Repair systems correct damage to DNA

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Repair systems correct damage to DNA

A structural distortion is a change in the conformation of DNA caused by bases or base pairs that do not fit into the normal duplex.
A pyrimidine dimer is formed when ultraviolet irradiation generates a covalent link directly between two adjacent pyrimidine bases in DNA. It blocks DNA replication and transcription.
Photoreactivation uses a white-light-dependent enzyme to split cyclobutane pyrimidine dimers formed by ultraviolet light.
Mismatch repair corrects recently inserted bases that do not pair properly. The process preferentially corrects the sequence of the daughter strand by distinguishing the daughter strand and parental strand, sometimes on the basis of their states of methylation.
Excision repair describes a type of repair system in which one strand of DNA is directly excised and then replaced by resynthesis using the complementary strand as template.
Recombination-repair is a mode of filling a gap in one strand of duplex DNA by retrieving a homologous single strand from another duplex.
Error-prone synthesis occurs when DNA incorporates noncomplementary bases into the daughter strand.

Repair systems recognize DNA sequences that do not conform to standard base pairs.
Excision systems remove one strand of DNA at the site of damage and then replace it.
Recombination-repair systems use recombination to replace the double-stranded region that has been damaged.
All these systems are prone to introducing errors during the repair process.
Photoreactivation is a nonmutagenic repair system that acts specifically on pyrimidine dimers.

Any event that introduces a deviation from the usual double-helical structure of DNA is a threat to the genetic constitution of the cell. We can divide such changes into two general classes:

Figure 15.32

Deamination of cytosine creates a U-G base pair. Uracil is preferentially removed from the mismatched pair.

Figure 15.33

A replication error creates a mismatched pair that may be corrected by replacing one base; if uncorrected, a mutation is fixed in one daughter duplex.

Figure 15.34

Ultraviolet irradiation causes dimer formation between adjacent thymines. The dimer blocks replication and transcription.

Figure 15.35

Methylation of a base distorts the double helix and causes mispairing at replication.

Figure 15.36

Depurination removes a base from DNA, blocking replication and transcription.

Single base changes affect the sequence but not the overall structure of DNA. They do not affect transcription or replication, when the strands of the DNA duplex are separated. So these changes exert their damaging effects on future generations through the consequences of the change in DNA sequence. The cause of this type of effect is the conversion of one base into another that is not properly paired with the partner base. They may be happen as the result of mutation of a base in situ or by replication errors. Figure 15.32 shows that deamination of cytosine to uracil (spontaneously or by chemical mutagen) creates a mismatched U•G pair. Figure 15.33 shows that a replication error might insert adenine instead of cytosine to create an A•G pair. Similar consequences could result from covalent addition of a small group to a base that modifies its ability to base pair. These changes may result in very minor structural distortion (as in the case of a U•G pair) or quite significant change (as in the case of an A•G pair), but the common feature is that the mismatch persists only until the next replication. So only limited time is available to repair the damage before it is fixed by replication.
Structural distortion s may provide a physical impediment to replication or transcription. Introduction of covalent links between bases on one strand of DNA or between bases on opposite strands inhibits replication and transcription. Figure 15.34 shows the example of ultraviolet irradiation, which introduces covalent bonds between two adjacent thymine bases, giving an intrastrand pyrimidine dimer. Figure 15.35 shows that similar consequences could result from addition of a bulky adduct to a base that distorts the structure of the double helix. A single-strand nick or the removal of a base, as shown in Figure 15.36, prevents a strand from serving as a proper template for synthesis of RNA or DNA. The common feature in all these changes is that the damaged adduct remains in the DNA, continuing to cause structural problems and/or induce mutations, until it is removed.

Injury to DNA is minimized by systems that recognize and correct the damage. The repair systems are as complex as the replication apparatus itself, which indicates their importance for the survival of the cell. When a repair system reverses a change to DNA, there is no consequence. But a mutation may result when it fails to do so. The measured rate of mutation reflects a balance between the number of damaging events occurring in DNA and the number that have been corrected (or miscorrected).

Figure 15.37

Repair genes can be classified into pathways that use different mechanisms to reverse or bypass damage to DNA.

