DNA replication plays an important role in cellular growth and development. It is a semi-discontinuous process of duplicating the DNA molecules. However, some undesirable events happen in the cell leading to errors in DNA replication. Hence, the cells have internal DNA damage repair mechanisms for protecting the DNA from getting degraded. The cell employs many enzymes in repairing the damaged DNA. Not all the damage gets repaired. In some cases, the cell becomes inefficient in repairing the damage (cancer). Certain mutations damage the DNA including spontaneous and induced mutations.
Direct reversal of DNA damage:
DNA damage occurs mostly during enzymatic proofreading during the process of replication or gets damaged due to physical or chemical agents. The most damaging physical agent includes UV rays. These rays produce thymine dimers or other pyrimidine dimers. Chemical agents such as base modifying agents, alkylating agents modify the bases or transfer alkyl groups to the bases. The direct reversal mechanisms of the DNA repair involve repair of the errors during replication or damage done by physical or chemical agents.
Mismatch repair:
It involves a mechanism in repairing the damage done during DNA polymerase proofreading. During the new strand synthesis, DNA polymerase sometimes goes wrong in inserting the nucleotides. The role of DNA polymerase also involves proofreading the mismatched bases and acts in 3’to 5’ direction. In this way, DNA polymerase corrects the wrong bases inserted into the DNA. The exonuclease proofreading activity helps in reducing the mutation rates in the cell. UV induced pyrimidine dimers get repaired through light repair mechanisms. The process of repairing pyrimidine dimers is known as photoreactivation. The process involves reverting them to their original form using near-UV light with a wavelength of 320-370 nm. An enzyme known as photolyase gets activated in this process. Photolyase is a product of phr gene. It gets activated by the light and helps in reverting the dimers to their original form. Chemical agents such as alkylating agents mostly induce damage to the DNA. Repair of alkylation damage also involves certain enzymes. Alkylating agents transfer the alkyl groups to various bases. For example, E. coli cells employ an enzyme known as an O6-methylguanine methyltransferase for repairing alkylation damage. An ADA gene encodes this enzyme. It removes the methyl group and changes the base to its original form.
Image 1: Mismatch repair
Base excision repair:
The damaged bases get removed through repair mechanisms for inserting the correct bases. It also recognizes regions that do not show bulkiness. An enzyme known as repair glycosylase recognizes the damaged base. Next, it removes the base from the DNA by cleaving the bond between the base and the deoxyribose sugar.
Nucleotide excision repair:
It helps in removing the UV induced DNA damage. UV light induces bulky DNA adducts such as thymine dimers and 6,4-photoproducts. NER pathway removes the region consisting of the lesion. The undamaged DNA strand acts as a template for synthesizing new strand. Consider the NER system in E coli. It involves uvr mutants (UV repair mutants). The NER system involves four main proteins such as UvrA, UvrB, UvrC, and UvrD. The first step involves scanning the damaged DNA. First, the Uvr A and Uvr B form a complex known as a UvrAB complex. This complex serves in finding the damage. The UvrA gets released. Now, comes the role of UvrC. Next step involves cleavage at 5’ (done by UvrC) and 3’(done by UvrB) sites of the damage. UvrB gets released facilitating the binding of Uvr D. Uvr D unwinds the region between the cuts since it acts as a helicase enzyme. An enzyme known as DNA polymerase helps in the gap filling process. Ligating enzyme finally ligates the gaps.
An autosomal recessive disorder known as Xeroderma pigmentosum affects the repair mechanisms involved in UV induced DNA damage. It leads to sensitivity to the sunlight and causes malignancies. Another disease known as Fanconi anemia is an autosomal recessive disease affecting the repair mechanisms involved in UV induced thymine dimers. It involves changes in the skin pigmentation, malformations of heart and limbs, genital defects, and anemia.
Image 2: Nucleotide excision repair
Methyl-directed mismatch repair:
First, it recognizes a mismatch, excises the incorrect base and then repairs it. Genes involved in this type of repair mechanism include mutS, mutL, and mutH genes. The products of these genes help in mismatch repair. In E coli, the GATC sequence gets methylated at the adenine base position. The parental strand has a methylated A in its GATC sequence. However, after replication, the daughter strand does not have a methylated A at the GATC sequence. First, the MutS protein binds to the mismatch. Then, it forms a complex with MutL and MutH. It helps in bringing the unmethylated GATC sequence near to the mismatch. MutH nicks the unmethylated GATC. The exonuclease helps in removing the mismatch. Finally, the DNA gets ligated. Humans have similar genes involved in mismatch repair. An E coli mutS homolog known as hMSH2 is present in humans. Similarly, hMLH1, hPMS1, and hPMS2 genes have homologies to E coli mutL gene. Loss of function of such genes results in mutator genes causing uncontrolled accumulation of mutations in the genome. Hereditary non-polyposis colon cancer is an autosomal dominant disorder. It affects the mismatch repair.
SOS system:
Sometimes the cell allows replication past the lesions in case of emergency. This kind of DNA damage activates SOS response mechanisms. It allows the cell to survive in the lethal mutations. Genes such as lexA and recA contribute to the SOS repair mechanisms. The gene known as lexA encodes a protein which helps in repressing the transcription of the genes involved in the process of DNA damage. The gene known as rexA encodes a protein. Both the protein products are known as LexA and Rec A proteins respectively. The RecA protein activates the LexA protein cleavage and helps in enhancing the transcription of DNA repair genes. One of the repair genes encodes for a DNA polymerase enzyme which helps in the translesion DNA synthesis. SOS system is more related to mutagenesis than repair. It helps pass the lesion and replicates the strand across from the lesion.
References:
[1] DNA Repair and Mutagenesis, edited by Errol C. Friedberg
[2] DNA Repair Mechanisms, Philip Hanawalt
[3] DNA Damage Recognition, Wolfram Siede, Paul W. Doetsch
[4] Molecular Biology of the Cell, Bruce Alberts
[5] Cell And Molecular Biology, S. C. Rastogi
[1] DNA Repair and Mutagenesis, edited by Errol C. Friedberg
[2] DNA Repair Mechanisms, Philip Hanawalt
[3] DNA Damage Recognition, Wolfram Siede, Paul W. Doetsch
[4] Molecular Biology of the Cell, Bruce Alberts
[5] Cell And Molecular Biology, S. C. Rastogi
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