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3 5 MutL binds: Methylation signal located MutH endonuclease nicks DNA at GATC site G T MutU binds and unwinds nicked progeny strand G T
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Figure 12.32 Mismatch repair. The MutS protein discovers mismatches; MutL binds and the MutH endonuclease nicks the progeny strand at the 3 -CTAG-5 sequence. MutU helicase unwinds the nicked oligonucleotide with the mismatch (red). Exonuclease digestion, followed by DNA polymerase III and DNA ligase repair, completes the operation.
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III. Molecular Genetics
12. DNA: Its Mutation, Repair, and Recombination
The McGraw Hill Companies, 2001
Twelve
DNA: Its Mutation, Repair, and Recombination
copies of the same protein nds the mismatch. MutL, also in the form of a homodimer, then binds, and together they nd the methylation signal.They also activate the endonuclease MutH, which then nicks the unmethylated strand at the 3 -CTAG-5 recognition site, which can be one thousand to two thousand bases away from the mismatch. At the recognition site, the MutS-MutL tetramer loads the helicase MutU (UvrD), which then unwinds the nicked strand. Any one of at least four different exonucleases then attacks the unwound oligonucleotide. DNA polymerase III then repairs the gap, and DNA ligase seals it.This sequence of events highlights a common theme in DNA repair: Once a lesion is found, the damaged DNA has some protein bound to it until the repair is nished. Our understanding of DNA damage and repair helps provide an answer to an evolutionary question Why does DNA have thymine while RNA has uracil If we live in an RNA world, in which RNA evolved rst, why don t DNA and RNA both contain uracil One answer is that a common damage to cytosine, spontaneous deamination, results in uracil. If uracil were a normal base in DNA, the conversion of cytosine to uracil by deamination would not leave any clue to a mismatch repair system that a mutation had occurred. Thus, thymine replaces uracil in DNA, since thymine is not confused with any other normal base in DNA by common spontaneous changes. In fact, cytosine, guanine, adenine, and thymine are not converted simply to any other of the bases in DNA. Hence, changes of these bases leave clues for the repair systems.
piece of DNA homologous to the broken piece. The method is very similar to our current model of DNA recombination and is discussed in the section entitled Recombination later in the chapter.
Postreplicative Repair
When DNA polymerase III encounters certain damage in E. coli, such as thymine dimers, it cannot proceed. Instead, the polymerase stops DNA synthesis and, leaving a gap, skips down the DNA to resume replication as far as eight hundred or more bases away. If allowed to remain, this gap will result in de cient and broken DNA. Since part of one strand is absent and the other has damage, there appears to be no viable template for replicating new DNA. However, the cell has two mechanisms to repair this gap: one uses polymerases that can replicate these lesions, and the other is a repair process that uses homologous DNA. Originally, several proteins were known to facilitate the replication of DNA with lesions; they were believed to interact with the polymerase to make it capable of using damaged DNA as a template. We now know that these proteins are, in fact, polymerases that have the ability to replicate damaged DNA. In E. coli, polymerase V can copy damaged DNA. In yeast, polymerases and , also called REV3/7 and RAD30 polymerases, respectively, can also copy damaged DNA. Some of these polymerases are relatively error free; polymerase V and polymerases put adenine-containing nucleotides opposite dimerized thymines. However, polymerases and the E. coli polymerase IV, which also appears during times of damage, are error prone in their replicative roles. One possible reason for this is that the error-prone polymerases developed by evolutionary processes: They create mutations at a time when the cell might need variability. That is, DNA damage can occur when the environment is stressful for the cell; variability might help the cell survive. As we will see later, the cell can sense DNA damage and act appropriately. In addition to using repair polymerases, the cell can use a second repair mechanism to replicate damaged DNA when the polymerase leaves a gap. A replication fork creates two DNA duplexes. Thus, an undamaged copy of the region with the lesion exists on the other daughter duplex. A group of enzymes, with one speci ed by the recA locus having central importance, repairs the gap. Since the repair takes place at a gap created by the failure of DNA replication, the process is called postreplicative repair. The recA locus was originally discovered and named in the recombination process. In fact, postreplicative repair is sometimes called recombinational repair, and it shares many enzymes with recombination.
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