of other tumors. For example, hereditary nonpolyposis
colorectal cancer (HNPCC, or Lynch syndrome) results from defective DNA mismatch repair. HNPCC is not rare as
many as 1 in 200 people will develop this form of cancer. Mutations in two genes, called hMSH2 and hMLH1, account
for most cases of this hereditary predisposition to cancer. The striking finding is that these genes encode the human
counterparts of MutS and MutL of E. coli. The MutS protein binds to mismatched base pairs (e.g., G-T) in DNA. An
MutH protein, together with MutL, participates in cleaving one of the DNA strands in the vicinity of this mismatch to
initiate the repair process (Figure 27.51). It seems likely that mutations in hMSH2 and hMLH1 lead to the accumulation
of mutations throughout the genome. In time, genes important in controlling cell proliferation become altered, resulting
in the onset of cancer.
27.6.6. Some Genetic Diseases Are Caused by the Expansion of Repeats of Three
Nucleotides
Some genetic diseases are caused by the presence of DNA sequences that are inherently prone to errors in the
course of replication. A particularly important class of such diseases are characterized by the presence of long
tandem arrays of repeats of three nucleotides. An example is Hunt-ington disease, an autosomal dominant neurological
disorder with a variable age of onset. The mutated gene in this disease expresses a protein called huntingtin, which is
expressed in the brain and contains a stretch of consecutive glutamine residues. These glutamine residues are encoded by
a tandem array of CAG sequences within the gene. In unaffected persons, this array is between 6 and 31 repeats,
whereas, in those with the disease, the array is between 36 and 82 repeats or longer. Moreover, the array tends to become
longer from one generation to the next. The consequence is a phenomenon called anticipation: the children of an
affected parent tend to show symptoms of the disease at an earlier age than did the parent.
The tendency of these trinucleotide repeats to expand is explained by the formation of alternative structures in DNA
replication (Figure 27.52). Part of the array within the daughter strand can loop out without disrupting base-pairing
outside this region. DNA polymerase extends this strand through the remainder of the array, leading to an increase in the
number of copies of the trinucleotide sequence.
A number of other neurological diseases are characterized by expanding arrays of trinucleotide repeats. How do these
long stretches of repeated amino acids cause disease? For huntingtin, it appears that the polyglutamine stretches become
increasingly prone to aggregate as their length increases; the additional consequences of such aggregation are still under
active investigation.
27.6.7. Many Potential Carcinogens Can Be Detected by Their Mutagenic Action on
Bacteria
Many human cancers are caused by exposure to chemicals. These chemical carcinogens usually cause mutations, which
suggests that damage to DNA is a fundamental event in the origin of mutations and cancer. It is important to identify
these compounds and ascertain their potency so that human exposure to them can be minimized. Bruce Ames devised a
simple and sensitive test for detecting chemical mutagens. In the Ames test, a thin layer of agar containing about 109
bacteria of a specially constructed tester strain of Salmonella is placed on a petri dish. These bacteria are unable to grow
in the absence of histidine, because a mutation is present in one of the genes for the biosynthesis of this amino acid. The
addition of a chemical mutagen to the center of the plate results in many new mutations. A small proportion of them
reverse the original mutation, and histidine can be synthesized. These revertants multiply in the absence of an external
source of histidine and appear as discrete colonies after the plate has been incubated at 37°C for 2 days (Figure 27.53).
For example, 0.5 µg of 2-aminoanthracene gives 11,000 revertant colonies, compared with only 30 spontaneous
revertants in its absence. A series of concentrations of a chemical can be readily tested to generate a dose-response curve.
These curves are usually linear, which suggests that there is no threshold concentration for mutagenesis.
Some of the tester strains are responsive to base-pair substitutions, whereas others detect deletions or additions of base
pairs (frameshifts). The sensitivity of these specially designed strains has been enhanced by the genetic deletion of their
excision-repair systems. Potential mutagens enter the tester strains easily because the lipopolysaccharide barrier that
normally coats the surface of Salmonella is incomplete in these strains.
