1. Chen Yonggang Zhejiang Univ. School of Medicine Research Building C-616 Chenyg9@163.com A DNA Repair Overview

2. Excellent Review Articles Friedberg, EC (2003) DNA damage and repair. Nature 421:436-440. Sancar A, Lindsey-Boltz LA, Unsal- Kacmaz K, Linn S (2004) Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 73: 39-85.

3. Importance of Repair DNA is the only biological macromolecule that is repaired. All others are replaced. More than 100 genes are required for DNA repair, even in organisms with very small genomes. Cancer is a consequence of inadequate DNA repair.

4. DNA can be damaged by a variety of processes 1, Some spontaneously: deamination C U 2, Others catalyzed by enviromental agents a)UV light: dimer b)Chemicals: (1) deaminating agents (2) alkylating agents c) Oxidative damage: hydrogen peroxide, hydroxyl radicals, superoxide radicals

5. Spontaneous base loss: Several thousand purines and serval thousand pyrimidines per haploid genome per day! AP Site: apyrimidinic site or apurinic site

6. Spontaneous deamination: ~100 uracils per haploid genome per day. Also: Adenine to hypoxanthine Guanine to xanthine 5-methyl cytosine to thymine

7. “Reactive Oxygen Species” (ROS) include O, O-O, HOOH, OH ThymineThymine Glycol

8. Spontaneous production of 3-Methyl Adenine by S-Adenosylmethionine: Several hundred per haploid genome per day!

9. Effects of Sunlight: (photodamage) Cyclobutane pyrimidine dimers (CPDs) T-T>T-C, C-T>C-C DNA helix bends 7-9°

10. Effects of Sunlight: (photodamage) Pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) T-C>C-C>T-T>C-T DNA helix bends 44°

11. Some Additional Types of Damage: Replication errors Intra- and inter-strand crosslinks DNA-protein crosslinks Strand breaks

12. Types of DNA Repair  Direct repair(Direct reversal of damage)  Excision repair(Excision of damaged region, followed by precise replacement)  Recombination repair(strand break repair)  Damage bypass

13. An Example of Direct Repair: “Photoreactivation” MTHF or 8-HDF FADH -

14. Additional Examples of Direct Repair 6-4 photolyases Ligation of nicks

15. Excision Repair Takes advantage of the double-stranded (double information) nature of the DNA molecule.  Mismatch repair  Base excision repair  Nucleotide excision repair

16. Mismatch repair in E. coli Excision by UvrD (Helicase II and single- strand exonuclease) Gap filling by Polymerase I(in E. coli); Ligation by DNA ligase

19. Base Excision Repair

20. Several variations, depending on nature of damage, nature of glycosylase, and nature of DNA polymerase. All have in common the following steps: 1.Removal of the incorrect base by an appropriate DNA N-glycosylase to create an AP site. 2.An AP endonuclease nicks on the 5’ side of the AP site to generate a 3’-OH terminus. 3.Extension of the 3’-OH terminus by a DNA polymerase.

21. An example of a DNA N- glycosylase: Pinch-push-pull mechanism suggested by crystal structures of glycosylases.

22. Some DNA N- glycosylases have AP lyase activity.

23. Initial steps of base- excision repair

24. Final steps of base- excision repair (DNA polymerase β pathway; short patch repair

25. Final steps of base-excision repair (replication pathway)

26. Nucleotide Excision Repair Extremely flexible Corrects any damage that distorts the DNA molecule In all organisms, NER involves the following steps: 1.Damage recognition 2.Binding of a multi-protein complex at the damaged site 3.Double incision of the damaged strand several nucleotides away from the damaged site, on both the 5’ and 3’ sides 4.Removal of the damage-containing oligonucleotide from between the two nicks 5.Filling in of the resulting gap by a DNA polymerase 6.Ligation

