What is DNA repair?

DNA Structure and DNA Damage

All living things are continually exposed to agents that can damage their genetic material. Damage to or mutations in DNA can occur as a result of ionizing radiation, from assault by mutagenic chemicals, or as a by-product of other cellular processes, such as failure of the DNA mismatch repair (DMMR) pathway. As DNA is the blueprint for directing the functions of the cell, it must be accurately maintained. The integrity of DNA is also important because daughter cells receive copies of a parent cell’s DNA during mitosis. DNA damage can include a break in a DNA molecule, the abnormal bonding of two nucleotides, or by the attaching or removal of a chemical group to or from a nucleotide. Mutations typically occur as a result of a copying error and can follow from DNA damage. To a bacterial cell, DNA damage may mean death. To a multicellular organism, damaged DNA in some of its cells may mean loss of function of organs or tissues or it may lead to cancer.

DNA is assembled from nucleotides, each defined by the base it contains. If the DNA double helix is pictured as a twisted ladder, the outside supports, sometimes referred to as the “backbone” of the DNA, are composed of alternating phosphates and ribose sugars. The “rungs” of the ladder are bases. Four bases are found in DNA: the double-ring purines, adenine and guanine, and the single-ring pyrimidines, cytosine and thymine. The structure of each base makes two base pairings most likely. In James Watson and Francis Crick’s model of DNA, adenine pairs with thymine, and cytosine pairs with guanine. This base pairing holds the two strands of the double helix together and is essential for the synthesis of new DNA molecules (DNA replication) and for the transfer of information from DNA to RNA in the process of transcription. DNA replication is carried out by an enzyme called DNA polymerase, which reads the information (the sequence of bases) on a single strand of DNA, brings the appropriate nucleotide to pair with the template strand one nucleotide at a time, and joins it to the end of the new DNA chain. Transcription occurs through a process similar to DNA replication, except that a RNA polymerase copies only the portion of one DNA strand which codes for a gene, making an RNA copy. The RNA can be used as a template for synthesizing a particular protein, which is the final product of most genes.

One frequent form of DNA damage is the loss of a base. Purines are particularly unstable, and many are lost each day in human cells. If a base is absent, the DNA cannot be copied correctly during DNA replication. Another common type of DNA damage is a pyrimidine dimer, an abnormal linkage between two cytosines, two thymines, or a cytosine and an adjacent thymine in a DNA strand. These are caused by the absorption of ultraviolet light by the two bases. A pyrimidine dimer creates a distortion in the double helix that interferes with the processes of DNA replication and transcription. Another form of DNA damage is a break in the backbone of one or both strands of the double helix. Breaks can block DNA replication, create problems during cell division, or cause rearrangements in the chromosomes. DNA replication itself can cause problems by inserting an incorrect base or an additional or too few bases in a new strand. While DNA replication errors are not DNA damage as such, they can also lead to mutations and are subject to repair.

DNA Repair Systems

DNA repair systems are found in most organisms. Even some viruses, such as bacteriophages (viruses which infect bacteria) and herpes viruses (which infect animals), are capable of repairing some damage to their genetic material. The DNA repair systems of single-celled organisms, including bacteria and yeasts, have been extensively studied for many years. Techniques including the use of recombinant DNA methods revealed that DNA repair systems of multicellular organisms such as humans, animals, and plants are quite similar to those of microorganisms.

Scientists generally classify DNA repair systems into three categories on the basis of complexity, mechanism, and the fate of the damaged DNA. “Damage reversal” systems are the simplest: They usually require only a single enzyme to directly act on the damage and restore it to normal, usually in a single step. “Damage removal” systems are somewhat more complicated: These involve cutting out and replacing a damaged or inappropriate base or section of nucleotides and require several proteins to act together in a series of steps. “Damage tolerance” systems are those that respond to and act on damaged DNA but do not actually repair the original damage. Instead, they are ways for cells to cope with DNA damage in order to continue growth and division.

Damage Reversal Systems

Photoreactivation is one of the simplest and perhaps oldest known repair systems: it consists of a single enzyme that can split pyrimidine dimers in the presence of light. An enzyme called photolyase catalyzes this reaction; it is found in many bacteria, lower eukaryotes, insects, and plants but seems to be absent in mammals (including humans). A similar gene is present in mammals but may code for a protein that functions in another type of repair.

X-rays and some chemicals, such as peroxides, can cause breaks in the backbone of DNA. Simple breaks in one strand are rapidly repaired by the enzyme DNA ligase. Mutant strains of microorganisms with reduced DNA ligase activity tend to have high levels of recombination since DNA ends are very “sticky” and readily join with any other fragment of DNA. While recombination is important in generating genetic diversity during sexual reproduction, it can also be dangerous if DNA molecules are joined inappropriately. The result can be aberrant chromosomes that do not function properly.

