Oxidative Damage of DNA Oxidative damage results from aerobic metabolism, environmental toxins, activated macrophages, and signaling molecules (NO) Compartmentation limits oxidative DNA damage

Oxidation of Guanine Forms 8-Oxoguanine The most common mutagenic base lesion is 8-oxoguanine guanine 8-oxoguanine from Banerjee et al., Nature 434, 612 (2005)

Repair of 8-oxo-G Replication of the 8-oxoG strand preferentially mispairs with A and mimics a normal base pair and results in a G-to-T transversion 8-oxoguanine DNA glycosylase/ b-lyase (OGG1) removes 8-oxo-G and creates an AP site MUTYH removes the A opposite 8-oxoG

Oxidation of dNTPs are Mutagenic cGTP is oxidized to 8-OH-dGTP and is misincorporated opposite A MutT converts 8-OH-dGTP to 8-OH-dGMP

UV-Irradiation Causes Formation of Thymine Dimers from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-38

Nonenzymatic Methylation of DNA Formation of 600 3-me-A residues/cell/day are caused by S-adnosylmethionine 3-me-A is cytotoxic and is repaired by 3-me-A-DNA glycosylase 7-me-G is the main aberrant base present in DNA and is repaired by nonenzymatic cleavage of the glycosyl bond

Effect of Chemical Mutagens Nitrous acid causes deamination of C to U and A to HX U base pairs with A HX base pairs with C

Repair Pathways for Altered DNA Bases from Lindahl and Wood, Science 286, 1897 (1999)

Direct Repair of DNA Photoreactivation of pyrimidine dimers by photolyase restores the original DNA structure O6-methylguanine is repaired by removal of methyl group by MGMT 1-methyladenine and 3-methylcytosine are repaired by oxidative demethylation

Base Excision Repair of a G-T Mismatch BER works primarily on modifications caused by endogenous agents At least 8 DNA glcosylases are present in mammalian cells DNA glycosylases remove mismatched or abnormal bases AP endonuclease cleaves 5’ to AP site AP lyase cleaves 3’ to AP site from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-36

DNA Glycosylases from Xu et al., Mech.Ageing Dev. 129, 366 (2008) Each glycosylase has limited substrate specificity, but there is redundancy in damage recognition

Mechanism of hOGG1 Action from David, Nature 434, 569 (2005) hOGG1 binds nonspecifically to DNA Contacts with C results in the extrusion of corresponding base in the opposite strand G is extruded into the G-specific pocket, but is denied access to the oxoG pocket oxoG moves out of the G-specific pocket, enters the oxoG-specific pocket, and excised from the DNA

Nucleotide excision repair mainly works on helix distortion and damage caused by environmental mutagens

Recognition of Helix Distortion for Nucleotide Excision Repair RNA pol II stalls at a damaged base on the transcribed strand DDB1-DDB2 recognizes lesions on either DNA strand XPC-HR23 is then recruited Ubiquitylation of DDB2 and XPC may mediate the hand-off of the lesion to XPC-HR23 from Chu and Yang, Cell 135 (1172 (2008)

Nucleotide Excision Repair in Human Cells NER works mainly on helix-distorting damage caused by environmental mutagens The only pathway to repair thymine dimers in humans is nucleotide excision repair Mutations in at least seven XP genes inactivate nucleotide excision repair and cause xeroderma pigmentosum XPC recognizes damaged DNA Helicase activities of XPB and XPD of TFIIH create sites for XPF and XPG cleavage An oligonucleotide containing the lesion is released and the gap is filled by POL d or e and sealed by LIG1 from Lindahl and Wood, Science 286, 1897 (1999)

Transcription-coupled Repair Repair of the transcribed strand of active genes is corrected 5-10-fold as fast as the nontranscribed strand All the factors required for NER are required for transcription-coupled repair except XPC The arrest of POL II progression at a lesion served as a damage recognition signal Recruitment of NER factors also involves CS-A and CS-B

Nucleotide Excision Repair Pathway in Mammals Cockayne’s Syndrome and Trichothiodystrophy are multisystem disorders defective in transcription-coupled DNA repair

Mismatch Repair Repairs DNA replication errors and insertion-deletion loops Decreases mutation frequency by 102 - 103 Plays a role in triplet repeat expansion, somatic hypermutation and class switch recombination

