DNA Repair Mechanisms
Since replication errors and a variety of mutagens can alter the nucleotide sequence, a microorganism must be able to repair changes in the sequence that might be fatal. DNA is repaired by several different mechanisms besides proofreading by replication enzymes (DNA polymerases can remove an incorrect nucleotide immediately after its addition to the growing end of the chain).
It is a general repair system that corrects damage which causes distortions in the double helix. A repair endonuclease or uvrABC endonuclease removes the damaged bases alongwith some bases on either side of the lesion. This system also removes thymine dimers and repair almost any other injury that produces a detectable distortion in DNA.
Besides this general excision repair system, specialized versions of the system excise specific sites on the DNA where the sugar phosphate backbone is intact but the bases have been removed to form apurinic or apyrimidinic sites (AP sites). Special endonucleases called AP endonucleases recognize these locations and nick the backbone at the site. Excision repair then commences, beginning with the excision of a short stretch of nucleotides.
Another type of excision repair employs DNA glycosylases. These enzymes remove damaged or unnatural bases yielding AP sites that are then repaired as just described.
Removal of Lesions
Thymine dimmers and alkylated bases often are directly repaired. Photoreactivation is the repair of thymine dimmers by splitting them apart into separate thymines with the help of visible light in a photochemical reaction catalyzed by the enzyme photolyase. Because this repair mechanism does not remove and replace nucleotides, it is error free.
Methyls and some other alkyl groups that have been added to the O-6 position of guanine can be removed with the help of an enzyme known as alkyltransferase or methylguanine methyltransferase. Thus damage to guanine from mutagens such as methyl nitrosoguanidine can be repaired directly.
Despite the accuracy of DNA polymerase action and continual proofreading, errors still are made during DNA replication. Remaining mismatched bases and other errors are usually detected and repaired by the mismatch repair system in E.coli. The mismatch correction enzyme scans the newly replicated DNA for mismatched pairs and removes a stretch of newly synthesized DNA around the mismatch. A DNA polymerase then replaces the excised nucleotides, and the resulting nick is sealed with a ligase. Post-replication repair is a type of excision repair.
Successful post replication repair depends on the ability of enzymes to distinguish between old and newly replicated DNA strands. This distinction is possible because newly replicated DNA strands lack methyl groups on their bases whereas older DNA has methyl groups on the bases of both strands.
In recombination repair, damaged DNA for which there is no remaining template is restored. This situation arises if both bases of a pair are missing or damaged, or if there is a gap opposite a lesion. In this type of repair, the recA protein cuts a piece of template of DNA from a sister molecule and puts it into the gap or uses it to replace a damaged strand. Although bacteria are haploid, another copy of the damaged segment often is available because either it has recently been replicated or the cell is growing rapidly and has more than one copy of its chromosome. Once the template is in place, the remaining damage can be corrected by another repair system.
The recA protein also participates in a type of inducible repair known as SOS repair. In this instance, the DNA damage is so great that synthesis stops completely, leaving many large gaps. RecA will bind to the gaps and initiate strand exchange. Simultaneously it takes on a proteolytic function that destroys the lexA repressor protein, which regulates the function of many genes involved in DNA repair and synthesis. As a result, many more copies of these enzymes are produced, accelerating the replication and repair processes. The system can quickly repair extensive damage caused by agents such as UV radiation, but it is error prone and does produce mutations. However, it is extremely better to have a few mutations than no DNA replication at all.
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