nucleotide excision repair
Wednesday 19 November 2003
Definition: Nucleotide excision repair is a DNA repair mechanism. It is a process carried out by mammalian cells that involves the recognition, removal and resynthesis of the restored DNA following DNA damage by bulky lesions.
Nucleotide excision repair (NER) is one of several DNA repair mechanisms by which damaged bases are removed from the genome. The process incorporates the excision of such bases as part of an oligonucleotide fragment, in contrast to base excision repair (BER), by which damaged or inappropriate bases are excised as a free base, or mismatch repair (MMR), by which mispaired bases are excised as single nucleotides.
NER in human cells is a complex biochemical process that requires several proteins (See components). The human proteins required for NER assemble in an ordered, stepwise fashion at sites of base damage that are substrates for NER.
Studies in yeast, an informative model for many aspects of NER in humans, indicate that some of this complex might be preassembled in cells not deliberately exposed to DNA damage. However, the conclusions of these studies have proved controversial.
The repair complex is a versatile ’NER machine’ that can recognize many types of base damage that often bear little, if any, structural or chemical similarity, incise (nick) DNA at precise distances on either side of the base damage exclusively on the damaged DNA strand, and excise oligonucleotide fragments that include the base damage.
Eukaryotic cells can repair many types of DNA damage. Among the known DNA repair processes in humans, one type - nucleotide excision repair (NER) - specifically protects against mutations caused indirectly by environmental carcinogens. Humans with a hereditary defect in NER suffer from xeroderma pigmentosum and have a marked predisposition to skin cancer caused by sunlight exposure.
DNA constantly requires repair due to chemical damage that can occur to bases, and nucleotide excision repair (NER) and base excision repair (BER) are mechanisms by which the cell can prevent unwanted mutations caused by base damage.
While the base excision repair (BER) machinery recognizes specific lesions in the DNA and can correct only damaged bases that can be removed by a specific DNA glycosylase, the nucleotide excision repair enzymes recognize distortions in the shape of the DNA double helix.
Recognition of these distortions leads to the removal of a short single-stranded DNA segment that includes the lesion, creating a single-strand gap in the DNA, which is subsequently filled in by DNA polymerase, which uses the undamaged strand as a template.
Steps of the NER system
The essential features of nucleotide excision repair.
1. Nucleotide excision repair (NER) operates on base damage caused by exogenous agents (such as mutagenic and carcinogenic chemicals and photoproducts generated by sunlight exposure) that cause alterations in the chemistry and structure of the DNA duplex .
2. Such damage is recognized by a protein called XPC, which is stably bound to another protein called HHRAD23B.
3. The binding of the XPC-HHRAD23 heterodimeric subcomplex is followed by the binding of several other proteins, as XPA, RPA, TFIIH and XPG. XPA and RPA are believed to facilitate specific recognition of base damage. TFIIH is a subcomplex of the RNA polymerase II transcription initiation machinery which also operates during NER.
It consists of six subunits and contains two DNA helicase activities (XPB and XPD) that unwind the DNA duplex in the immediate vicinity of the base damage.
This local denaturation generates a bubble in the DNA, the ends of which comprise junctions between duplex and single-stranded DNA.
4. The subsequent binding of the ERCC1-XPF heterodimeric subcomplex generates a completely assembled NER multiprotein complex.
5. XPG is a duplex/single-stranded DNA endonuclease that cuts the damaged strand at such junctions 3’ to the site of base damage. Conversely, the ERCC1-XPF heterodimeric protein is a duplex/single-stranded DNA endonuclease that cuts the damaged strand at such junctions 5’ to the site of base damage.
This bimodal incision generates an oligonucleotide fragment 27-30 nucleotides in length which includes the damaged base.
6. This fragment is excised from the genome, concomitant with restoring the potential 27-30 nucleotide gap by repair synthesis. Repair synthesis requires DNA polymerases or , as well as the accessory replication proteins PCNA, RPA and RFC. The covalent integrity of the damaged strand is then restored by DNA ligase.