Repair systems often can recognize a range of distortions in DNA as signals for action, and a cell is likely to have several systems able to deal with DNA damage. The importance of DNA repair in eukaryotes is indicated by the identification of >130 repair genes in the human genome (for review see 2398). We may divide them into several general types (for review see 5849). Figure 15.37 summarizes the types of pathways:

Some enzymes directly reverse specific sorts of damage to DNA.
Pathways that function by removing damaged material include base excision repair, nucleotide excision repair, and mismatch repair.
Some systems function by using recombination to retrieve an undamaged copy that then replaces a damaged duplex sequence.
The nonhomologous end-joining pathway rejoins broken double-stranded ends.
Several different DNA polymerases that may be involved in resynthesizing stretches of replacement DNA.

Direct repair is rare and involves the reversal or simple removal of the damage. Photoreactivation of pyrimidine dimers, in which the offending covalent bonds are reversed by a light-dependent enzyme, is a good example. This system is widespread in nature, and appears to be especially important in plants. In E. coli it depends on the product of a single gene (phr) that codes for an enzyme called photolyase.

Mismatches between the strands of DNA are one of the major targets for repair systems. Mismatch repair is accomplished by scrutinizing DNA for apposed bases that do not pair properly. Mismatches that arise during replication are corrected by distinguishing between the "new" and "old" strands and preferentially correcting the sequence of the newly synthesized strand. Mismatches also occur when hybrid DNA is created during recombination, and their correction upsets the ratio of parental alleles (see Figure 15.18). Other systems deal with mismatches generated by base conversions, such as the result of deamination. The importance of these systems is emphasized by the fact that cancer is caused in human populations by mutation of genes related to those involved in mismatch repair in yeast.

Mismatches are usually corrected by excision repair, which is initiated by a recognition enzyme that sees an actual damaged base or a change in the spatial path of DNA. There are two types of excision repair system.

Figure 15.38

Excision-repair directly replaces damaged DNA and then resynthesizes a replacement stretch for the damaged strand.

Base excision repair systems directly remove the damaged base and replace it in DNA. A good example is DNA uracil glycolase, which removes uracils that are mispaired with guanines (see Base flipping is used by methylases and glycosylases).
Nucleotide excision repair systems excise a sequence that includes the damaged base(s); then a new stretch of DNA is synthesized to replace the excised material. Figure 15.38 summarizes the main events in the operation of such a system. Such systems are common. Some recognize general damage to DNA. Others act upon specific types of base damage. There are often multiple excision repair systems in a single cell type.

Recombination-repair systems handle situations in which damage remains in a daughter molecule, and replication has been forced to bypass the site, typically creating a gap in the daughter strand. A retrieval system uses recombination to obtain another copy of the sequence from an undamaged source; the copy is then used to repair the gap.

A major feature in recombination and repair is the need to handle double-strand breaks. DSBs initiate crossovers in homologous recombination. They can also be created by problems in replication, when they may trigger the use of recombination-repair systems. When DSBs are created by environmental damage (for example, by radiation damage) or because of the shortening of telomeres (see Genetic instability is a key event in cancer), they can cause mutations. One system for handling DSBs can join together nonhomologous DNA ends.

Mutations that affect the ability of E. coli cells to engage in DNA repair fall into groups, which correspond to several repair pathways (not necessarily all independent). The major known pathways are the uvr excision repair system, the methyl-directed mismatch-repair system, and the recB and recF recombination and recombination-repair pathways. The enzyme activities associated with these systems are endonucleases and exonucleases (important in removing damaged DNA), resolvases (endonucleases that act specifically on recombinant junctions), helicases to unwind DNA, and DNA polymerases to synthesize new DNA. Some of these enzyme activities are unique to particular repair pathways, but others participate in multiple pathways.

The replication apparatus devotes a lot of attention to quality control. DNA polymerases use proofreading to check the daughter strand sequence and to remove errors. Some of the repair systems are less accurate when they synthesize DNA to replace damaged material. For this reason, these systems have been known historically as error-prone systems.

When the repair systems are eliminated, cells become exceedingly sensitive to ultraviolet irradiation. The introduction of UV-induced damage has been a major test for repair systems, and so in assessing their activities and relative efficiencies, we should remember that the emphasis might be different if another damaged adduct were studied.

Last Revised on March 25, 2005

2398 Wood, R. D., Mitchell, M., Sgouros, J., and Lindahl, T. (2001). Human DNA repair genes. Science 291, 1284-1289. PubMed Journal
5849 Sancar, A., Lindsey-Boltz, L. A., Unsal-Kaçmaz, K., and Linn, S. (2004). Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 73, 39-85. PubMed

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