Figure 5– 41 A comparison of two major DNA repair pathways. (A) Base excision repair. This pathway starts with a DNA glycosylase. Here, the enzyme uracil DNA glycosylase removes an accidentally deaminated cytosine in DNA. After the action of this glycosylase (or another DNA glycosylase that recognizes a different kind of damage), the sugar phosphate with the missing base is cut out by the sequential action of AP endonuclease and a phosphodiesterase. (These same enzymes begin the repair of depurinated sites directly.) The gap of a single nucleotide is then filled by DNA polymerase and DNA ligase. The net result is that the U that was created by accidental deamination is restored to a C. AP endonuclease is so-named because it recognizes any site in the DNA helix that contains a deoxyribose sugar with a missing base; such sites can arise either by the loss of a purine (apurinic sites) or by the loss of a pyrimidine (apyrimidinic sites). (B) Nucleotide excision repair. In bacteria, after a multienzyme complex has recognized a lesion such as a pyrimidine dimer (see Figure 5–39), one cut is made on each side of the lesion, and an associated DNA helicase then removes the entire portion of the damaged strand. The excision repair machinery in bacteria leaves the gap of 12 nucleotides shown. In humans, once the damaged DNA is recognized, a helicase is recruited to unwind the DNA duplex locally. Next, the excision nuclease enters and cleaves on either side of the damage, leaving a gap of about 30 nucleotides. The nucleotide excision repair machinery in both bacteria and humans can recognize and repair many different types of DNA damage.
The second major repair pathway is called nucleotide excision repair. This mechanism can repair the damage caused by almost any large change in the structure of the DNA double helix. Such “bulky lesions” include those created by the covalent reaction of DNA bases with large hydrocarbons (such as the carcinogen benzopyrene, found in tobacco smoke, coal tar, and diesel exhaust), as well as the various pyrimidine dimers (T-T, T-C, and C-C) caused by sunlight. In this pathway, a large multienzyme complex scans the DNA for a distortion in the double helix, rather than for a specific base change. Once it finds a lesion, it cleaves the phosphodiester backbone of the abnormal strand on both sides of the distortion, and a DNA helicase peels away the single-strand oligonucleotide containing the lesion. The large gap produced in the DNA helix is then repaired by DNA polymerase and DNA ligase (see Figure 5–41B).
An alternative to base and nucleotide excision repair processes is direct chemical reversal of DNA damage, and this strategy is selectively employed for the rapid removal of certain highly mutagenic or cytotoxic lesions. For example, the alkylation lesion O6-methylguanine has its methyl group removed by direct transfer to a cysteine residue in the repair protein itself, which is destroyed in the reaction. 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