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DNA repair mechanisms
©2000 written by Gary Roberts, edited by Timothy Paustian, University of Wisconins-Madison
III C. DNA REPAIR MECHANISMS
There are a number of enzyme systems in the cell that perform damage to DNA. Some of these are specific for a particular type of damage (e.g. a particular base modification) while other can handle a range of mutation types. These systems also differ in the degree to which they are able to restore the wild-type sequence. The following lists some of the best describe categories of repair systems:
Photoreactivation (utilizing near UV light as well as an appropriate enzyme system) is specific for pyrimidine dimers formed by UV. It is error-free because it merely breaks the pyrimidine dimer and restores the wild-type sequence. (It is therefore prudent, if one wishes to mutagenize cells with UV, to wrap the cells in some opaque wrapper following exposure to UV to avoid photoreactivation.)
Nucleotide excision repair also works on base dimers. It involves an endonucleolytic cleavage near the dimer, followed by a polymerase which cuts out the thymine dimer with a 5'-3' exonucleolytic activity. This polymerase (the polA gene product) simultaneously synthesizes an appropriate matching strand. This system and photoreactivation share the property that they both function effectively when they are able to repair the dimer before a replication fork comes to that dimer. If a growing fork or replication fork comes upon a thymine dimer before repair, one gets a large stretch of single-stranded DNA on the strand opposite the dimer.
Recombination repair (or post-replication repair) repairs damage by a strand exchange from the other daughter chromosome. Since it involves homologous recombination, it is largely error- free. It has been argued that this may be the predominant reason for the very existence of recsystems (and you probably thought it was just so we could do genetics!)
Base excision repair allows the identification and excision of aberrant bases, typically due to deamination of normal bases, but also from chemical modification.
Mismatch repair is a multi-enzyme system that recognizes inappropriately matched bases in DNA and replaces one of the two bases with one that "matches" the other. The major problem this system has to face is how to recognize which of the mismatched bases is the incorrect one (and therefore which one to excise and replace). E. coli figures this out using a sequence specific DNA methylation system:
During replication, only one strand (the old one) is already methylated so that the new and old strands can be discriminated. An endonucleolytic attack can then take place on the new, unmethylated strand allowing removal of the incorrectly incorporated base (and everything else between the mutant site and the methylation site!). The "half-sites" on the new strand are modified subsequently. The error need not be in the immediate vicinity of the methylation site, but rather the methylation system simply allows discrimination between old and new DNA strands.
Adaptive/inducible repair describes several protein activities that recognize very specific modified bases, typically methylated, and transfers the modifying group from the DNA to themselves. In doing so, they destroy their own function and are therefore not enzymes. They are inducible since they tend to be negative regulators of their own synthesis, so exposure to modifying agents induces more synthesis and therefore adaptation.
SOS repair or inducible error-prone repair is induced by single-stranded gaps and/or the presence of DNA degradation products. This system is capable of replication opposite thymine dimers or apurinic sites and apparently does so by putting in most any base. It therefore causes a very broad spectrum of mutations, including duplications and deletions. This system is often the cause of mutations following either chemical or UV mutagenesis. Obviously such a repair system must be a desperate recourse for the cell, allowing replication past a region where the wild-type sequence has been "lost".
Other repair systems are less well understood but some seem to be specific for certain mismatches. What is known about these systems has generally been found through the analysis of mutators (see below). This is presumably because they lack an error-prone repair system, so that they never "mutagenize" themselves in response to UV damage.
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