RecQ helicases play an important role in preserving genomic integrity, and their cellular roles in DNA repair, recombination, and replication have been of considerable interest. Of the five human RecQ helicases identified, three are associated with genetic disorders characterized by an elevated incidence of cancer or premature aging: Werner syndrome, Bloom syndrome, and Rothmund-Thomson syndrome. Although the biochemical properties and protein interactions of the WRN and BLM helicases defective in Werner syndrome and Bloom syndrome, respectively, have been extensively investigated, less information is available concerning the functions of the other human RecQ helicases. We have focused our attention on human RECQ1, a DNA helicase whose cellular functions remain largely uncharacterized. In this work, we have characterized the DNA substrate specificity and optimal cofactor requirements for efficient RECQ1-catalyzed DNA unwinding and determined that RECQ1 has certain properties that are distinct from those of other RecQ helicases. RECQ1 stably bound to a variety of DNA structures, enabling it to unwind a diverse set of DNA substrates. In addition to its DNA binding and helicase activities, RECQ1 catalyzed efficient strand annealing between complementary single-stranded DNA molecules. The ability of RECQ1 to promote strand annealing was modulated by ATP binding, which induced a conformational change in the protein. The enzymatic properties of the RECQ1 helicase and strand annealing activities are discussed in the context of proposed cellular DNA metabolic pathways that are important in the maintenance of genomic stability.Cellular processes such as DNA replication, recombination, and repair often involve steps that require unwinding of double-stranded DNA (dsDNA) 1 to form transient single-stranded DNA (ssDNA) intermediates. Helicases are a class of enzymes that unwind DNA duplexes with a distinct directional polarity, either 3Ј to 5Ј or 5Ј to 3Ј with respect to the strand on which the helicase is presumed to translocate, deriving energy from the hydrolysis of ATP

Werner syndrome is a hereditary premature aging disorder characterized by genome instability. The product of the gene defective in WS, WRN, is a helicase/exonuclease that presumably functions in DNA metabolism. To understand the DNA structures WRN acts upon in vivo, we examined its substrate preferences for unwinding. WRN unwound a 3'-single-stranded (ss)DNA-tailed duplex substrate with streptavidin bound to the end of the 3'-ssDNA tail, suggesting that WRN does not require a free DNA end to unwind the duplex; however, WRN was completely blocked by streptavidin bound to the 3'-ssDNA tail 6 nucleotides upstream of the single-stranded/double-stranded DNA junction. WRN efficiently unwound the forked duplex with streptavidin bound just upstream of the junction, suggesting that WRN recognizes elements of the fork structure to initiate unwinding. WRN unwound two important intermediates of replication/repair, a 5'-ssDNA flap substrate and a synthetic replication fork. WRN was able to translocate on the lagging strand of the synthetic replication fork to unwind duplex ahead of the fork. For the 5'-flap structure, WRN specifically displaced the 5'-flap oligonucleotide, suggesting a role of WRN in Okazaki fragment processing. The ability of WRN to target DNA replication/repair intermediates may be relevant to its role in genome stability maintenance.

Modulation of DNA repair proteins by small molecules has attracted great interest. An in vitro helicase activity screen was used to identify molecules that modulate DNA unwinding by Werner syndrome helicase (WRN), mutated in the premature aging disorder Werner syndrome. A small molecule from the National Cancer Institute Diversity Set designated NSC 19630 [1-(propoxymethyl)-maleimide] was identified that inhibited WRN helicase activity but did not affect other DNA helicases [Bloom syndrome (BLM), Fanconi anemia group J (FANCJ), RECQ1, RecQ, UvrD, or DnaB). Exposure of human cells to NSC 19630 dramatically impaired growth and proliferation, induced apoptosis in a WRN-dependent manner, and resulted in elevated γ-H2AX and proliferating cell nuclear antigen (PCNA) foci. NSC 19630 exposure led to delayed S-phase progression, consistent with the accumulation of stalled replication forks, and to DNA damage in a WRN-dependent manner. Exposure to NSC 19630 sensitized cancer cells to the G-quadruplex–binding compound telomestatin or a poly(ADP ribose) polymerase (PARP) inhibitor. Sublethal dosage of NSC 19630 and the chemotherapy drug topotecan acted synergistically to inhibit cell proliferation and induce DNA damage. The use of this WRN helicase inhibitor molecule may provide insight into the importance of WRN-mediated pathway(s) important for DNA repair and the replicational stress response.

