Dna Damage and Repair

Mammalian cells can make use of a variety of DNA repair pathways. An overview of these is presented in Figure 3. Most studies over the years have been based on the assumption that the DNA repair pathways listed were confined to the removal of specific lesions within certain categories. For example, nucleotide excision repair (NER) was the system that removed bulky lesions in DNA that dramatically changed the DNA structure. In contrast, base excision repair (BER) was the process responsible for the removal of simple lesions in DNA, which are considered to cause only small structural changes in DNA and may not represent major blocks to transcription and replication. This concept has changed somewhat in recent years as it has become evident that many of the DNA repair pathways listed in Figure 3 are overlapping and share components. Thus, although it is useful to think of repair pathways as confined to the removal of different types of DNA lesions, that distinction is of limited validity. It would be much too ambitious to review all the pathways listed in Figure 3. Two of the most predominant pathways are NER and BER, and these will be discussed in more detail. The mismatch repair pathway is of particular interest in relation to cancer.

In general terms, the DNA repair process consists of a number of steps that act in concert to accomplish the complete repair of DNA damage. The first step is the recognition of the DNA lesion, and this is accomplished by proteins that constantly survey the DNA for any unwanted Figure 2 Some consequences of DNA damage. Lesions in DNA can instigate a number of DNA related transactions, discussed in the text, that ultimately lead to genomic instability and other features of cancer and aging. SOURCE: Author modifications. In the next step, incision, enzymes are cut into the DNA to remove the damaged DNA base. This step is complex and involves many proteins. When the damaged base has been removed, there is a step of resynthesis, in which new DNA is made to replace that which was removed in the incision step. This is accomplished by proteins called DNA polymerases, and there are several kinds of these in each mammalian cell. Since the DNA damage was in one strand of DNA, the other strand has the information required to copy itself. After the DNA synthesis, there is a ligation process in which the gaps in the DNA are sealed and a new, intact double helix is formed.

Base excision repair. Base excision repair (BER) of oxidative DNA damage is initiated by DNA glycosylases, a class of enzymes that recognize and remove damaged bases from DNA by hydrolytic cleavage of the base-sugar bond, leaving an abasic site (AP site). There are at least two pathways for further processing of the AP site. One of these is catalyzed by AP endonuclease, and results in a single-nucleotide gap that is then filled and sealed.

An alternative pathway, long patch BER, has been reported. In addition to a DNA glycosylase and AP endonuclease, it also involves a single-strand flap structure that is recognized and excised, and then the DNA is ligated (Klugland and Lindahl). These repair events result in a repair patch two to seven nucleotides long. There has been much research activity in the BER area (see Krokan et al.; Friedberg et al.).

Nucleotide excision repair. Most of the understanding of the nucleotide excision repair (NER) pathway has come through the study of the human disorder xeroderma pigmentosum (XP). There are seven genetically different types of this disease, designated A–G. XP proteins are designated after the cell line in which they are Figure 3 Some of the major pathways of DNA repair in mammalian systems such as humans. These pathways can operate independently, but also are interactive. (TCR is the abbreviation for transcription coupled repair.) SOURCE: Author mutated (e.g., the XPA protein is the one mutated in XPA cells). The individuals afflicted with this condition suffer from high incidences of skin and internal cancers, hyperpigmentation, and premature aging (Friedburg et al.). Cells from XP patients cannot incise their DNA at a site of a UV-induced lesion, and thus are in general deficient in the incision process of NER. The enzymatic steps involved in NER are recognition of the lesion, incision of the DNA, excision of the damaged DNA template, resynthesis of new DNA based on the intact template, and ligation of the newly formed DNA repair patch into the reconstructed double helix. A number of reviews have discussed NER in much more detail (see, e.g., Friedberg).

Genomic heterogeneity of NER. A major advance in the study of DNA repair has been the insight that NER and possibly other repair pathways operate with considerable heterogeneity over the mammalian genome. The NER pathway can thus be subdivided into pathways relating to the functional and structural organization of the genome. Only about 1 percent of the genome is transcriptionally active, and a repair pathway called transcription coupled repair (TCR) operates here. The remainder of the genome, the 99 percent that is inactive, has a separate pathway, general genome repair (GGR). Much work has been dedicated to the further delineation and clarification of these pathways. For a more thorough review and discussion of the repair in genes, see Balajee and Bohr, which also discusses the human premature aging syndrome, Cockayne syndrome (CS), where TCR is deficient. CS is a rare and severe clinical condition in which patients appear to be much older than their chronological age. It is a premature aging disorder because many of the clinical signs and symptoms are those seen in the aging process in normal individuals.