1
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Keahi DL, Sanders MA, Paul MR, Webster ALH, Fang Y, Wiley TF, Shalaby S, Carroll TS, Chandrasekharappa SC, Sandoval-Garcia C, MacMillan ML, Wagner JE, Hatten ME, Smogorzewska A. G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604431. [PMID: 39091814 PMCID: PMC11291086 DOI: 10.1101/2024.07.20.604431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Biallelic pathogenic variants in the essential DNA repair gene BRCA2 causes Fanconi anemia, complementation group FA-D1. Patients in this group are highly prone to develop embryonal tumors, most commonly medulloblastoma arising from the cerebellar granule cell progenitors (GCPs). GCPs undergo high proliferation in the postnatal cerebellum under SHH activation, but the type of DNA lesions that require the function of the BRCA2 to prevent tumorigenesis remains unknown. To identify such lesions, we assessed both GCP neurodevelopment and tumor formation using a mouse model with deletion of exons three and four of Brca2 in the central nervous system, coupled with global Trp53 loss. Brca2 Δex3-4 ;Trp53 -/- animals developed SHH subgroup medulloblastomas with complete penetrance. Whole-genome sequencing of the tumors identified structural variants with breakpoints enriched in areas overlapping G-quadruplexes (G4s). Brca2-deficient GCPs exhibited decreased replication speed in the presence of the G4-stabilizer pyridostatin. Pif1 helicase, which resolves G4s during replication, was highly upregulated in tumors, and Pif1 knockout in primary MB tumor cells resulted in increased genome instability upon pyridostatin treatment. These data suggest that G4s may represent sites prone to replication stalling in highly proliferative GCPs and without BRCA2, G4s become a source of genome instability. Tumor cells upregulate G4-resolving helicases to facilitate rapid proliferation through G4s highlighting PIF1 helicase as a potential therapeutic target for treatment of BRCA2-deficient medulloblastomas.
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Affiliation(s)
- Danielle L. Keahi
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
| | - Mathijs A. Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Matthew R. Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | | | - Yin Fang
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA
| | - Tom F. Wiley
- Comparative Bioscience Center, The Rockefeller University, New York, NY, USA
| | - Samer Shalaby
- Flow Cytometry Resource Center, The Rockefeller University, New York, NY, USA
| | - Thomas S. Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Settara C. Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - John E. Wagner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Mary E. Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
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2
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Hong Z, Byrd AK, Gao J, Das P, Tan VQ, Malone EG, Osei B, Marecki JC, Protacio RU, Wahls WP, Raney KD, Song H. Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge. Nat Commun 2024; 15:6104. [PMID: 39030241 PMCID: PMC11275212 DOI: 10.1038/s41467-024-50575-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 07/16/2024] [Indexed: 07/21/2024] Open
Abstract
G-quadruplexes (G4s) formed by guanine-rich nucleic acids induce genome instability through impeding DNA replication fork progression. G4s are stable DNA structures, the unfolding of which require the functions of DNA helicases. Pif1 helicase binds preferentially to G4 DNA and plays multiple roles in maintaining genome stability, but the mechanism by which Pif1 unfolds G4s is poorly understood. Here we report the co-crystal structure of Saccharomyces cerevisiae Pif1 (ScPif1) bound to a G4 DNA with a 5' single-stranded DNA (ssDNA) segment. Unlike the Thermus oshimai Pif1-G4 structure, in which the 1B and 2B domains confer G4 recognition, ScPif1 recognizes G4 mainly through the wedge region in the 1A domain that contacts the 5' most G-tetrad directly. A conserved Arg residue in the wedge is required for Okazaki fragment processing but not for mitochondrial function or for suppression of gross chromosomal rearrangements. Multiple substitutions at this position have similar effects on resolution of DNA duplexes and G4s, suggesting that ScPif1 may use the same wedge to unwind G4 and dsDNA. Our results reveal the mechanism governing dsDNA unwinding and G4 unfolding by ScPif1 helicase that can potentially be generalized to other eukaryotic Pif1 helicases and beyond.
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Affiliation(s)
- Zebin Hong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Poulomi Das
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore
| | - Vanessa Qianmin Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore
| | - Emory G Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Bertha Osei
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Reine U Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Haiwei Song
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore.
