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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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12. DNA: Its Mutation, Repair, and Recombination
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The McGraw Hill Companies, 2001
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Like base excision repair, nucleotide excision repair is present in all organisms. In yeast, approximately twelve genes are involved, many in what is called the RAD3 group. In human beings, twenty- ve proteins are involved; they remove twenty-seven to twenty-nine nucleotides, as compared to twelve to thirteen in E. coli. Transcription and nucleotide excision repair are linked in eukaryotes.Transcription factor TFIIH (see chapter 11) is involved in repair of UV damage; it has helicase activity and is found in both processes. Since it has been shown that genes that are actively being transcribed are preferentially repaired, we can now envision a model in which transcription, when blocked by a DNA lesion like a thymine dimer, signals the formation of a repair complex, using TFIIH in both processes. In prokaryotes, RNA polymerase dissociates from the DNA in this circumstance, losing the nascent transcript. This would be inef cient in eukaryotes, whose genes are much longer and more expensive to transcribe; for example, the human dystrophin gene, defective in the disease Duchenne muscular dystrophy, is 2.4 million bases long and takes almost eight hours to transcribe. We believe that eukaryotic RNA polymerase II backs up when stalled at a DNA lesion and continues after the lesion is repaired, without losing the transcript. Much active research is going on in this area. In human beings, the autosomal recessive trait xeroderma pigmentosum is caused by an inability to repair thymine dimerization induced by UV light. Persons with this trait freckle heavily when exposed to the UV rays of the sun, and they have a high incidence of skin cancer. There are seven complementation groups (loci XPA-XPG) whose protein products are involved in the rst steps of nucleotide excision repair and whose defects cause xeroderma pigmentosum in human beings. One of them, XPD, is a component of TFIIH. Excision repair triggered by mismatches is referred to as mismatch repair, which encompasses about 99% of all DNA repairs. As DNA polymerase replicates DNA, some errors are made that the proofreading polymerase does not correct. For example, a template G can be paired with a T rather than a C in the progeny strand.The GT base pair does not t correctly in the DNA duplex. The mismatch repair system, which follows behind the replicating fork, recognizes this problem. This system, whose members in E. coli are speci ed by the mutH, mutL, mutS, and mutU genes, is responsible for the removal of the incorrect base by an excision repair process. (The genes are called mut for mutator because mutations of these genes cause high levels of spontaneous mutation in the cells. The mutU gene is also known as uvrD.) The mismatch repair enzymes initiate the removal of the incorrect base by nicking the DNA strand on one side of the mismatch. You might wonder how the mismatch repair system recognizes the progeny, rather than the template, base as
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the wrong one. After all, in a mismatch, there are no defective bases theoretically, either partner could be the wrong base. In E. coli, the answer lies in the methylation state of the DNA. DNA methylase, the product of the dam locus, methylates 5 -GATC-3 sequences, which are relatively common in the DNA of E. coli, at the adenine residue. Since the mismatch repair enzymes follow the replication fork of the DNA, they usually reach the site of mismatch before the methylase does. Template strands will be methylated, whereas progeny strands, being newly synthesized, will not be. Thus, the methylation state of the DNA cues the mismatch repair enzymes to eliminate the progeny-strand base for repair. After the methylase passes by, both strands of the DNA are methylated, and the methylation cue is gone. In gure 12.32, we present one model of mismatch repair.The MutS protein, in the form of a homodimer two
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