DNA Repair

DNA is  most important molecule for working of cell. Although it directly not take part in metabolic pathways, but it keep information safe to generate proteins those take part in metabolic pathways. It is DNA which carry such information to next generation to work cell normally. 

During replication, as it is a fast process and cell DNA might be long enough, some time some mistakes are made during making its copies. Or there might be some external factors, influence of them may change the DNA sequence at the time of replication. A microorganism must be able to repair changes in the sequence that might be lethal.

DNA is repaired by several different mechanisms beside proofreading by replication enzymes (DNA polymerases can remove an incorrect nucleotide immediately after its addition to the growing end of the chain).

E.coli DNA or replication is most studied and best understood.

Excision Repair

Excision repair corrects damage that causes distortions in the double helix. Two type of excision repair system have been described: nucleotide excision repair and base excision repair. they are distinguished by the enzymes used to correct DNA damage. However, they both do the same work: remove the damage portion of DNA strand and use the intact complementary strand as the template for synthesis of new DNA.

In Nucleotide excision repair, a repair enzyme called UvrABC endonuclease removes damaged bases and some bases on either side of the lesion. This result in single stranded gap, about 12 nucleotides long, is filled by DNA polymerase I, and DNA ligand joins the fragments. This system can remove thymine diners and repair almost any other injury that produces a detectable distortion in DNA.

Base excision repair employs DNA glycosylases to remove damaged or unnatural bases. Special endonucleases called AP endonucleases recognize the damaged DNA and nick the backbone at the APsite. DNA polymerase I removes the damaged region, using its 5’ to 3’ exonuclease activity. It then fill the gap, and DNA ligand joins the DNA fragments.

Direct Repair

Thymine dimmer and alkylated bases often are corrected by direct repair. Photoreactivation is the repair of thymine diners by splitting them apart into separate thymines with the help of visible light in a photochemical reaction catalyzed by the enzyme photolyase.

Mismatch Repair

Although DNA replication is very accurate in itself. But DNA polymerase and continual proofreading, errors still are made during DNA replication. Remaining mismatched bases are usually detected and repaired by mismatch repair system in E. coli. 

The mismatch correction enzyme MutS scans the newly replicated DNA for mismatched pair. Another enzyme MutH, 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 ligand.

Successful mismatch repair depends on the ability of enzymes to distinguish between old and new strand of DNA. 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. DNA methylation is catalyzed by DNA methyltransferases.

Recombinational Repair

This repair system corrects damaged DNA in which both bases of a pair are missing or damaged, or where there is a gap opposite a lesion. In this type of repair the RecA protein cuts a piece of template DNA from a sister molecule and puts it into the gap or uses it to replace a damaged strand. Although procaryotes are haploid, another copy of the damaged segment often is available because wither 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 SOS Response

Despite having multiple repair systems, sometimes the damage to an organism’s DNA is so great that the normal repair mechanisms just described cannot repair all the damage. As a result, DNA synthesis stops completely. In such situations, a global control network called the SOS response is activated. The SOS response, like recombinational repair, is dependent on the activity of the RecA protein. 

RecA binds to single or double stranded DNA  breaks and gaps generated by cessation of DNA synthesis. RecA binding initiates recombinantional repair. Simultaneously, RecA takes on a proteolytic function that destroys a repressor protein called LexA.  LexA negatively regulates the function of many genes involved in DNA repair and synthesis.

Reference: Prescott Microbiology