Excision Repair
EXCISION REPAIR MECHANISMS
• Fixes replication errors missed by DNA Pol proofreading (cannot repair damage)
Base excision repair
• Damaged bases removed and replaced
• Deamination & depurination (most common spontaneous damages)
• Alkylation (except for O6-alkyl guanine)
• Oxidation
Nucleotide excision repair
• Damaged nucleotides removed and replaced
• 2 types: global genomic NER (transcriptionally inactive) & transcription-coupled
• Repairs wider variety of lesions that distort DNA helix
• Pyrimidine dimers and other intrastrand adducts
• Bulky group addition (via carcinogen-exposure)
BASE EXCISION REPAIR
• Model: cytosine spontaneously deaminates to uracil
1. DNA glycosylase excises uracil: cleaves N-glycosidic bond between base & deoxyribose
• Produces apyrimidinic site (AP site)
2. AP endonuclease cleaves deoxyribose backbone adjacent to AP site
• Excises deoxyribose moiety
3. DNA polymerase and ligase fill/seal gap with cytosine
• Prokaryotes: DNA Pol. I
• Eukaryotes: DNA Pol. beta
NUCLEOTIDE EXCISION REPAIR
• Model: thymine dimer in E. Coli (prokaryotes)
Global genomic NER: transcriptionally inactive region
• Uvr genes: discovered in E. Coli, mutations conferred extreme UV light sensitivity
1. UvrA recognizes helical distortion as damage
2. UvrA recruits uvrB and uvrC
Intertextual variation exists for above step.
3. Uvr B and C cleave DNA on either side of damage
• Uvr ABC complex: excinuclease
4. Helicase unwinds DNA and releases damaged segment
5. DNA polymerase fills gap and ligase seals it
• DNA Pol. fills gap in 5' to 3' direction
• Prokaryotes: DNA Pol. I
• Eukaryotes: DNA Pol. delta and epsilon
Transcription-coupled NER: transcriptionally active region
• Repairs more rapidly than global genomic pathway
1. NER enzymes recognize RNA polymerase stalled by lesion and displace it
• E. Coli: NER enzymes are Mfd proteins
• Humans: RNA polymerase II (prokaryotes only have one RNA Pol.) & CS proteins
2. Mfd proteins (E. Coli) and CS proteins (humans) recruit other proteins to site
• E. Coli: Mfd proteins recruit uvr proteins
• Humans: CS proteins recruit more CS and XP proteins (amongst others)
3. Recruited proteins cleave and excise damaged oligomer
4. Identical to Step 5 in global genomic pathway
CLINICAL CORRELATION
Xeroderma pigmentosum (XP)
• Rare genetic defect produces dysfunctional XP proteins
• Patients extremely sensitive to UV light: develop skin cancers in sun-exposed areas