Concept
To prevent that DNA damage and errors remain in the cell, having serious consequences or being passed on to offspring, the cell has several mechanisms that correct errors and maintain genome integrity, called DNA repair mechanisms. Both eukaryotes and prokaryotes have these mechanisms.
The importance of DNA repair
DNA is the basis of the entire structure of an organism, whether eukaryotic or prokaryotic, making it the key to the storage of all genetic information, in evolution and development. Although it is necessary that occur genetic variation for the evolution of the species, taking into account the importance of DNA, is known that the genome of organisms must be stable for survival and cannot undergo major changes. However, DNA is daily and constantly subject to modifications, such as errors occurring during replication and damage induced by exposure to radiation and mutagens present in the environment, which if not corrected can lead to mutations. To protect its DNA against daily aggressions and maintain genome integrity, cells have developed mechanisms capable of correcting these modifications, which are known as DNA repair mechanisms. These mechanisms have been extensively studied in E. coli which has made possible the knowledge of its steps and the enzymes involved.
DNA repair mechanisms can be divided into two broad groups: those involving the repair of errors or damage that occur in only one of the double-helix DNA strands (DNA polymerase repair, mismatch repair, DNA excision base repair and repair by nucleotide excision) and those involving repair of damage occurring in both the double-helix DNA strands (non-homologous junction and homologous recombination).
Mechanisms of DNA repair
DNA polymerase
Many errors occur during DNA replication (insertion of 1 wrong base in every 104 bases added in bacteria), these errors are automatically corrected by the intrinsic proof-reading ability of DNA polymerase. This feature provides the DNA polymerase with the ability to recognize an incorrectly copied base, go back in the strand, and replace the wrong base with the correct base.
Mismatch
Mismatch errors that persist after replication are fixed by mismatch repair. In these errors only one basis is involved which is not correct according to the rule of complementarity of bases – hence the term mismatch. The mechanism of repair of these errors is based on the detection of the mismatched base, its removal and the addition of the correct base by the DNA polymerase, that use the other DNA strand as a template. In the end, the DNA ligase closes the DNA strand.
Base excision
Bases that have been subject to deamination, alkylation or oxidation are fixed by base excision repair. In this mechanism, specific enzymes, called exonucleases, recognize the base that is damaged and catalyze its hydrolytic removal. Then a repair DNA polymerase uses the other DNA strand which is undamaged as template and does the correct replication of the base. To conclude the process, the DNA ligase promotes the formation of the phosphodiester bond between the bases and the double DNA helix is complete and error-free.
Nucleotide excision
DNA damage caused by covalent reactions with carcinogens and by thymine dimers caused by UV rays (the most common DNA damage) are repaired by nucleotide excision. In this repair pathway a complex formed by several enzymes (including exonucleases) looks for DNA double-helix distortions and, when found it, cleaves the DNA strand containing the distortion and remove it (an oligonucleotide) through the action of the DNA helicase. Subsequently, a repair DNA polymerase fills the space with the non-cleaved and undamaged strand as template and a DNA ligase promotes formation of the phosphodiester linkage in order to close the fixed strand.
Junction of non-homologous ends
Ionizing radiation, oxidizing agents and some metabolic products are responsible for DNA double-strand breaks. These damaged, which damage both DNA double-helix strands, are quite dangerous since no strand remains to serve as a template. For this type of damaged, the repair by junction of non-homologous ends is the simplest and occurs through the junction of the free left ends by the damage, which are reunited and linked. One of the disadvantage of this mechanism is that bases are lost and are not recovered again, which can lead to information losses. On the other hand, it has the advantage that it can be activated rapidly by the cell at any stage of the cell cycle, being predominant in multicellular organisms, and functions as an emergency mechanism for the repair of double-strand breaks.
Homologous recombination
Another way of repairing double strand breaks in DNA is by homologous recombination. This mechanism is based on the existence of homologous chromosomes in the cell, which means that there are two copies of each double-helix strand. The repair occurs through the ‘invasion’ of the homologous chromosome that has not been damaged by the damaged double-helix. An enzyme complex is responsible for finding complementarity zones and for directing the non-injured homologous chromosome to near the damaged chromosome. Each chain then uses its complementary as template, the DNA polymerase synthesizes the new strand, and the DNA ligase closes them. At the end, the homologous chromosomes separate and the chromosome that was damaged is fixed, with no loss of information or changes in the DNA sequence.
Consequences of non-repair of DNA
If lesions or mismatches are not rectified, serious consequences may occur in the cell, such as mutations, changes in the three-dimensional structure of DNA, protein synthesis without function or deficient function, among many others. It is known that, ultimately, DNA damage or changes in its sequence lead to the development of tumors.
References:
Alberts B., Johnson A., Lewis J., Raff M., Keith R., Walter P. (2007). Molecular Biology of the Cell (5th edition). Garland Science, New York.
Cooper G.M. (2000). The Cell: A Molecular Approach (2nd edition). Sinauer Associates, Sunderland (MA).
Griffiths A.J.F., Miller J.H., Suzuki D.T., Lewontin R.C., Gelbart W.M. (2000). An Introduction to Genetic Analysis (7th edition). W. H. Freeman, New York.
Lodish H., Berk A., Zipursky S.L., Matsudaira P., Baltimore D., Darnell J. (2000). Molecular Cell Biology (4th edition). W. H. Freeman, New York.