Mismatch repair in E. coli GATC sequences are methylated by dam methylase Newly replicated DNA is transiently hemimethylated MutS recognizes a mismatch of small IDL MutS bends DNA, recruits MutL and forms a small dsDNA loop MutH nicks the unmethylated GATC Helicase unwinds the nicked DNA which is degraded past the mismatch Gap is repaired by Pol III and ligase from Marra and Schar, Biochem.J. 338, 1 (1998)

Mismatch Repair in Eukaryotes MutS homologs recognize mismatch and form a ternary complex with MulL homologs and the mismatch PMS2 is a mismatch-activated strand- specific nuclease, and the break is directed to the strand contain the preexisting nick EXO1 excises the mismatch The gap is filled in by PCNA, Pold and DNA ligase Defective mismatch repair is the primary cause of certain types of human cancers from Hsieh and Yamane, Mech.Ageing Dev. 129, 391 (2008)

Causes of and Responses to ds Breaks DSBs result from exogenous insults or normal cellular processes DSBs result in cell cycle arrest, cell death, or repair Repair of DSBs is by homologous recombination or nonhomologous end joining from van Gent et al., Nature Rev.Genet. 2, 196 (2001)

Initiation of Double-stranded Break Repair MRN complex recognizes DSB ends and recruits ATM ATM phosphorylates H2A.X and recruits MDC1 to spread gH2A.X TIP60 and UBC13 modify H2A.X MDC1 recruits RNF8 which ubiquitylates H2A.X RNF168 forms ubiquitin conjugates and recruits BRCA1 from van Attikum and Gasser, Trends Cell Biol. 19, 204 (2009)

ATM Mediates the Cell’s Response to DSBs DSBs activate ATM ATM phosphorylation of p53, NBS1 and H2A.X influence cell cycle progression and DNA repatr from van Gent et al., Nature Rev.Genet. 2, 196 (2001)

Repair of ds Breaks by Homologous Recombination ssDNAs with 3’ends are formed and coated with Rad51, the RecA homolog Rad51-coated ssDNA invades the homologous dsDNA in the sister chromatid The 3’-end is elongated by DNA polymerase, and base pairs with ss 3-end of the other broken DNA DNA polymerase and DNA ligase fills in gaps from Lodish et al., Molecular Cell Biology, 5th ed. Fig 23-31

Role of BRCA2 in Double-stranded Break Repair BRCA2 mediates binding of RAD51 to ssDNA RAD51-ssDNA filaments mediate invasion of ssDNA to homologous dsDNA from Zou, Nature 467, 667 (2010)

Repair of ds Breaks by Nonhomologous End Joining KU heterodimer recognizes DSBs and recruits DNA-PK Mre11 complex tethers ends together and processes DNA ends DNA ligase IV and XRCC4 ligates DNA ends from van Gent et al., Nature Rev.Genet. 2, 196 (2001)

Translesion DNA Synthesis Replicative polymerase encounters DNA damage on template strand Catalytic site of replicative polymerases is intolerant of misalignment between template and incoming nucleotide Replicative polymerase is replaced by TLS polymerase which inserts a base opposite lesion Base pairing is restored beyond the lesion and replicative polymerase replaces TLS polymerase TLS can occur in S or G2 from Sale et al., Nature Rev.Mol.Cell Biol. 13, 141 (2012)

There are Multiple TLS Polymerases TLS polymerases are recruited by interactions with the sliding clamp There are multiple TLS polymerases TLS polymerases have low processivity and low fidelity, and lack 3’-5’ exonucleases TLS polymerases are selective for certain lesions from Sale et al., Nature Rev.Mol.Cell Biol. 13, 141 (2012) Most mutations caused by DNA lesions are caused by TLS polymerases

TLS Polymerases Can Be Accurate or Error-prone Pol k bypasses an abasic site and often causes a -1 frameshift Pol h bypasses a thymine dimer and inserts AA Pol i is accurate with dA template and error-prone with dT template Replicative polymerases insert dC or dA opposite 8-oxo-G, Pol i inserts dC The likelihood that TLS polymerases are error-prone depends on the nature of the lesion and the TLS polymerase that is utilized

Somatic Hypermutation of Ig Genes Depends on TLS Polymerases AID deaminates dC to dU Uracil DNA glycosylase forms an abasic site, and REV1 incorporates dC opposite the site MMR proteins lead to the formation of a ss gap, PCNA is ubiquitylated, and Pol h is recruited, generating mutations at A-T from Sale et al., Nature Rev.Mol.Cell Biol. 13, 141 (2012)