Damage Removal Systems

Damage removal systems are accurate and efficient but require the action of several enzymes and are more energetically “expensive” to the cell. There are three types of damage removal systems that work in the same general way but act on different forms of DNA damage. In base excision repair, an enzyme called a DNA glycosylase recognizes a specific damaged or inappropriate base and cuts the base-sugar linkage to remove the base. The backbone then is cut by another protein (an endonuclease) that removes the baseless sugar, and a new nucleotide is inserted to replace the damaged one by a DNA polymerase enzyme. The remaining break in the backbone is reconnected by DNA ligase. There are a number of specific glycosylases for particular types of DNA damage caused by radiation and chemicals.

The nucleotide excision repair system works on DNA damage that is “bulky” and that creates a block to DNA replication and transcription, such as ultraviolet-induced pyrimidine dimers and some kinds of DNA damage created by chemicals. It probably does not recognize a specific abnormal structure but sees a distortion in the double helix. Several proteins joined in a complex scan the DNA for helix distortions. When one is found, the complex binds to the damage and creates two cuts in the DNA strand containing the damaged bases on either side of the damage. The short segment with the damaged bases (around thirty nucleotides in humans) is removed from the double helix, leaving a short gap that can be filled by DNA polymerase using the intact nucleotides in the other DNA strand as a guide. In the last step, DNA ligase rejoins the strand. Mutants that are defective in nucleotide excision repair have been isolated in many organisms and are extremely sensitive to mutation by ultraviolet light and similar-acting chemical mutagens.

Mismatch repair occurs during DNA replication as a last “spell check” on its accuracy. By comparing mutation rates in
Escherichia coli
bacteria that either have or lack mismatch repair systems, scientists have estimated that this process adds between one hundred and one thousand times more accuracy to the replication process. It is carried out by a group of proteins that can scan DNA and look for incorrectly paired bases (or unpaired bases). The incorrect nucleotide is removed as part of a short stretch, and then a DNA polymerase attempts to insert the correct sequence. In 1993, Richard Fishel, Bert Vogelstein, and their colleagues isolated the first genes for human mismatch repair proteins and showed that they are very similar to those of the bacterium Escherichia coli and the simple eukaryote baker’s yeast. Further studies in the 1990s revealed that mismatch repair genes are defective in people with hereditary forms of colon cancer.

Nucleotide Excision Repair: Xeroderma Pigmentosum

Humans with the hereditary disease xeroderma pigmentosum (XP)
are extremely sensitive to ultraviolet light and are at nearly a 100 percent risk of skin cancer in their lifetime. XP results when a child inherits genetic defects in the nucleotide excision repair system (NER) from both parents. Studies have shown that XP patients often are born to parents who share a common ancestor. This remote inbreeding is also referred to as consanguinity. These children often begin to exhibit symptoms of XP between the ages of one and two. The affected are often hypersensitive to light and are prone to sunburn, skin, and eye defects, such as cataracts. Eight different forms of the disease, labeled A through G and V, correspond to mutations in different components of the NER system. Rates of XP presentation vary, but have been estimated at 1 in 1 million in the United States, according to 2014 data from the US National Library of Medicine.

Variation in symptoms depends on the function of the specific NER system protein affected. Functions of specific NER system proteins implicated in XP fit within two NER subtypes, known as transcription-coupled repair (TCR), which works on damage in the genome undergoing transcription, and global genome repair (GGR), which works on damage in the entire genome and is slower than TCR. Recognition of damage in GGR occurs through XPC and DDB1 complexes. Recognition events in TCR and GGR activate unwinding of DNA through the ERCC2 and ERCC3 helicases. Subsequently, XPA binds and presents binding sites for the XPG
nuclease and ERCC1-ERCC4 nuclease complex. Mutations in these specific genes generally lead to the corresponding form of XP, though mutations in other proteins that form complexes with XP proteins can lead to XP, such as the mutation in DDB2. The variant form of XP is the result of a mutation in DNA polymerase eta, also called hRAD30, which is not a part of the NER system, but functions after DNA replication. DNA polymerase eta is able to bypass many forms of DNA lesions that would stop the main DNA polymerase complex.

Of the eight forms of XP, mutations in genes found only in GGR, such as XPC, DDB1, and DNA polymerase eta produce the fewest symptoms beyond an increased risk of cancer. However, mutations in one or more of the other components of TCR can produce more complicated arrays of symptoms, including neurodegenerative and developmental disorders.