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3
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Gao J, Proffitt D, Marecki J, Protacio R, Wahls W, Byrd A, Raney K. Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth. Nucleic Acids Res 2024; 52:6543-6557. [PMID: 38752483 PMCID: PMC11194084 DOI: 10.1093/nar/gkae403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
Pif1 helicase functions in both the nucleus and mitochondria. Pif1 tightly couples ATP hydrolysis, single-stranded DNA translocation, and duplex DNA unwinding. We investigated two Pif1 variants (F723A and T464A) that have each lost one site of interaction of the protein with the DNA substrate. Both variants exhibit minor reductions in affinity for DNA and ATP hydrolysis but have impaired DNA unwinding activity. However, these variants translocate on single-stranded DNA faster than the wildtype enzyme and can slide on the DNA substrate in an ATP-independent manner. This suggests they have lost their grip on the DNA, interfering with coupling ATP hydrolysis to translocation and unwinding. Yeast expressing these variants have increased gross chromosomal rearrangements, increased telomere length, and can overcome the lethality of dna2Δ, similar to phenotypes of yeast lacking Pif1. However, unlike pif1Δ mutants, they are viable on glycerol containing media and maintain similar mitochondrial DNA copy numbers as Pif1 wildtype. Overall, our data indicate that a tight grip of the trailing edge of the Pif1 enzyme on the DNA couples ATP hydrolysis to DNA translocation and DNA unwinding. This tight grip appears to be essential for the Pif1 nuclear functions tested but is dispensable for mitochondrial respiratory growth.
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Affiliation(s)
- Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - David R Proffitt
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Reine U Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, AR 72205, USA
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4
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Lee RS, Geronimo CL, Liu L, Twarowski JM, Malkova A, Zakian VA. Identification of the nuclear localization signal in the Saccharomyces cerevisiae Pif1 DNA helicase. PLoS Genet 2023; 19:e1010853. [PMID: 37486934 PMCID: PMC10399864 DOI: 10.1371/journal.pgen.1010853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/03/2023] [Accepted: 07/02/2023] [Indexed: 07/26/2023] Open
Abstract
Saccharomyces cerevisiae Pif1 is a multi-functional DNA helicase that plays diverse roles in the maintenance of the nuclear and mitochondrial genomes. Two isoforms of Pif1 are generated from a single open reading frame by the use of alternative translational start sites. The Mitochondrial Targeting Signal (MTS) of Pif1 is located between the two start sites, but a Nuclear Localization Signal (NLS) has not been identified. Here we used sequence and functional analysis to identify an NLS element. A mutant allele of PIF1 (pif1-NLSΔ) that lacks four basic amino acids (781KKRK784) in the carboxyl-terminal domain of the 859 amino acid Pif1 was expressed at wild type levels and retained wild type mitochondrial function. However, pif1-NLSΔ cells were defective in four tests for nuclear function: telomere length maintenance, Okazaki fragment processing, break-induced replication (BIR), and binding to nuclear target sites. Fusing the NLS from the simian virus 40 (SV40) T-antigen to the Pif1-NLSΔ protein reduced the nuclear defects of pif1-NLSΔ cells. Thus, four basic amino acids near the carboxyl end of Pif1 are required for the vast majority of nuclear Pif1 function. Our study also reveals phenotypic differences between the previously described loss of function pif1-m2 allele and three other pif1 mutant alleles generated in this work, which will be useful to study nuclear Pif1 functions.
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Affiliation(s)
- Rosemary S. Lee
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Carly L. Geronimo
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Liping Liu
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Jerzy M. Twarowski
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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5
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Mustafi M, Kwon Y, Sung P, Greene EC. Single-molecule visualization of Pif1 helicase translocation on single-stranded DNA. J Biol Chem 2023; 299:104817. [PMID: 37178921 PMCID: PMC10279920 DOI: 10.1016/j.jbc.2023.104817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Pif1 is a broadly conserved helicase that is essential for genome integrity and participates in numerous aspects of DNA metabolism, including telomere length regulation, Okazaki fragment maturation, replication fork progression through difficult-to-replicate sites, replication fork convergence, and break-induced replication. However, details of its translocation properties and the importance of amino acids residues implicated in DNA binding remain unclear. Here, we use total internal reflection fluorescence microscopy with single-molecule DNA curtain assays to directly observe the movement of fluorescently tagged Saccharomyces cerevisiae Pif1 on single-stranded DNA (ssDNA) substrates. We find that Pif1 binds tightly to ssDNA and translocates very rapidly (∼350 nucleotides per second) in the 5'→3' direction over relatively long distances (∼29,500 nucleotides). Surprisingly, we show the ssDNA-binding protein replication protein A inhibits Pif1 activity in both bulk biochemical and single-molecule measurements. However, we demonstrate Pif1 can strip replication protein A from ssDNA, allowing subsequent molecules of Pif1 to translocate unimpeded. We also assess the functional attributes of several Pif1 mutations predicted to impair contact with the ssDNA substrate. Taken together, our findings highlight the functional importance of these amino acid residues in coordinating the movement of Pif1 along ssDNA.