We have investigated the DNA substrate specificity of BACH1 (BRCA1-associated C-terminal helicase). The importance of various DNA structural elements for efficient unwinding by purified recombinant BACH1 helicase was examined. The results indicated that BACH1 preferentially binds and unwinds a forked duplex substrate compared with a duplex flanked by only one single-stranded DNA (ssDNA) tail. In support of its DNA substrate preference, helicase sequestration studies revealed that BACH1 can be preferentially trapped by forked duplex molecules. BACH1 helicase requires a minimal 5 ssDNA tail of 15 nucleotides for unwinding of conventional duplex DNA substrates; however, the enzyme is able to catalytically release the third strand of the homologous recombination intermediate D-loop structure irrespective of DNA tail status. In contrast, BACH1 completely fails to unwind a synthetic Holliday junction structure. Moreover, BACH1 requires nucleic acid continuity in the 5 ssDNA tail of the forked duplex substrate within six nucleotides of the ssDNA-dsDNA junction to initiate efficiently DNA unwinding. These studies provide the first detailed information on the DNA substrate specificity of BACH1 helicase and provide insight to the types of DNA structures the enzyme is likely to act upon to perform its functions in DNA repair or recombination.Germ line mutations in BRCA1 lead to an increased lifetime risk of breast and/or ovarian cancer. Cellular studies have revealed that the BRCA1 tumor suppressor gene is required for the maintenance of genomic integrity and a normal level of resistance to DNA damage (for review see Refs. 1-3). The nuclear phosphoprotein BRCA1 contains tandem C-terminal BRCT motifs, a conserved protein sequence found in a large number of DNA damage-response proteins (4). The integrity of the BRCT motifs is required for the role of BRCA1 in double strand break repair (DSBR) 1 and homologous recombination (5-8). Tumor-predisposing missense and deletion mutations in the BRCA1 BRCT domain, all of which render BRCA1 defective in its DSBR function, also disrupt the ability of BRCA to bind BACH1. BACH1 is a member of the DEAH subfamily of superfamily 2 helicases (9). Consistent with its predicted helicase domain, BACH1 was recently shown to catalyze DNA unwinding of M13 partial duplex substrates and have a 5Ј to 3Ј polarity on a linearized M13 directionality substrate (10). A role of BACH1 helicase in DSBR was suggested by the observation that overexpression of a BACH1 allele (K52R) carrying a mutation in its ATP-binding pocket that inactivates its ATPase/ helicase function (10) resulted in a marked decrease in the ability of cells to repair DSBs, and that this dominant negative phenotype depended on a specific interaction between BACH1 and BRCA1 (9). More recently, it was shown that the interaction between BRCA1 and BACH1 depends on the phosphorylation status of BACH1 (11-13), and that this phosphorylationdependent interaction is required for DNA damage-induced checkpoint control during the G 2 /M phase of the ...

