NUCLEOTIDE EXCISION REPAIR PATHWAY

Major DNA repair pathways:

• Nucleotide excision repair (NER)-- deals with broad class of helix –distorting lesions that disrupt transcription and replication

• Base excision repair (BER)-- deals with small chemical alterations of bases. Particularly relevant for preventing mutation.

• Double-strand break (DSB) repair—Homologous recombination (HR) and Nonhomologous end-joining (NHEJ)

• Mismatch repair (MMR)– corrects replication errors, and can repair alkylated bases.

Excision repair directly replaces damaged DNA and then re-synthesizes a replacement stretch for the damaged strand.

WHAT IS NER?! NUCLEOTIDE EXCISION REPAIR (NER) is a

versatile repair pathway, involved in the removal of a variety of bulky DNA lesions such as UV induced cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PP). NER is a complex process in which basically the following steps can be distinguished:

recognition of a DNA lesion; separation of the double helix at the DNA lesion site; single strand incision at both sides of the lesion; excision of the lesion-containing single stranded DNA

fragment; DNA repair synthesis to replace the gap and ligation of the remaining single stranded nick.

The NER pathway involves at least 28 genes. Three NER genes are also part of the basal transcription factor, TFIIH. Mutations in 11 NER genes have been associated with clinical diseases with at least eight overlapping phenotypes.

NER is involved in protection against sunlight-induced DNA damage.

Several of the genes involved in NER also affect somatic growth and development.

Patients with the rare genetic disorders, xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS) have defects in DNA nucleotide excision repair (NER).

The clinical features of these patients have some similarities but also have marked differences. While XP patients have 1000-fold increase in susceptibility to skin cancer, TTD and CS patients have normal skin cancer risk. Some patients have short stature and immature sexual development. TTD patients have sulfur deficient brittle hair. Progressive sensorineural deafness is an early feature of XP and CS. Many of these clinical diseases are associated with developmental delay and progressive neurological degeneration. The main neuropathology of XP is a primary neuronal degeneration. In contrast, CS and TTD patients have reduced myelination of the brain. These complex neurological abnormalities are not related to sunlight exposure but may be caused by developmental defects as well as faulty repair of DNA damage to neuronal cells induced by oxidative metabolism or other endogenous processes.

Excision Repair Systems in E. coli

The UVR system makes incisions ~12 bases apart on both sides of damaged DNA, removes the DNA between them, and re-synthesizes new DNA.

incision : an endonuclease recognizes the damaged area in the DNA, and isolates it by cutting the DNA strand on both sides of the damage. excision : a 5’-3’ exonuclease removes a stretch of the damaged strand.

Excision repair systems vary in their specificity, but share the same general features. Each system removes impaired or damaged bases from DNA and then synthesizes a new stretch of DNA to replace them.

Excision-repair removes and replaces a stretch of DNA that includes the damaged base(s).

The UVR system operates in stages in which UVRAB recognizes damage, UVRBC nicks the DNA, and UVRD unwinds the marked region. (The UVR system of excision repair includes three genes, UVRA, B, and C, which code for the components of a repair endonuclease. UVRD is a helicase. In almost all (99%) of cases, the average length of replaced DNA is ∼12 nucleotides (short-patch repair).

Excision-Repair Pathways in Mammalian Cells

Mammalian excision repair is triggered by directly removing a damaged base from DNA. Base removal triggers the removal and replacement of a stretch of polynucleotides. The nature of the base removal reaction determines which of two pathways for excision repair is activated. The polδ/ε pathway replaces a long polynucleotide stretch; the polβ pathway replaces a short stretch.

The general principle of excision-repair in mammalian cells is similar to that of bacteria. The process usually starts in a different way, however, with the removal of an individual damaged base. Enzymes that remove bases from DNA are called glycosylases and lyases.

IN A NUTSHELL!!

1. Damage recognition

2. Local unwinding

3. Strand dual incision

4. Repair synthesis and strand ligation

5. Repaired DNA

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