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Affiliation(s)
- Mainak Mustafi
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, USA.
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6
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Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. Int J Mol Sci 2022; 23:ijms23073736. [PMID: 35409096 PMCID: PMC8998199 DOI: 10.3390/ijms23073736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Pif1 helicases are a multifunctional family of DNA helicases that are important for many aspects of genomic stability in the nucleus and mitochondria. Pif1 helicases are conserved from bacteria to humans. Pif1 helicases play multiple roles at the replication fork, including promoting replication through many barriers such as G-quadruplex DNA, the rDNA replication fork barrier, tRNA genes, and R-loops. Pif1 helicases also regulate telomerase and promote replication termination, Okazaki fragment maturation, and break-induced replication. This review highlights many of the roles and regulations of Pif1 at the replication fork that promote cellular health and viability.
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Affiliation(s)
- Emory G. Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Matthew D. Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: ; Tel.: +1-501-526-6488
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7
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Zhang B, Zhang Q, Zhu X, Li D, Duan X, Jin J, Wang K, Xie Y, Liu Y. Mechanistic Insight Into Cadmium- and Zinc-Induced Inactivation of the Candida albicans Pif1 Helicase. Front Mol Biosci 2022; 8:778647. [PMID: 35127815 PMCID: PMC8815974 DOI: 10.3389/fmolb.2021.778647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Zinc and cadmium are environmental contaminants that can cause disease by affecting the activity of DNA-repair proteins. In this study, we investigated the effect of Zn2+ and Cd2+ on the Candida albicans Pif1, a DNA-repair helicase that plays a critical role in ensuring genomic stability. We show that Zn2+ and Cd2+ strongly inhibit both the ATPase and the unwinding activities of CaPif1, but have no effect on its DNA binding activity. High concentrations of Cd2+ may bind to the cysteine residues of CaPif1, and its inhibition appears to be difficult to be restored by ethylene diamine tetraacetic acid, while inhibition due to Zn2+ can. When the two ions are at low concentrations, increasing the concentration of ATP in the reaction can appropriately weaken the inhibitory effect of Zn2+, while cysteine can reduce the inhibitory effect of Cd2+. In addition, we found that for both Cd2+ and Zn2+ the inhibition effects were nearly 100 times greater in reduced environments than in non-reducing environments. When heavy metals stimulate the body’s response, the environment of the body becomes less reducing, and thus the tolerance of CaPif1 to heavy metals will be stronger. We propose that CaPif1 may resist the toxicity of heavy metals through this mechanism. Altogether, our results provide new insights into the mechanisms by which heavy metals are toxic to DNA-repair proteins.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Yan Xie, ; Bo Zhang,
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Dayu Li
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaolei Duan
- Medical Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiao Jin
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- College of Life Sciences, Guizhou University, Guiyang, China
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Yan Xie, ; Bo Zhang,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Yan Xie, ; Bo Zhang,
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8
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Obi I, Rentoft M, Singh V, Jamroskovic J, Chand K, Chorell E, Westerlund F, Sabouri N. Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication. Nucleic Acids Res 2020; 48:10998-11015. [PMID: 33045725 PMCID: PMC7641769 DOI: 10.1093/nar/gkaa820] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022] Open
Abstract
G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.
