Mechanisms of Disease: DNA Repair Defects and Neurological Disease

Kalluri Subba Rao

Disclosures

Nat Clin Pract Neurol. 2007;3(3):162-172. 

In This Article

DNA Repair Pathways in Mammalian Cells

The mammalian DNA repair process has evolved over time into a number of complex pathways to cope with all of the alterations that can occur to the structure of DNA. The past 30 years have seen a great advancement in our understanding of the various DNA repair pathways, both in prokaryotes and in higher organisms. An updated inventory of about 150 human DNA repair genes was recently compiled by Wood et al.,[3] and excellent reviews have also appeared in recent times regarding our current knowledge of the DNA repair pathways in eukaryotes,[1,2,4,5,6,7,8] of which two have dealt specifically with DNA repair pathways in the brain.[1,8] In mammalian cells there are at least four major pathways: first, a simple reversal of the damage; second, nucleotide excision repair (NER), including mismatch and transcription-coupled repair; third, base excision repair (BER); and last, recombination repair including nonhomologous end joining.

Bacterial photolysis activity is an example of direct reversal of DNA damage. In this repair system an enzyme, with the help of light, monomerizes the pyrimidine dimers in DNA. It is not clear, however, whether a comparable process occurs in humans, so this mode of repair will not be discussed further here.

Excision Repair Pathways

The excision repair pathway is the predominant, and perhaps universal, mechanism for the maintenance of genomic integrity. This pathway is responsible for repairing a wide variety of DNA lesions, ranging from simple base methylations, to interstrand adduct formation that results in major distortion of the DNA structure. The basic process involved in this pathway consists of four steps: first, recognition and demarcation of the damaged site; second, excision of the damaged portion of DNA and certain adjacent sequences; third, resynthesis of the excised portion using the second strand as a template; and last, ligation of the newly synthesized portion to the existing downstream sequence. As knowledge of the excision repair pathway increased, it became clear that it can be viewed as two distinct streams—NER and BER.

Nucleotide Excision Repair. NER is a multistep process[9] that seems to come into operation to repair such DNA damage as the distinct helical distortion caused by ultraviolet-induced photoproducts. At least 20–30 proteins are involved in the pathway in a sequential manner, and an outline of the pathway is given in Figure 1. The first step involves damage recognition and demarcation, and requires, possibly among many other factors, three proteins—the xeroderma pigmentosum complementing proteins DDB1 (XPE) and XPC, and RD23B–centrin 2. The second step involves the simultaneous arrival of the DNA excision repair proteins ERCC5 (XPG; 3'-endonuclease) and ERCC4 (XPF; 5'-endonuclease complexed with excision repair cross-complementing protein 1), resulting in a dual incision on either side of the damage and removal of an oligonucleotide consisting of around 29 nucleotides. In the third step, the lengthy gap created by removal of the damage-harboring portion is resynthesized using the other strand as a template. In the final step, the newly synthesized portion is ligated to complete the repair process, yielding the repaired DNA product.

Figure 1.

An outline of the nucleotide excision repair pathway, which includes global genomic repair (1B) and transcription-coupled repair (1A). The damaged base in the DNA is indicated by a green star. In global genomic repair, the damage is recognized by the heterotrimeric complex of XPC, RD23B and centrin 2, whereas when the damage is in a gene that is being actively transcribed by RNA pol II, the Cockayne's syndrome factors ERCC8 and ERCC6 have a crucial role in stalling the transcription process so that repair of the transcribed gene can be initiated. From this point onwards, the repair pathway is common to both mechanisms, and it proceeds by recruiting several other factors, as shown in (2), to effect unwinding, bubble formation of the strand harboring the damage, incision of the strand at discrete points on the 5' and 3' sides, and excision of the fragment containing the damage. The size of the bubble will depend on the nature of damage, which in turn is likely to determine the incision points for the removal of the damaged portion. In step (3), the gap created by the excision of the damaged strand is resynthesized by DNA pol δ/ε, with the help of auxiliary factors such as PCNA and RPA–RFC. Finally, DNA ligase I ligates the newly synthesized fragment to the downstream strand to complete the repair process and yield the repaired product (4). Abbreviations: DDB1, xeroderma pigmentosum E; ERCC1, DNA excision repair protein ERCC-1; ERCC2–5, excision repair complementing factors (formerly known as XPD/XPB/XPF/XPG); ERCC6/8, Cockayne's syndrome factor B/A; PCNA, proliferating cell nuclear antigen; pol δ/ε, polymerase δ/ε; RD23B, RAD23 homolog B (Saccharomyces cerevisiae); RFC, replication factor C; RNA pol II, RNA polymerase II; RPA, replication protein A; XPA, xeroderma pigmentosum A; XPC, xeroderma pigmentosum C.

