DNA helicases involved in DNA repair and their roles in cancer

Abstract

Helicases have major roles in genome maintenance by unwinding structured nucleic acids. Their prominence is marked by various cancers and genetic disorders that are linked to helicase defects. Although considerable effort has been made to understand the functions of DNA helicases that are important for genomic stability and cellular homeostasis, the complexity of the DNA damage response leaves us with unanswered questions regarding how helicase-dependent DNA repair pathways are regulated and coordinated with cell cycle checkpoints. Further studies may open the door to targeting helicases in order to improve cancer treatments based on DNA-damaging chemotherapy or radiation.

Figure 1. Molecular functions of DNA helicases

DNA helicases (beige triangles) catalytically disrupt base pairs between complementary strands in an ATP-dependent manner (a), and may have specialized functions. For example, Fanconi anaemia group J protein (FANCJ), the Werner syndrome helicase (WRN), the Bloom syndrome helicase (BLM), and PIF1 disrupt G-quadruplex (G4) DNA structures (b). RECQL5 and FANCJ strip off proteins (for example, RAD51) that are bound to DNA (c). Some helicases (for example, RECQL1, RECQL4, RECQL5, WRN and BLM) carry out strand annealing by promoting base pairing (d). Strand annealing directionality by a DNA helicase has not been demonstrated. ATP inhibits strand annealing and promotes duplex unwinding by inducing a conformational change in the helicase protein (for example, RECQL1 (REF. 213)). Some helicases (for example, BLM and regulator of telomere elongation helicase 1 (RTEL1)) suppress homologous recombination (HR)-mediated repair by unwinding displacement loop (D-loop) intermediates (e). Branch-migration of three- or four-stranded joint DNA molecules by a DNA helicase (for example, BLM, WRN or RECQL1) (f) can suppress or promote the formation of Holliday Junction (HJ) structures that can be resolved by specialized endonucleases to create crossover products that are responsible for loss of heterozygosity and cancer predisposition. The BLM helicase, together with topoisomerase 3α (TOP3α) and RecQ-mediated genome instability 1 (RMI1) and RMI2, dissolves double HJ structures (g) during HR or at converging replication forks to generate non-crossover DNA molecules. See the main text for details.

Figure 2. Involvement of helicases in nucleotide excision and interstrand crosslink DNA repair mechanisms

Basic steps of nucleotide-excision repair (NER) (a) and interstrand crosslink (ICL) DNA repair (b) are shown, highlighting the roles of helicases. a | After DNA damage recognition by proteins including xeroderma pigmentosum complementation group C (XPC), XPE and RAD23B, the XPB and XPD helicases act with XPA to create a single-stranded bubble coated by replication protein A (RPA) that is processed by nucleases (the XPF–ERCC1 complex and XPG) to remove the damaged strand in NER^,. b | Multiple helicases are implicated in crosslink resistance pathways that intersect with the Fanconi anaemia (FA) pathway. After lesion detection, nuclease-catalysed incisions on each side of the crosslink remove (unhook) it from one strand, leaving a small gap that converts the fork to a double-strand break (DSB). Parallel pathways resolve the lesion. For simplicity, the double replication fork model is not shown. HR, homologous recombination; Pol, DNA polymerase; ssDNA, single-stranded DNA.

Figure 3. Involvement of helicases in homologous recombination and base excision DNA repair mechanisms

Basic steps of homologous recombination (HR)-mediated DNA repair (a) and base-excision repair (BER) (b) are shown, highlighting the roles of helicases. a | Helicases participate in various steps of conservative HR-mediated repair in somatic cells. Suppression of crossover and rearrangement events can occur pre- and post-synaptically. Specific roles for helicases are being identified. Helicase disruption of displacement loops (D-loops) promotes synthesis-dependent strand annealing by decreasing double Holliday Junction (HJ) formation. b | The Werner syndrome helicase (WRN) participates in long-patch BER by unwinding 5′ flaps and interacting with BER proteins, including flap endonuclease 1 (FEN1) (REF. 217). APE1, apurinic/apyrimidinic endonuclease 1; DNA2, DNA replication helicase/nuclease 2; EXO1, exonuclease 1; FANCJ, Fanconi anaemia complementation group J protein; NBS1, Nijmegen breakage syndrome protein 1; OGG1, 8-oxoguanine DNA glycosylase; POLβ, DNA polymerase-β; RTEL1, regulator of telomere elongation helicase 1.

Figure 4. Roles of DNA helicases during replication stress

a | When the replisome (not shown) encounters a replication-blocking lesion (green oval) or other form of replication stress (for example, nucleotide starvation), certain helicases (for example, the Werner syndrome helicase (WRN) or Bloom syndrome helicase (BLM)^,), carry out fork regression to create a Holliday Junction (HJ)-like ‘chicken-foot’ DNA structure. Reverse branch-migration of the regressed fork by a helicase (for example, WRN or RECQL1 (REF. 129)) potentially allows replication bypass of the lesion in a non-recombinogenic mode. b | The WRN or BLM helicases can stimulate flap endonuclease 1 (FEN1)-catalyzed cleavage of 5′ flap structures that might arise during lagging-strand synthesis. BLM stimulates FEN1-mediated cleavage on flaps with secondary 5′ flap structure, and WRN is involved with DNA polymerase-δ in a hairpin repair pathway. DNA replication helicase/nuclease 2 (DNA2) also facilitates FEN1-mediated cleavage of 5′ flaps. c | Based on evidence from studies of Escherichia coli replication, accessory DNA helicases (blue triangle) may coordinate with a eukaryotic minichromosome maintenance (MCM) helicase complex (purple) and replication machinery to displace a protein (orange oval) bound to duplex DNA that impedes fork progression. Replication fork reversal has a role in bacterial replication restart. Further studies are required to substantiate this model for eukaryotes.

Figure 5. Helicase functions at telomeres and potential for anticancer therapy

Helicases that regulate telomere capping may be targeted for depletion by RNA interference (RNAi) or small-molecule inhibition to selectively kill cancer cells. a | 3′ single-stranded DNA (ssDNA) tail invasion into adjacent telomeric double-stranded DNA (dsDNA) results in displacement of the complementary strand to create a displacement loop (D-loop), the so-called T-loop structure. Human DNA helicases (regulator of telomere elongation helicase 1 (RTEL1) and the Werner syndrome helicase (WRN); indicated by the beige triangles) resolve T-loops to enable telomere replication or repair. Helicase deficiency by mutation or RNAi-mediated depletion results in the persistence of T-loops which can be nucleolytically cleaved, leading to telomere instability. A helicase inhibitor (purple circle) may prevent T-loop unwinding, thus resulting in telomere instability. b | ssDNA that arises at telomeres or during lagging-strand synthesis can form a G-quadruplex (G4). Certain human helicases with 5′ to 3′ polarity (RTEL, Fanconi anaemia complementation group J protein (FANCJ) and PIF1) or 3′ to 5′ polarity (WRN and the Bloom syndrome helicase (BLM)) may resolve G4 structures to enable replication or repair. Helicase deficiency by mutation or RNAi-mediated depletion results in telomere fragility. A helicase inhibitor or G4-specific ligand (green circle) may prevent G4 resolution at telomeres or other G-rich genomic sequences. Telomere instability can lead to cellular senescence of rapidly dividing cancer cells. Figure is modified, with permission, from REF. © (2012) Elsevier Science.