7. Collectively, these biochemical events return the damaged DNA to its native chemistry and configuration.
Mutations in genes on the nucleotide excision repair pathway (NER system) are associated with diseases, such as xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy, that involve skin cancer and developmental and neurological symptoms.
These mutations cause the defective repair of damaged DNA and increased transcription arrest but, except for skin cancer, the links between repair and disease have not been obvious.
Widely different clinical syndromes seem to result from mutations in the same gene, even when the mutations result in complete loss of function.
The mapping of mutations in recently solved protein structures has begun to clarify the links between the molecular defects and phenotypes, but the identification of additional sources of clinical variability is still necessary.
Nucleotide-excision repair diseases exhibit cancer, complex developmental disorders and neurodegeneration.
Cancer is the hallmark of xeroderma pigmentosum (XP), and neurodegeneration and developmental disorders are the hallmarks of Cockayne syndrome and trichothiodystrophy.
A distinguishing feature is that the DNA-repair or DNA-replication deficiencies of XP involve most of the genome, whereas the defects in CS are confined to actively transcribed genes.
Many of the proteins involved in repair are also components of dynamic multiprotein complexes, transcription factors, ubiquitylation cofactors and signal-transduction networks. Complex clinical phenotypes might therefore result from unanticipated effects on other genes and proteins.
The fact that these three different diseases (XP, CS and TTD) may be mutated in the same genes (as is the case of XPB, XPD and XPG) is intriguing.
The clinical symptoms of these genetic disorders are distinct specially concerning the increased frequency of skin tumors, observed in XP but not in CS or TTD patients.
These different symptoms may simply express differences in the abilities of the mutated cells to perform either DNA repair or transcription, depending on the mutation on the gene.
However, recent data have shone some light onto this very interesting question. Working with cells derived from XPG patients associated or not with CS, Cooper et al. (1997) have found evidence that the developmental CS defects may be due to a defective preferential repair of active genes by oxidative damage.
On the other hand, Ahrens et al. (1997) have found that the high risk of cancer in XPD patients may be due to a decreased immunological response to UVB irradiation, not found on cells from TTD patients (mutated in the same XPD gene).
The author propose that the XPD protein might have a transcriptional role controlling the expression of immunological relevant genes. Thus, mutations that affect this control (such as those found in XP patients, but not in TTD) may increase the skin cancer risk.
Pathology (nucelotide excision repair diseases)
In these diseases, the nucleotide-excision repair pathway (NER) does not remove UV-induced DNA lesions efficiently.
germline mutations in ERCC1 have been reported in (cerebrooculofacioskeletal syndrome 4) (cerebro-oculo-facio-skeletal syndrome 4) (COFS4). (17273966)
Jaspers NG, Raams A, Silengo MC, Wijgers N, Niedernhofer LJ, Robinson AR, Giglia-Mari G, Hoogstraten D, Kleijer WJ, Hoeijmakers JH, Vermeulen W. First reported patient with human ERCC1 deficiency has cerebro-oculo-facio-skeletal syndrome with a mild defect in nucleotide excision repair and severe developmental failure. Am J Hum Genet. 2007 Mar;80(3):457-66. PMID: 17273966
The NER pathway
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Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity. Cleaver JE, Lam ET, Revet I. Nat Rev Genet. 2009 Nov;10(11):756-68. PMID: 19809470
Cleaver JE. Cancer in xeroderma pigmentosum and related disorders of DNA repair. Nat Rev Cancer. 2005 Jul;5(7):564-73. PMID: 16069818
Bergmann E, Egly JM. Trichothiodystrophy, a transcription syndrome. Trends Genet. 2001 May;17(5):279-86. PMID: 11335038
de Boer J, Hoeijmakers JH. Nucleotide excision repair and human syndromes. Carcinogenesis. 2000 Mar;21(3):453-60. PMID: 10688865