The mechanism described above can repair damage to any part of the genome. There is, however, an alternative NER pathway that can be used in the early stage of the recognition process to preferentially recognize and repair damage in a genomic area where transcription is occurring simultaneously. This type of NER repair, which is termed transcription-coupled repair, was first described by Bohr et al.,[10] and subsequently gained clinical importance.[11] It is not yet completely clear how damage in a gene that is being transcribed is preferentially recognized and repaired, although it seems that the factor involved in general recognition of the damage, XPC, is dispensable for transcription-coupled repair.[12] Interestingly, Mu and Sancar[13] have shown that damage recognition and initiation of repair can be mediated by certain other factors, by blocking RNA polymerase II and dissociating it from the DNA strand to allow repair to proceed first. A role for the Cockayne's syndrome genes ERCC8 (CSA) and ERCC6 (CSB) is envisaged in this function (Figure 1).[9]

Mismatch repair is responsible for correcting mismatches, such as guanine–thymine nucleotide pairs. Mismatches can result from many factors, including replication errors, spontaneous deamination of bases, oxidation, methylation, and homologous recombination intermediates. Depending on the individual situation, mismatch repair seems to be instigated not only through NER, but also through the other DNA repair pathways such as BER and homologous recombination.[14] Indeed, in the brain, the main pathway for mismatch repair is thought to be BER, although many other proteins involved in NER are also found in this organ.[8]

Base excision repair. BER is perhaps the most fundamental and ubiquitous DNA repair mechanism in all higher organisms that depend on oxygen for the sustenance of life. This pathway has evolved to handle the numerous minor alterations—including spontaneous modification, oxidation, deamination and loss of bases—that can occur in the structure of DNA as a result of cellular metabolic activity. This mode of repair is of particular importance in postmitotic tissues such as those of the brain, where simple base modifications are more likely to occur than is major damage to DNA. An outline of the BER pathway, including the two subpathways known as the short-patch and long-patch repair pathways, is shown in Figure 2. For a more detailed discussion of the BER pathway, the reader is referred to recent reviews.[1,15,16,17]

Figure 2.

Outline of base excision repair showing the two subpathways: (A) the 'short-patch' or single-nucleotide pathway, and (B) the 'long-patch' pathway. Crossing over of the pathways can occur at points (3) and (9). As with nucleotide excision repair, there are essentially four steps in the base excision repair pathway. First, when an altered base is detected (1) the surveillance glycosylases remove that base (2). Next, the endonuclease that is specific for an apurinic or apyrimidinic site cleaves the strand on the 5' side of the abasic site (3). This is followed by filling in of the gap with a correct nucleotide by DNA pol β, and at the same time releasing the dRP (4). Finally, DNA ligase III ligates the newly introduced nucleotide with the downstream sequence (5), thereby restoring the repaired DNA (6). There are several variations in this process that depend on the nature of the abasic site and the size of the gap to be filled. Sometimes, other DNA polymerases such as DNA polymerase δ or ε, along with PCNA, are involved in filling larger sized gaps, also in a strand-displacement manner (long-patch repair [B]; steps 7–12). A more detailed discussion than that supplied in the main text can be obtained from recent review articles[1,15,16,17] It has recently been suggested that one of the several newly discovered DNA polymerases, DNA polymerase λ, has similar properties to that of pol β and might participate in base excision repair.[61] Abbreviations: APE1, human apurinic/apyrimidinic endonuclease 1; DB, damaged base; dNTPs, deoxynucleoside triphosphates; dRP, deoxyribose 5'-phosphate; FEN1, flap structure-specific endonuclease 1; gly, DNA glycosylase; lig I/III, DNA ligase I/III; PARP1, poly (ADP-ribose) polymerase 1; PCNA, proliferating cell nuclear antigen; PNKP, polynucleotide kinase 3'-phosphatase; pol β/δ/ε, DNA polymerase β/δ/ε; WRN, Werner syndrome ATP-dependent helicase; XRCC1, X-ray repair cross-complementing protein 1. Permission obtained from Elsevier B.V. © Rao KS (2006) DNA repair in aging rat neurons. Neuroscience [doi:10.1016/j.neuroscience.2006.09.032].

Recombination Repair Pathways

Damage to DNA that occurs in the form of a double-strand break, for instance as a result of ionizing radiation or chemicals that induce interstrand and intrastrand cross-links, eliminates the possibility of using one of the strands as a template for the repair process. Such damage is therefore addressed by recombination repair.[18,19] Recombination repair is of two types: homologous recombination and nonhomologous end joining. Homologous recombination is a complex and poorly understood process that involves using an intact homologous DNA strand as a template to repair a double-strand break. Nonhomologous end joining, by contrast, involves religation of the broken ends without any regard to homology, and is consequently relatively error-prone,[7] but it is nevertheless a major pathway for double-strand-break repair in mammalian cells and is thought to be of vital importance in postmitotic tissue. Indeed, the existence of this activity in adult as well as aging brain cells has been demonstrated.[20,21] Finally, a new dimension has been added to our understanding of the DNA repair mechanisms in mammalian cells, with the discovery of a number of novel DNA polymerases that have the capacity to carry out DNA synthesis across a damaged or altered base; this process is known as translesion synthesis.[22,23] These polymerases have differing substrate specificities, enabling them to deal with many different types of damaged bases.

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