Damage Tolerance Systems

Not all DNA damage is or can be removed immediately; some of it may persist for a time. If a DNA replication complex encounters DNA damage such as a pyrimidine dimer, it will normally act as a block to further replication of that DNA molecule. In eukaryotes, however, DNA replication initiates at multiple sites and may be able to resume downstream of a damage site, leaving a “gap” of single-stranded, unreplicated DNA in one of the two daughter molecules. The daughter-strand gap is potentially just as dangerous as the original damage site, if not more so. The reason for this is that if the cell divides with a gap in a DNA molecule, there will be no way accurately to repair that gap or the damage in one of its two daughter cells. To avoid this problem, cells have developed a way to repair daughter-strand gaps by recombination with an intact molecule of identical or similar sequence. The recombinational repair process, which requires a number of proteins, yields two intact daughter molecules, one of which still contains the original DNA damage. In addition to dealing with daughter-strand gaps, recombinational repair systems can also repair single- and double-strand breaks caused by the action of x-rays and certain chemicals on DNA. Many of the proteins required for recombinational repair are also involved in the genetic recombination that occurs in meiosis, the process which produces sperm and egg cells in organisms which reproduce sexually. In 1997, it was shown that the products of the breast cancer susceptibility genes BRCA1
and BRCA2 participate in both recombinational repair and meiotic recombination.

An alternative choice for a DNA polymerase blocked at a DNA damage site is to change its specificity so that it can insert any nucleotide opposite the normally nonreadable damage and continue DNA replication. This type of “damage bypass” is very likely to cause a mutation, but if the cell cannot replicate its DNA, it will not be able to divide. In Escherichia coli bacteria, there is a set of genes that are turned on when the bacteria have received a large amount of DNA damage. Some of these gene products alter the DNA polymerase and allow damage bypass. This system has been termed the SOS response to indicate that it is a system of last resort. Other organisms, including humans, seem to have similar damage bypass mechanisms that allow a cell to continue growth despite DNA damage at the price of mutations. For this reason, damage bypass systems are sometimes referred to as error-prone or mutagenic repair systems.

Impact and Applications

DNA repair systems are an important component of the metabolism of cells. Studies in microorganisms have shown that as little as one unrepaired site of DNA damage per cell can be lethal or lead to permanent changes in the genetic material. The integrity of DNA is normally maintained by an elaborate series of interrelated checks and surveillance systems. The greatly increased risk of cancer suffered by humans with hereditary defects in DNA repair shows how important these systems are in avoiding genetic changes. As the relationship between genes and cancer susceptibility becomes clearer, this information may be used in directing the course of cancer therapy and possibly in providing gene therapy for cancer.

In 2015, Tomas Lindahl, Paul Modrich, and Aziz Sancar won the Nobel Prize in Chemistry for their work on mapping DNA repair mechanisms. Lindahl has studied base excision repair, Modrich mismatch repair, and Sancar nucleotide excision repair. The Nobel Foundation honored the three scientists because their insights into DNA repair could be used to develop new cancer treatments.

Key Terms




base


:

the component of a nucleotide that gives it its identity and special properties





nucleotide


:

the basic unit of DNA, consisting of a five-carbon sugar, a nitrogen-containing base, and a phosphate group





Bibliography

Dizdaroglu, Miral, and Ali Esat Karakaya, eds. Advances in DNA Damage and Repair: Oxygen Radical Effects, Cellular Protection, and Biological Consequences. New York: Plenum, 1999. Print.

Fernholm, Ann. DNA Repair—Providing Chemical Stability for Life. Trans. Peter Wennersten. Stockholm: Royal Swedish Academy of Sciences, 2015. PDF file.

Fischman, Josh. "Discovery of DNA Repair Methods Nails 2015 Chemistry Nobel Prize." Scientific American. Scientific American, 7 Oct. 2015. Web. 2 Nov. 2015.

Gilchrest, Barbara A., and Vilhelm A. Bohr, eds. The Role of DNA Damage and Repair in Cell Aging. New York: Elsevier, 2001. Print.

Haber, James. Genome Stability: DNA Repair and Recombination. New York: Garland, 2014. Print.

Hartl, Daniel L. Essential Genetics: A Genomics Perspective. 6th ed. Burlington: Jones, 2014. Print.

Henderson, Daryl S., ed. DNA Repair Protocols. 2nd ed. Totowa: Humana, 2005. Print.

Mills, Kevin D. Silencing, Heterochromatin, and DNA Double Strand Break Repair. Boston: Kluwer Academic, 2001. Print.

Sancar, Aziz, Laura A. Lindsey-Boltz, Keziban Unsal-Kacmaz, and Stuart Linn. “Molecular Mechanisms of Mammalian DNA Repair and the DNA Damage Checkpoints.” Annual Review of Biochemistry 73 (2004): 39–85. Print.

Smith, Paul J., and Christopher J. Jones, eds. DNA Recombination and Repair. New York: Oxford UP, 1999. Print.

Strachan, Tom, Judith Goodship, and Patrick Chinnery. Genetics and Genomics in Medicine. New York: Garland, 2015. Print.

Vaughan, Pat, ed. DNA Repair Protocols: Prokaryotic Systems. Totowa: Humana, 2000. Print.

"Xeroderma Pigmentosum." Genetics Home Reference. National Library of Medicine, 21 July 2014. Web. 25 July 2014.