The single-stranded DNA-binding protein replication protein A (RPA) interacts with several human RecQ DNA helicases that have important roles in maintaining genomic stability; however, the mechanism for RPA stimulation of DNA unwinding is not well understood. To map regions of Werner syndrome helicase (WRN) that interact with RPA, yeast two-hybrid studies, WRN affinity pull-down experiments and enzyme-linked immunosorbent assays with purified recombinant WRN protein fragments were performed. The results indicated that WRN has two RPA binding sites, a high affinity N-terminal site, and a lower affinity C-terminal site. Based on results from mapping studies, we sought to determine if the WRN N-terminal region harboring the high affinity RPA interaction site was important for RPA stimulation of WRN helicase activity. To accomplish this, we tested a catalytically active WRN helicase domain fragment (WRN H-R ) that lacked the N-terminal RPA interaction site for its ability to unwind long DNA duplex substrates, which the wild-type enzyme can efficiently unwind only in the presence of RPA. WRN H-R helicase activity was significantly reduced on RPAdependent partial duplex substrates compared with full-length WRN despite the presence of RPA. These results clearly demonstrate that, although WRN H-R had comparable helicase activity to full-length WRN on short duplex substrates, its ability to unwind RPAdependent WRN helicase substrates was significantly impaired. Similarly, a Bloom syndrome helicase (BLM) domain fragment, BLM 642-1290 , that lacked its N-terminal RPA interaction site also unwound short DNA duplex substrates similar to wild-type BLM, but was severely compromised in its ability to unwind long DNA substrates that full-length BLM helicase could unwind in the presence of RPA. These results suggest that the physical interaction between RPA and WRN or BLM helicases plays an important role in the mechanism for RPA stimulation of helicase-catalyzed DNA unwinding.Within the last decade, several genetic disorders with premature aging and/or cancer have been identified in which a gene member of the RecQ helicase family is mutated (1, 2). RecQ helicases share a centrally located domain of ϳ450 residues that contains the seven conserved helicase motifs (for review, see Ref.3). The founding member of the RecQ family, Escherichia coli RecQ helicase, has been extensively studied biochemically and has been genetically implicated in DNA recombination. A single yeast RecQ helicase, Sgs1 or Rqh1, is found in the budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, respectively, and these helicases are thought to be important in the cellular response to DNA-damaging agents and maintenance of genome stability. RecQ helicases have also been identified in a number of higher eukaryotes, including Xenopus laevis (focus forming activity 1 (FFA-1) 1 ), Drosophila melanogaster (DmBLM and DmRecQ5), and Caenorhabditis elegans (WRN-1, Ce-RCQ5, HIM-6, and RECQL/Q1). These helicases have proposed functions in ...

Werner Syndrome is a premature aging disorder characterized by genomic instability, elevated recombination, and replication defects. It has been hypothesized that defective processing of certain replication fork structures by WRN may contribute to genomic instability. Fluorescence resonance energy transfer (FRET) analyses show that WRN and Flap Endonuclease-1 (FEN-1) form a complex in vivo that colocalizes in foci associated with arrested replication forks. WRN effectively stimulates FEN-1 cleavage of branch-migrating double-flap structures that are the physiological substrates of FEN-1 during replication. Biochemical analyses demonstrate that WRN helicase unwinds the chicken-foot HJ intermediate associated with a regressed replication fork and stimulates FEN-1 to cleave the unwound product in a structuredependent manner. These results provide evidence for an interaction between WRN and FEN-1 in vivo and suggest that these proteins function together to process DNA structures associated with the replication fork. INTRODUCTIONWerner Syndrome (WS) is a premature aging disorder characterized by genomic instability and increased cancer risk (Martin, 1978). The WRN gene product defective in WS belongs to the RecQ family of DNA helicases (Yu et al., 1996). In humans, mutations in RecQ family members BLM and RECQ4 are responsible for two other disorders associated with elevated chromosomal instability and cancer, Bloom and Rothmund-Thomson syndromes, respectively (Ellis et al., 1995;Kitao et al., 1998Kitao et al., , 1999. RecQ helicase mutants display defects in DNA replication, recombination, and DNA repair, suggesting a role for RecQ helicases in maintaining genomic integrity (Wu and Hickson, 2002;Cobb et al., 2002).A DNA processing defect during replication or recombination has been suggested to contribute to the molecular pathology of WS. WS cells have a prolonged S phase (Poot et al., 1992), slower rate of repair associated with DNA damage induced in S-phase, reduced induction of RAD51 foci, and higher level of DNA strand breaks (Pichierri et al., 2001).More recently, it was demonstrated that WS cells initiate recombination at a normal rate but fail to resolve recombination intermediates in a RAD51-dependent pathway (Prince et al., 2001;Saintigny et al., 2002). A DNA substrate for WRN was suggested by the demonstration that RusA, a bacterial enzyme that cleaves four-way junctions, rescued cell survival and restored the ability to generate viable recombinants following exposure of WRNϪ/Ϫ cells to DNA damaging agents (Saintigny et al., 2002).A stalled replication fork can be converted to a four-way junction resembling a Holliday Junction (HJ) by branch migration and reannealing of nascent DNA strands (McGlynn et al., 2001;Postow et al., 2001). WRN has been shown to unwind the HJ and catalyze branch fork migration on ␣-structures (Constantinou et al., 2000), suggesting a potential role in processing the recombination intermediate to prevent aberrant recombination events at sites of stalled replication forks. Evidence ...

