Nucleotide excision repair defects

Figure 36-24. Nucleotide excision-repair. This mechanism is employed to correct larger defects in DNA and generally involves more proteins than either mismatch or base excision-repair. After defect recognition (indicated by XXXX) and unwinding of the DNA encompassing the defect, an excision nuclease (exinucle-ase) cuts the DNA upstream and downstream of the defective region. This gap is then filled in by a polymerase (5/e in humans) and religated.

CSB/ERCC6 CSB Human Associates with a subset of Pol II complexes Mutation causes Cockayne syndrome, a defect in transcription coupled nucleotide excision repair [321,322]. Human Rad26p homolog... 

The repair of stalled replication forks entails a coordinated transition from replication to recombination and back to replication. The recombination steps function to fill the DNA gap or rejoin the broken DNA branch to recreate the branched DNA structure at the replication fork. Lesions left behind in what is now duplex DNA are repaired by pathways such as base-excision or nucleotide-excision repair. Thus a wide range of enzymes encompassing every aspect of DNA metabolism ultimately take part in the repair of a stalled replication fork. This type of repair process is clearly a primary function of the homologous recombination system of every cell, and defects in recombinational DNA repair play an important role in human disease (Box 25-1). 

Excision repair. The E. coli mismatch repair is a type of excision repair. However, a different nucleotide excision repair system (NER) is utilized by all organisms from bacteria to human to remove a variety of defects. These include thymine dimers, photohydrates, oxidized bases, adducts of cisplatin (Box 5-B), mutagens derived from polycyclic aromatic compounds,683 and poorly recognized OC mismatched pairs.692 In E. coli this excision repair process depends upon proteins encoded by genes UvrA, B, C, and D and also DNA polymerase I and DNA ligase.693 695a A dimer of protein UvrA forms a complex with helicase UvrB (Eq. 27-22).696 696a... 

While defects in protein XPD often cause typical XP symptoms, some defects in the same protein lead to trichothiodystrophy (TTD, brittle hair disease). The hair is sulfur deficient, and scaly skin (ichthyosis, Box 8-F), mental retardation, and other symptoms are observed.0 Like their yeast counterparts (proteins RAD3 and RAD25), XPB and XPD are both DNA helicases.0 They also constitute distinct subunits of the human transcription factor TFIIHP, which is discussed in Chapter 28. It seems likely that XPD is involved in transcription-coupled repair (TCR) of DNA.° °i-s This is a subpathway of the nucleotide excision repair (NER) pathway, which allows for rapid repair of the transcribed strand of DNA. This is important in tissues such as skin, where the global NER process may be too slow to keep up with the need for rapid protein synthesis. Transcription-coupled repair also appears to depend upon proteins CSA and CSB, defects which may result in the rare cockayne syndrome.13 0 4 11 Patients are not only photosensitive but have severe mental and physical retardation including skeletal defects and a wizened appearance. 

Kim, N., Kage, K., Matsuda, F., Lefranc, M.-P., Storb, U. (1997). B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes. J. Exp. Med. 186,413-419. 

Although the molecular defect of XPV is very different from that of the other XP patients (XPA, XPB, XPC, XPD, XPE, XPF, and XPG), who are deficient in nucleotide excision repair, the clinical manifestations of the diseases are quite similar. This is not surprising because the defect in either Polq or nucleotide excision repair results in a common problem genomic overload of TT dimers and perhaps other CPDs for error-prone translesion synthesis by other bypass polymerases during replication. The result is predictable elevated cytotoxicity and mutagenesis induced by the UV component of the sunlight, which constitute the cellular bases of XP diseases. 

The importance of the repair of damaged DNA in keeping the cells alive and preventing cancer is also apparent from mutations in genes involved in nucleotide excision repair. The enzymes involved in nucleotide excision repair are other tools that cells have to repair mismatched DNA. Defects in DNA nucleotide excision repair can cause skin cancer (xeroderma pigmentosa) and colon cancer. 

The DNA lesion 8,5 -cyclo-2 -dG, formed by attack of hydroxyl radicals, contains damage to both base and sugar, and is therefore repaired by nucleotide excision repair enzymes, and is involved in diseases with defective nucleotide excision repair. A mass spectroscopic assay has been developed for the quantitation of the lesion after enzymatic separation of the 5 (R) and 5 (S) isomers. The thermodynamic stability of ODNs containing the oxidative lesion, 2-hydroxy-dA has been examined. It was shown that when the lesion was in the middle of a DNA duplex it behaved as a universal base, in that there was no dilference in Tm when opposite any of the canonical bases. On the other hand, when it was near the termini, there was a preference for base pairing with thymidine, but it also formed base pairs with other nucleotides which was sequence dependent. The extent of oxoprenylation by malondialdehyde or adenine propenal has been investigated in DNA, see (139). ssDNA was found to be more sensitive to oxoprenylation, and supercoiled-DNA more susceptible than linearised plasmid DNA. A variety of intercalators were used, some of which inhibit oxoprenylation, e.g. netropsin, whilst others, like ethidium bromide, caused enhanced oxoprenylation. 

DNA repair, some associated with skin cancer19. Such disorders result from defects in nucleotide excision repair and are all genetically complex, with involvement of multiple genes. Here again, the Xiphophorus model offers a potential means of unraveling each of the many steps involved in these complex molecular events that underpin multifactorial phenotypes. 

Inherited defects in the nucleotide excision-repair pathway, as in individuals with xeroderma pigmentosum, predispose them to skin cancer. Inherited colon cancer frequently is associated with mutant forms of proteins essential for the mismatch repair pathway. 

Nucleotide excision repair involves the removal of "bulky" lesions in DNA such as thymine dimers. The human genetic disease xeroderma pigmentosum is the result of defects in nucleotide excision repair proteins. 

Nucleotide-excision repair is common for DNA lesions caused by ultraviolet or chemical means, which often lead to deformed DNA structures. Figure 10.16 demonstrates how a large section of DNA containing the lesion is removed by ABC excinuclease. DNA polymerase I and DNA ligase then work to fill in the gap. This type of repair is also the most common repair for ultraviolet damage in mammals. Defects in DNA repair mechanisms can have drastic consequences. One of the most remarkable examples is the disease xeroderma pigmentosum. Affected individuals develop numerous skin cancers at an early age because... 

A defect in nucleotide excision repair causes extreme ultraviolet (UV) sensitivity in E. coli and Saccharomyces cerevisiae. In humans, defects in... 

Roche, H. R., Gietz, R. D., and Kunz, B. A. (1994). Specificity of the rev3CS antimutator and EEV3 dependency of the mutator resulting from a defect (radlA) in nucleotide excision repair. Genetics 137, 637-646. 

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