Nucleotide excision repair steps

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). 

Figure 6 Nucleotide excision repair in (A) E. coli and (B) humans. There are five basic steps of nucieotide excision repair (1) damage recognition, (2) dual incisions, (3) release of the excised oligomer, (4) repair synthesis to fill in the gap, and (5) ligation.

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. 

Xeroderma pigmentation (XP) is an autosomal recessive human disease charactenzed by hypersensitivity to sunlight and a high incidence of skin cancer in sun-exposed area. XPA is a monomeric 31 kDa DNA-binding protem known to be involved in the damage recognition step of nucleotide excision repair processes. 

Fig. 1. Schematic illustration of nucleotide excision repair in prokaryotes and eukaryotes. The basic steps are conserved damage recognition and dual incisions to excise DNA damage, helicase activity to displace excised oligomer and repair factors, and resynthesis/ligation to restore the integrity of the DNA molecule. (See Color Insert.)...

Orren, D. K., Selby, C. P., Hearst, J. E., and Sancar, A. (1992). Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I. /. Biol. Chem. 267, 780-788. 

Figure 5 Base excision repair in mammalian cells. In base excision repair, the damaged nucleotide is removed in a two-step process. A glycosylase cleaves the glycosidic bond of the damaged base, releasing it, and then AP lyase and AP endonuclease cleave the phosphodlester bonds on either side of the abasic site, which releases the deoxyribose.

Nealon K, Nicholl ID, Kenny MK (1996) Characterization of the DNA polymerase requirement of human base excision repair. Nucleic Acids Res 24 3763-70 Dianov GL, Price A, Lindahl T (1992) Generation of single nucleotide repair patches following excision of uracil residues from DNA. Mol Cell Biol 12 1605-12 Singhal RK, Prasad R, Wilson SH (1995) DNA polymerase / conducts the gap-filling step in uracU-initiated base excision repair in a bovine testis nuclear extract. J Biol Chem 270 949-57... 

Base-excision repair involves the removal of nucleotides that have lost the base moiety as a result of depurination or by the action of DNA glycosylases (enzymes that remove abnormal bases such as deaminated cytosines). As in the other two repair systems, the first step is to remove the deoxyribose 5-phosphate through the action of an endonuclease and a phosphodiesterase which cleave the phosphate backbone and create a single nucleotide gap. 

Many DNA polymerases proofread the nascent product their 3 —> 5 exonuclease activity potentially edits the outcome of each polymerization step. A mispaired nucleotide is excised before the next step proceeds. In E. coli, DNA polymerase I repairs DNA and participates in replication. Fidelity is further enhanced by an induced fit that results in a catalytically active conformation only when the complex of enzyme, DNA, and correct dNTP is formed. Helicases prepare the way for DNA replication by using ATP hydrolysis to separate the strands of the double helix. 

---