Background: Mutations in ChlR1 (DDX11) are linked to Warsaw breakage syndrome. Results: ChlR1 unwinds forked duplex, 5Ј flap, D-loop, and two-stranded antiparallel G-quadruplex substrates, whereas a patient-derived mutation abolishes helicase activity. Conclusion: ChlR1 helicase unwinds key intermediates of DNA replication and recombination. Significance: Inactivation of catalytic activity by Warsaw breakage syndrome mutation suggests that ChlR1 helicase function is important in vivo.

Human Werner Syndrome is characterized by early onset of aging, elevated chromosomal instability, and a high incidence of cancer. Werner protein (WRN) is a member of the recQ gene family, but unlike other members of the recQ family, it contains a unique 335 exonuclease activity. We have reported previously that human Ku heterodimer interacts physically with WRN and functionally stimulates WRN exonuclease activity. Because Ku and DNA-PKcs, the catalytic subunit of DNAdependent protein kinase (DNA-PK), form a complex at DNA ends, we have now explored the possibility of functional modulation of WRN exonuclease activity by DNA-PK. We find that although DNA-PKcs alone does not affect the WRN exonuclease activity, the additional presence of Ku mediates a marked inhibition of it. The inhibition of WRN exonuclease by DNA-PKcs requires the kinase activity of DNA-PKcs. WRN is a target for DNA-PKcs phosphorylation, and this phosphorylation requires the presence of Ku. We also find that treatment of recombinant WRN with a Ser/Thr phosphatase enhances WRN exonuclease and helicase activities and that WRN catalytic activity can be inhibited by rephosphorylation of WRN with DNA-PK. Thus, the level of phosphorylation of WRN appears to regulate its catalytic activities. WRN forms a complex, both in vitro and in vivo, with DNA-PKC. WRN is phosphorylated in vivo after treatment of cells with DNA-damaging agents in a pathway that requires DNA-PKcs. Thus, WRN protein is a target for DNA-PK phosphorylation in vitro and in vivo, and this phosphorylation may be a way of regulating its different catalytic activities, possibly in the repair of DNA dsb. Werner syndrome (WS)1 is a human autosomal recessive disorder characterized by early onset of premature aging characteristics including graying and loss of hair, wrinkling and ulceration of skin, atherosclerosis, osteoporosis, and cataracts. In addition, WS patients exhibit an increased incidence of diabetes mellitus type 2, hypertension, and malignancies (1). The gene (WRN), defects in which are responsible for WS, encodes a 1,432-amino acid protein (WRN) (2) that has both 3Ј35Ј helicase and 3Ј35Ј exonuclease activities (3-7). Although WRN appears to play an important role in DNA metabolism, the precise cellular roles of both the helicase and exonuclease activities of WRN remain to be determined.Cells from patients with WS show premature replicative senesence compared with cells derived from normal individuals (8). The WS cellular phenotype suggests correlations among faulty DNA metabolism, genomic instability, and senescence. WS cells show hypersensitivity to selected DNA-damaging agents including 4-nitroquinoline-1-oxide (4NQO) (9), topoisomerase inhibitors (10), and certain DNA cross-linking agents (11). Compared with normal cells, WS cells also exhibit increased genomic instability including higher levels of DNA deletions, translocations, and chromosomal breaks (12, 13). These studies suggest that WRN plays an important role in DNA metabolism possibly by participating in DNA repair, re...