Functional interplay between ATM/ATR-mediated DNA damage response and DNA repair pathways in oxidative stress

Abstract

To maintain genome stability, cells have evolved various DNA repair pathways to deal with oxidative DNA damage. DNA damage response (DDR) pathways, including ATM-Chk2 and ATR-Chk1 checkpoints, are also activated in oxidative stress to coordinate DNA repair, cell cycle progression, transcription, apoptosis, and senescence. Several studies demonstrate that DDR pathways can regulate DNA repair pathways. On the other hand, accumulating evidence suggests that DNA repair pathways may modulate DDR pathway activation as well. In this review, we summarize our current understanding of how various DNA repair and DDR pathways are activated in response to oxidative DNA damage primarily from studies in eukaryotes. In particular, we analyze the functional interplay between DNA repair and DDR pathways in oxidative stress. A better understanding of cellular response to oxidative stress may provide novel avenues of treating human diseases, such as cancer and neurodegenerative disorders.

Fig. 1

Oxidative DNA damage and DNA repair pathways involved in oxidative stress. Base lesion [e.g., 8-oxo-G (8-oxoguanine)], AP site, SSB, and protein–DNA crosslink (e.g., Top1-DNA crosslink) are primarily repaired by BER/SSBR. Mismatched pairs with damaged bases (e.g., 8-oxo-G:T mismatch pairs) are repaired by MMR. NER is involved in removing tandem lesions (e.g., 8,5′-cyclo-2′-deoxyadenosine (cdA) and T-G intrastrand crosslink), whereas DSB is fixed by HR or NHEJ. Dashed circles in red highlight SSB and DSB

Fig. 2

Cellular responses to oxidative DNA damage. DNA repair pathways (BER, NER, MMR, and HR) and DNA damage response pathways (ATM-Chk2 and ATR-Chk1) are integrating into an interacting network in response to oxidative stress. Dashed arrows indicate that potential regulations require more investigations. Defective DNA repair and DDR pathways may lead to diseases such as cancer and neurodegenerative diseases

Fig. 3

ATM/ATR pathways promote BER/SSBR in response to oxidative DNA damage. AP site is formed after removal of damaged base by DNA glycosylase. SSBs are generated by APE1 at the 5′ side of AP site or bifunctional DNA glycosylase at the 3′ side of AP site, whereas SSBs may also be from other sources. SSBs can be recognized and bound by scaffolding protein XRCC1. A In the short patch sub-pathway, SSB is processed by Pol β to form 1 nt gap. The gap is filled and the final nick is sealed. TDP1 is in charge of removing Topoisomerase I from the protein–DNA crosslink. ATM phosphorylates TDP1 and Chk2. Chk2 then phosphorylates XRCC1. B In the long patch sub-pathway, the 3′ side of SSB is extended by PCNA-tethered DNA polymerases when the 5′ side of SSB can’t be processed into the normal 5′-phosphate. A short strand (~2–13 nt) at the 5′ side of SSB is displaced and further cleaved by PCNA-mediated FEN1. The subsequent nick in the long patch sub-pathway is finally sealed by LIG1. The 9-1-1 complex stimulates enzyme activities of DNA glycosylase, APE1, Pol β, FEN1, and LIG1

Fig. 4

ATM/ATR pathways interact with NER in response to oxidative DNA damage. In TC-NER, RNA Pol II stops at helix-distorting DNA lesions, which is recognized by CSA/CSB. In GG-NER, the damaged nucleotides are recognized by XPC. The fragment containing the damaged nucleotides is unwound by XPB/XPE together with TFIIH. A pre-incision complex is formed after RPA-mediated XPA recruitment. Dual incisions are achieved at the 5′ side by ERCC1/XPF and at the 3′ side by XPG. Repair synthesis is achieved by the PCNA-mediated DNA Pol δ/ε and followed by ligation via LIG3. XPC, XPA, and XPG regulate ATM directly, whereas XPA also regulates ATR. ATR phosphorylates XPA directly, which is required for the nuclear import and stability and XPA

Fig. 5

MMR crosstalks with ATM/ATR pathways in response to oxidative DNA damage. Mismatch pairs with damaged base are recognized by MutSα (MSH2 and MSH6) and MutSβ (MSH2 and MSH3), which are required for the binding of MutLα (MLH2 and PMS2) and MutLβ (MLH2 and PMS1), respectively. MutLα/MutLβ may slide away from mismatch pairs and create a nick by the endonuclease activity. The strand containing the mismatch pair may be excised by nucleases such as Exo1 in a PCNA-dependent manner. Pol δ/ε will switch back to fill the gap, and the final nick is sealed by DNA ligase. MSH2, MSH3, and MSH6 may be phosphorylated by ATM/ATR. MSH2 associates with Chk2 while ATM associates with MLH1. ATM phosphorylates MLH1. MSH2 recruits ATR and Chk1 to damaged sites

Fig. 6

ATM/ATR pathways regulate HR and NHEJ in response to oxidative DNA damage. DSBs can be resected by DNA nuclease, generating RPA-coated ssDNA. Rad51-coated filaments invade the homologous strand and strand synthesis continues to form the D loop. The Double Holliday junctions are resolved to generate crossover or non-crossover products. The Ku complex (KU70/Ku80) is bound to both DSB ends with the absence of homologous chromosome in the NHEJ pathway. The Ku complex is also regulated by ATM/ATR. Subsequently, the DSB ends are processed by the catalytic subunits of DNA-PK (DNA-PKcs) and the broken ends of DSB are finally ligated. The MRN complex at the site of DSB may be phosphorylated by ATM/ATR, whereas ATM may also regulate Rad51

Fig. 7

ATM/ATR pathways in response to oxidative stress. A Oxidative stress can induce dimerization of ATM via its cysteine residues, leading to structural change in ATM protein and elevated ATM kinase activity. After dissociating from its homodimer, ATM can associate with the MRN complex, which localizes at oxidative stress-derived DSBs, or ATM can associate with MDC1. H2AX is localized to the flanking region of DSB and its phosphorylation mediates the recruitment of MDC1. Activated ATM then phosphorylates its substrates including Chk2. Long stretch of ssDNA is generated through DSB end resection in the 5′–3′ direction via DNA nucleases such as CtIP and Exo1. B Oxidative stress-induced mismatch pairs with base lesion are recognized by MSH2-MSH6 complex. C The helix-distorting DNA lesions are recognized by XPC in GG-NER and further incised by dual enzyme complexes including XPG. A gap of ssDNA can be generated in MMR or NER pathways and extended in the 5′–3′ direction by end resection via DNA nucleases such as Exo1. D Unrepaired SSBs may be processed by PCNA-dependent APE2 in the 3′–5′ direction, generating RPA-coated ssDNA. ATR/ATRIP and the 9-1-1 complex are recruited to RPA-ssDNA independently. TopBP1 bridges the ATR/ATRIP and the 9-1-1 complex and activates ATR kinase directly. Then activated ATR phosphorylates its own downstream substrates, such as Chk1, RPA32, and Rad1