DNA repair mechanisms in dividing and non-dividing cells

Abstract

DNA damage created by endogenous or exogenous genotoxic agents can exist in multiple forms, and if allowed to persist, can promote genome instability and directly lead to various human diseases, particularly cancer, neurological abnormalities, immunodeficiency and premature aging. To avoid such deleterious outcomes, cells have evolved an array of DNA repair pathways, which carry out what is typically a multiple-step process to resolve specific DNA lesions and maintain genome integrity. To fully appreciate the biological contributions of the different DNA repair systems, one must keep in mind the cellular context within which they operate. For example, the human body is composed of non-dividing and dividing cell types, including, in the brain, neurons and glial cells. We describe herein the molecular mechanisms of the different DNA repair pathways, and review their roles in non-dividing and dividing cells, with an eye toward how these pathways may regulate the development of neurological disease.

Keywords: 6-4PPs; 8-oxoguanine DNA glycosylase; AOA1; AP; AP endonuclease 1; APE1; APTX; ATM; CPDs; CS; CSR; Cockayne syndrome; DAR; DNA double strand break repair; DNA polymerase β; DNA repair; DNA single strand break repair; DNA single strand breaks; DNA-PKcs; DNA-dependent protein kinase catalytic subunit; DSBR; Dividing and non-dividing; ERCC1; Endogenous DNA damage; FEN1; GG-NER; HNPCC; HR; IR; MAP; MCSZ; MGMT; MMR; MPG; MUTYH; MUTYH-associated polyposis; N-methylpurine-DNA glycosylase; NEIL1; NER; NHEJ; NSC; NTH1; Neural cells; Neurological disorder; O(6)-methylguanine-DNA methyltransferase; OGG1; PARP1; PCNA; PG; PNKP; PUA; Pol β; RFC; RNA polymerase; RNAP; RPA; SCAN1; SCID; SDSA; SSA; SSBR; SSBs; TC-NER; TDP1; TFIIH; TOP1; TTD; Top1 cleavage complex; Top1cc; UNG; X-ray repair cross-complementing protein 1; XP; XRCC1; aprataxin; apurinic/apyrimidinic; ataxia telangiectasia mutated; ataxia with ocular motor apraxia 1; class switch recombination; cyclobutane pyrimidine dimers; dRP; deoxyribose-5-phosphate; endonuclease III-like 1; endonuclease VIII-like 1; excision repair cross complementing 1; flap endonuclease 1; global genome-NER; hereditary nonpolyposis colorectal cancer; homologous recombination; human mutY homolog; ionizing radiation; microcephaly with early-onset, intractable seizures and developmental delay; mismatch repair; neural stem cells; nonhomologous end joining; nucleotide excision repair; phospho-α,β-unsaturated aldehyde; phosphoglycolate; poly(ADP-ribose) polymerase-1; polynucleotide kinase 3′-phosphatase; proliferating cellular nuclear antigen; pyrimidine-(6,4)-pyrimidone photoproducts.; replication factor C; replication protein A; severe combined immunodeficient; single-strand annealing; spinocerebellar ataxia with axonal neuropathy-1; synthesis-dependent strand annealing; topoisomerase 1; transcription domains-associated repair; transcription factor II H; transcription-coupled NER; trichothiodystrophy; tyrosyl-DNA phosphodiesterase 1; uracil-DNA glycosylase; xeroderma pigmentosum.

Figure 1. DNA damage and repair responses

DNA repair pathways (top) and examples of corresponding DNA damage (bottom). The detailed molecular mechanisms for the repair responses are provided in text. APTX, aprataxin; BER, base exicision repair; DSBR, DNA double strand break repair; HR, homologous recombination; MGMT, O⁶-methylguanine-DNA methyltransferase; MMR, mismatch repair; NER, nucleotide excision repair; NHEJ, nonhomologous end joining; PNKP, polynucleotide kinase 3’-phosphatase; SSBR, DNA single strand break repair; SSBs, DNA single strand breaks; TC-NER, transcription-coupled NER; TDP1, tyrosyl-DNA phosphodiesterase 1; G-Me, O⁶-Methylguanine; TˆT, thymine dimer; I, inosine; U, uracil; G^o, 8-oxoguanine.

Figure 2. Nucleotide excision repair pathways

Two subpathways of mammalian NER: GG-NER and TC-NER. (i) XPC-RAD23B recognizes DNA damage-induced structural change as the initiation step of GG-NER. TC-NER is initiated by stalling of an elongating RNAP at a blocking lesion on the transcribed strand within an active gene. After these initial recognition steps, GG-NER and TC-NER pathways involve many of the same protein components. (ii) Following recognition, the TFIIH complex is recruited. Through the activity of the helicase subunits, XPB and XPD, TFIIH promotes opening of the DNA duplex around the lesion, facilitating recruitment of XPA and RPA. (iii) The XPF–ERCC1 complex is recruited to the lesion via a direct interaction with XPA, while XPG is specifically engaged through an interaction with TFIIH. The two endonucleases, XPF–ERCC1 and XPG, are responsible for carrying out incision 5’ and 3’, respectively, to the DNA damage. (iv) After dual incision and removal of the damage-containing oligonucleotide fragment, a DNA polymerase carries out gap-filling repair synthesis in cooperation with RFC and PCNA. (v) Finally, the nick is sealed by either XRCC1–LIG3α or a FEN1–LIG1 complex. CAK, the cyclin-dependent kinase (CDK)-activating kinase; GG-NER, global genome-NER; RFC, replication factor C; RPA, replication protein A; TC-NER, transcription-coupled NER; TFIIH, transcription factor II H.

