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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Figure 5–42 The recognition of an
unusual nucleotide in DNA by baseflipping.
The DNA glycosylase family of
enzymes recognizes specific inappropriate
bases in the conformation shown. Each of
these enzymes cleaves the glycosyl bond
that connects a particular recognized base
(yellow) to the backbone sugar, removing it
from the DNA. (A) Stick model; (B) spacefilling
model.
(A)
(B)
removal of certain highly mutagenic or cytotoxic lesions. For example, the alkylation
lesion O 6 -methylguanine has its methyl group removed by direct transfer to
a cysteine residue in the repair protein itself, which is destroyed in the reaction.
MBoC6 m5.49/5.43
In another example, methyl groups in the alkylation lesions 1-methyladenine and
3-methylcytosine are “burnt off” by an iron-dependent demethylase, with release
of formaldehyde from the methylated DNA and regeneration of the native base.
Coupling Nucleotide Excision Repair to Transcription Ensures That
the Cell’s Most Important DNA Is Efficiently Repaired
All of a cell’s DNA is under constant surveillance for damage, and the repair mechanisms
we have described act on all parts of the genome. However, cells have a
way of directing DNA repair to the DNA sequences that are most urgently needed.
They do this by linking RNA polymerase, the enzyme that transcribes DNA into
RNA as the first step in gene expression, to the nucleotide excision repair pathway.
As discussed above, this repair system can correct many different types of DNA
damage. RNA polymerase stalls at DNA lesions and, through the use of coupling
proteins, directs the excision repair machinery to these sites. In bacteria, where
genes are relatively short, the stalled RNA polymerase can be dissociated from the
DNA; the DNA is repaired, and the gene is transcribed again from the beginning.
In eukaryotes, where genes can be enormously long, a more complex reaction is
used to “back up” the RNA polymerase, repair the damage, and then restart the
polymerase.
The importance of transcription-coupled excision repair is seen in people
with Cockayne syndrome, which is caused by a defect in this coupling. These individuals
suffer from growth retardation, skeletal abnormalities, progressive neural
retardation, and severe sensitivity to sunlight. Most of these problems are thought
to arise from RNA polymerase molecules that become permanently stalled at sites
of DNA damage that lie in important genes.
The Chemistry of the DNA Bases Facilitates Damage Detection
The DNA double helix seems optimal for repair. As noted above, it contains a
backup copy of all genetic information. Equally importantly, the nature of the
four bases in DNA makes the distinction between undamaged and damaged
bases very clear. For example, every possible deamination event in DNA yields
an “unnatural” base, which can be directly recognized and removed by a specific
DNA glycosylase. Hypoxanthine, for example, is the simplest purine base capable
of pairing specifically with C, but hypoxanthine is the direct deamination product
of A (Figure 5–43A). The addition of a second amino group to hypoxanthine