27. S. cerevisiae proteinHuman proteinProbable function Rad4 XPCGGR (also required for TC-NER in yeast); works with HR23B; binds damaged DNA; recruits other NER proteins Rad23HR23BGGR; cooperates with XPC (see above); contains ubiquitin domain; interacts with proteasome and XPC Rad14XPABinds and stabilizes open complex; checks for damage Rpa1,2,3RPAp70,p32,p14Stabilizes open complex (with Rad14/XPA) Ssl2 (Rad25)XPB3' to 5' helicase Tfb1GTF2H1? Tfb2GTF2H4? Ssl1GTF2H2Zn finger; DNA binding? Tfb4GTF2H3Ring finger; DNA binding? Tfb5TFB5; TTD-AStabilization of TFIIH Rad3XPD5' to 3' helicase Tfb3/Rig2MAT1CDK assembly factor Kin28Cdk7CDK; C-terminal domain kinase; CAK Ccl1CycHCyclin Rad2XPGEndonuclease (3' incision); stabilizes full open complex Rad1XPFPart of endonuclease (5' incision) Rad10ERCC1Part of endonuclease (5' incision) Proteins Required for Eukaryotic Nucleotide Excision Repair

28. Nucleotide Excision Repair

29. Early Stages of Global Genome Repair

30. Initial Steps of Transcription-Coupled NER

31. Final Steps of Eukaryotic NER

32. Some of the proteins required for eukaryotic NER S. CerevisiaeHuman ProteinProbable function Rad 4XPCGGR (also required for TC-NER in yeast; works with HR23B; binds damaged DNA; recruits other NER proteins Rad 23HR23BGGR: cooperates with XPC; contains ubiquitin domain; interacts with proteasome and XPC Rad 14XPABinds and stabilizes open complex; checks for damage Rpa1, 2, 3RPA p70, p32, p14Stabilizes open complex (with Rad14/XPA) Ssl2 (Rad25)XPB3’ to 5’ helicase Tfb1GTF2H1? Tfb2GTF2H4? Ssl1GTF2H2Zn Finger; DNA binding? Tfb4GTF2H3Ring Finger; DNA binding? Tfb5TFB5; TTD-AStabilization of TFIIH Rad3XPD5’ to 3’ helicase Tfb3MAT1CDK assembly factor Kin28Cdk7CDK; C-terminal domain kinase; CAK Ccl1CycHCyclin Rad 2XPGEndonuclease (3’ incision); stabilizes full open complex Rad1XPFPart of endonuclease (5’ incision) Rad10ERCC1Part of endonuclease (5’ incision)

33. NER and Human Genetic Diseases Xeroderma pigmentosum 1.Severe light sensitivity 2.Severe pigmentation irregularities 3.Frequent neurological defects 4.Early onset of skin cancer at high incidence 5.Elevated frequency of other forms of cancer Cockayne’s syndrome 1.Premature aging of some tissues 2.Dwarfism 3.Light sensitivity in some cases 4.Facial and limb abnormalities 5.Neuroligical abnormalities 6.Early death due to neurodegeneration Trichothiodystrophy 1.Premature aging of some tissues 2.Sulfur deficient brittle hair 3.Facial abnormalities 4.Short stature 5.Ichthyosis (fish-like scales on the skin) 6.Light sensitivity in some cases Mitchell, Hoeijmakers and Niedernhofer (Divide and conquer: nucleotide excision repair battles cancer and ageing. Current Opinion in Cell Biology 15:232-240, 2003).

34. Recombinational Repair

35. Strand-break repair Usually essential for cell survival Many pathways, whose relative importance varies between and within organisms  Double-strand break repair by homologous recombination (HR)  Double-strand break repair by non-homologous end joining (NHEJ)  Single-strand break repair (SSBR)

36. Homologous Recombination is Based on the Ability of Single DNA Strands to Find Regions of Near- Perfect Homology Elsewhere in the Genome Facilitation of Homology Searching by RecA and its Eukaryotic Homologs Eukaryotic proteins important in this process include Rad51, Rad52, Rad54, Rad55, Rad57, Rad59. BRCA1 and BRCA2 interact with Rad51 and may regulate it.

37. Bypass synthesis corrects defect occuring in replication Bypass polymerases with reduced fidelity can read through lesions, increasing the possiblity of inducing errors in the new DNA Such enzymes have low processivity, only synthesizing short fragments and limiting copy errors Excision repair can cut out damaged nucleotides and repair damage