A key feature of this detection system is the inclusion of a mammalian liver homogenate (Section 4.1.2). Recall that
some potential carcinogens such as aflatoxin are converted into their active forms by enzyme systems in the liver or
other mammalian tissues (Section 27.6.1). Bacteria lack these enzymes, and so the test plate requires a few milligrams of
a liver homogenate to activate this group of mutagens.
The Salmonella test is extensively used to help evaluate the mutagenic and carcinogenic risks of a large number of
chemicals. This rapid and inexpensive bacterial assay for mutagenicity complements epidemiological surveys and animal
tests that are necessarily slower, more laborious, and far more expensive. The Salmonella test for mutagenicity is an
outgrowth of studies of gene-protein relations in bacteria. It is a striking example of how fundamental research in
molecular biology can lead directly to important advances in public health.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.41. Base Pair with Mutagenic Tautomer. The bases of DNA can exist in rare tautomeric forms. The imino
tautomer of adenine can pair with cytosine, eventually leading to a transition from A-T to G-C.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.42. Base Pair with 5-Bromouracil. This analog of thymine has a higher tendency to form an enol tautomer
than does thymine itself. The pairing of the enol tautomer of 5-bromouracil with guanine will lead to a transition from TA to C-G.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.43. Chemical Mutagenesis. Treatment of DNA with nitrous acid results in the conversion of adenine into
hypoxanthine. Hypoxanthine pairs with cytosine, inducing a transition from A-T to G-C.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.44. Acridines. Acridine dyes induce frameshift mutations by intercalating into the DNA, leading to the
incorporation of an additional base on the opposite strand.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.45. Aflatoxin Reaction. The compound, produced by molds that grow on peanuts, is activated by cytochrome
P450 to form a highly reactive species that modifies bases such as guanine in DNA, leading to mutations.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.46. Cross-Linked Dimer of Two Thymine Bases. Ultraviolet light induces cross-links between adjacent
pyrimidines along one strand of DNA.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.47. Repair Pathways. Three different pathways are used to repair damaged regions in DNA. In base-excision
repair, the damaged base is removed and replaced. In direct repair, the damaged region is corrected in place. In
nucleotide-excision repair, a stretch of DNA around the site of damage is removed and replaced.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.48. Structure of DNA-Repair Enzyme. A complex between the DNA-repair enzyme AlkA and an analog of
an apurinic site. Note that the damaged base is flipped out of the DNA double helix into the active site of the
enzyme for excision.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.49. Excision Repair. Repair of a region of DNA containing a thymine dimer by the sequential action of a
specific excinuclease, a DNA polymerase, and a DNA ligase. The thymine dimer is shown in blue, and the new region of
DNA is in red. [After P. C. Hanawalt. Endevour 31(1982):83.]
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.50. Uracil Repair. Uracil bases in DNA, formed by the deamination of cytosine, are excised and replaced by
cytosine.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.51. Mismatch Repair. DNA mismatch repair in E. coli is initiated by the interplay of MutS, MutL, and MutH
proteins. A G-T mismatch is recognized by MutS. MutH cleaves the backbone in the vicinity of the mismatch. A
segment of the DNA strand containing the erroneous T is removed by exonuclease I and synthesized anew by DNA
polymerase III. [After R. F. Service. Science 263(1994):1559.]
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.52. Triplet Repeat Expansion. Sequences containing tandem arrays of repeated triplet sequences can be
expanded to include more repeats by the looping out of some of the repeats before replication.
III. Synthesizing the Molecules of Life
27. DNA Replication, Recombination, and Repair
27.6. Mutations Involve Changes in the Base Sequence of DNA
Figure 27.53. Ames Test. (A) A petri dish containing about 109 Salmonella bacteria that cannot synthesize histidine and
(B) a petri dish containing a filter-paper disc with a mutagen, which produces a large number of revertants that can