Figure 3. Base excision repair pathways

In BER, base damage is recognized and removed by a lesion-specific DNA glycosylase. Monofunctional DNA glycosylases include UNG and MPG, whereas bifunctional DNA glycosylases are OGG1, MUTYH, NTH1 and NEIL1. The monofunctional DNA glycosylases create an AP site by removing the substrate base. Such AP sites are incised by APE1, creating a 5’-dRP and 3’-OH strand break product. Pol β removes the 5’-dRP moiety via an intrinsic lyase activity. Bifunctional DNA glycosylases excise a damaged base, and can also incise the DNA backbone immediately 3’ to the AP site product and produce a SSB with a 3’-PUA or 3’-P, respectively. APE1 removes the 3’-PUA residue, while PNKP excises the 3’-P moiety. TOP1cc can be removed by TDP1, leaving behind a 3′-P and 5′-OH terminus; both ends of this SSB are converted by PNKP to 3′-OH and 5′-P. APTX processes 5’-AMP groups, resulting from a failed DNA ligation event, to normal 5’-P ends at nicks or breaks. After creating the 3’-OH and 5’-P termini at a SSB, SP- or LP-BER performs repair synthesis and ligation. In SP-BER, Pol β replaces the missing nucleotide and the XRCC1 LIG3α complex seal the nick. In LP-BER, Pol δ/ε, RFC and PCNA incorporate 2–13 nucleotides and then FEN1–LIG1 completes the repair process. AMP, adenosine monophosphate; AP, apurinic/apyrimidinic; APE1, AP endonuclease 1; APTX, aprataxin; FEN1, flap endonuclease 1; LIG1, DNA ligase I; LIG3, DNA ligase III; MPG, N-methylpurine-DNA glycosylase; MUTYH, mutY homolog; NEIL1, endonuclease VIII-like 1; NTH1, endonuclease III-like 1; OGG1, 8-oxoguanine DNA glycosylase; PCNA, proliferating cellular nuclear antigen; PG, phosphoglycolate; PNKP, polynucleotide kinase 3’-phosphatase; Pol β, polymerase β; SSBR, DNA single strand break repair; SSBs, DNA single strand breaks; TDP1, tyrosyl-DNA phosphodiesterase 1; TOP1, topoisomerase 1; Top1cc, Top1 cleavage complex; UNG, uracil-DNA glycosylase; 3’-PUA, 3’-phospho-α,β-unsaturated aldehyde.

Figure 4. Recombination pathways

DSBR is divided into two major pathways: HR and NHEJ. HR operates in dividing cells and in S phase, whereas NHEJ can function in both dividing and non-dividing cells and independent of cell cycle. HR has been proposed to be initiated by recognition of the DSB by the MRN complex (MRE11-RAD50-NBS1). The MRN complex associates with CtIP, which initiates 5′–3′ end resection to create the 3′ ssDNA overhang. Further resection is carried out by exonucleases (possibly EXO1), and the resulting ssDNA is stabilized by binding of RPA. RAD52 is recruited to RPA. The RAD51-BRCA2 complex then replaces the RAD52-RPA complex to form RAD51 nucleoprotein filaments, whereas, in SSA, RPA and RAD52 carry out the recombination process in a RAD51-independent manner. RAD51-coated ssDNA enables strand invasion of the intact homologous DNA region. In classic DSBR, the second DSB end can be captured by the D-loop to form an intermediate with double Holliday junctions, which can result in a non-crossover (cleavage at blue arrows) or a crossover (cleavage at blue arrows on one side and red arrows on other side) products. In SDSA, the newly synthesized strand is displaced to permit annealing to the other DSB end, resulting in a non-crossover product. NHEJ is initiated by recognition of the DSB ends by the Ku (Ku70/Ku80) complex, followed by recruitment of DNA-PKcs. DNA-PKcs activates Artemis, which generates terminal overhangs prior to ligation. To complete the process, DNA synthesis is performed to fill-in the gaps and end joining is carried out by XRCC4–LIG4 in collaboration with XLF. CtIP, C-terminal binding protein-interacting protein; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; DSBR, DNA double strand break repair; HR, homologous recombination; NHEJ, nonhomologous end joining; SDSA, synthesis-dependent strand annealing; SSA, single-strand annealing; XRCC4, X-ray repair cross-complementing protein 4.