Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

DNA REPAIR
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produces G, which cannot be formed from A by spontaneous deamination, and
whose deamination product (xanthine) is likewise unique.
As discussed in Chapter 6, RNA is thought, on an evolutionary time scale,
to have served as the genetic material before DNA, and it seems likely that the
genetic code was initially carried in the four nucleotides A, C, G, and U. This raises
the question of why the U in RNA was replaced in DNA by T (which is 5-methyl U).
We have seen that the spontaneous deamination of C converts it to U, but that this
event is rendered relatively harmless by uracil DNA glycosylase. However, if DNA
contained U as a natural base, the repair system would not be able to distinguish
a deaminated C from a naturally occurring U.
A special situation occurs in vertebrate DNA, in which selected C nucleotides
are methylated at specific CG sequences that are associated with inactive
genes (discussed in Chapter 7). The accidental deamination of these methylated
C nucleotides produces the natural nucleotide T (Figure 5–43B) in a mismatched
base pair with a G on the opposite DNA strand. To help in repairing deaminated
methylated C nucleotides, a special DNA glycosylase recognizes a mismatched
base pair involving T in the sequence T-G and removes the T. This DNA repair
mechanism must be relatively ineffective, however, because methylated C nucleotides
are exceptionally common sites for mutations in vertebrate DNA. It is striking
that, even though only about 3% of the C nucleotides in human DNA are methylated,
mutations in these methylated nucleotides account for about one-third of
the single-base mutations that have been observed in inherited human diseases.
Special Translesion DNA Polymerases Are Used in Emergencies
If a cell’s DNA suffers heavy damage, the repair mechanisms that we have discussed
are often insufficient to cope with it. In these cases, a different strategy is
called into play, one that entails some risk to the cell. The highly accurate replicative
DNA polymerases stall when they encounter damaged DNA, and in emergencies
cells employ versatile, but less accurate, backup polymerases, known as
translesion polymerases, to replicate through the DNA damage.
Human cells have seven translesion polymerases, some of which can recognize
a specific type of DNA damage and correctly add the nucleotide required to
restore the initial sequence. Others make only “good guesses,” especially when the
template base has been extensively damaged. These enzymes are not as accurate
as the normal replicative polymerases when they copy a normal DNA sequence.
For one thing, the translesion polymerases lack exonucleolytic proofreading
activity; in addition, many are much less discriminating than the replicative polymerase
in choosing which nucleotide to incorporate initially. Presumably for this
reason, each such translesion polymerase is given a chance to add only one or a
few nucleotides before the highly accurate replicative polymerase resumes DNA
synthesis.
Despite their usefulness in allowing heavily damaged DNA to be replicated,
these translesion polymerases do, as noted above, pose risks to the cell. They are
probably responsible for most of the base-substitution and single-nucleotide
deletion mutations that accumulate in genomes; although they generally produce
mutations when copying damaged DNA (see Figure 5–40), they probably also create
mutations—at a low level—on undamaged DNA. Clearly, it is important for
the cell to tightly regulate these polymerases, releasing them only at sites of DNA
damage. Exactly how this happens for each translesion polymerase remains to
be discovered, but a conceptual model is given in Figure 5–44. The principle of
this model applies to many of the DNA repair processes discussed in this chapter:
because the enzymes that carry out these reactions are potentially dangerous to
the genome, they must be brought into play only at sites of damage.
Double-Strand Breaks Are Efficiently Repaired
An especially dangerous type of DNA damage occurs when both strands of the
double helix are broken, leaving no intact template strand to enable accurate