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Affiliation(s)
- Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Matilda Rentoft
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
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9
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Su N, Byrd AK, Bharath SR, Yang O, Jia Y, Tang X, Ha T, Raney KD, Song H. Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases. Nat Commun 2019; 10:5375. [PMID: 31772234 PMCID: PMC6879534 DOI: 10.1038/s41467-019-13414-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022] Open
Abstract
Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA, but the mechanism by which Pif1 unwinds forked dsDNA remains elusive. Here we report the structure of Bacteroides sp Pif1 (BaPif1) in complex with a symmetrical double forked dsDNA. Two interacting BaPif1 molecules are bound to each fork of the partially unwound dsDNA, and interact with the 5′ arm and 3′ ss/dsDNA respectively. Each of the two BaPif1 molecules is an active helicase and their interaction may regulate their helicase activities. The binding of BaPif1 to the 5′ arm causes a sharp bend in the 5′ ss/dsDNA junction, consequently breaking the first base-pair. BaPif1 bound to the 3′ ss/dsDNA junction impacts duplex unwinding by stabilizing the unpaired first base-pair and engaging the second base-pair poised for breaking. Our results provide an unprecedented insight into how two BaPif1 coordinate with each other to unwind the forked dsDNA. Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA. Here the authors solve the structure of Bacteroides sp Pif1 (BaPif1) in complex with a symmetrical double forked dsDNA and provide unprecedented insights into forked dsDNA unwinding by BaPif1.
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Affiliation(s)
- Nannan Su
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Yu Jia
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Haiwei Song
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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10
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Pohl TJ, Zakian VA. Pif1 family DNA helicases: A helpmate to RNase H? DNA Repair (Amst) 2019; 84:102633. [PMID: 31231063 DOI: 10.1016/j.dnarep.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 01/21/2023]
Abstract
An R-loop is a structure that forms when an RNA transcript stays bound to the DNA strand that encodes it and leaves the complementary strand exposed as a loop of single stranded DNA. R-loops accumulate when the processing of RNA transcripts is impaired. The failure to remove these RNA-DNA hybrids can lead to replication fork stalling and genome instability. Resolution of R-loops is thought to be mediated mainly by RNase H enzymes through the removal and degradation of the RNA in the hybrid. However, DNA helicases can also dismantle R-loops by displacing the bound RNA. In particular, the Pif1 family DNA helicases have been shown to regulate R-loop formation at specific genomic loci, such as tRNA genes and centromeres. Here we review the roles of Pif1 family helicases in vivo and in vitro and discuss evidence that Pif1 family helicases act on RNA-DNA hybrids and highlight their potential roles in complementing RNase H for R-loop resolution.
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Affiliation(s)
- Thomas J Pohl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States.
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11
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Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in Saccharomyces cerevisiae. Genetics 2018; 211:105-119. [PMID: 30442759 PMCID: PMC6325707 DOI: 10.1534/genetics.118.301710] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
Pif1 family helicases are found in virtually all eukaryotes. Saccharomyces cerevisiae (Sc) encodes two Pif1 family helicases, ScPif1 and Rrm3 ScPif1 is multifunctional, required not only for maintenance of mitochondrial DNA but also for multiple distinct nuclear functions. Rrm3 moves with the replication fork and promotes movement of the fork through ∼1400 hard-to-replicate sites, including centromeres. Here we show that ScPif1, like Rrm3, bound robustly to yeast centromeres but only if the centromere was active. While Rrm3 binding to centromeres occurred in early to mid S phase, about the same time as centromere replication, ScPif1 binding occurred later in the cell cycle when replication of most centromeres is complete. However, the timing of Rrm3 and ScPif1 centromere binding was altered by the absence of the other helicase, such that Rrm3 centromere binding occurred later in pif1-m2 cells and ScPif1 centromere binding occurred earlier in rrm3Δ cells. As shown previously, the modest pausing of replication forks at centromeres seen in wild-type cells was increased in the absence of Rrm3 While a lack of ScPif1 did not result in increased fork pausing at centromeres, pausing was even higher in rrm3Δ pif1Δ cells than in rrm3Δ cells. Likewise, centromere function as monitored by the loss rate of a centromere plasmid was increased in rrm3Δ but not pif1Δ cells, and was even higher in rrm3Δ pif1Δ cells than in rrm3Δ cells. Thus, ScPif1 promotes centromere replication and segregation, but only in the absence of Rrm3 These data also hint at a potential post-S phase function for ScPif1 at centromeres. These studies add to the growing list of ScPif1 functions that promote chromosome stability.
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Mohammad JB, Wallgren M, Sabouri N. The Pif1 signature motif of Pfh1 is necessary for both protein displacement and helicase unwinding activities, but is dispensable for strand-annealing activity. Nucleic Acids Res 2018; 46:8516-8531. [PMID: 30053106 PMCID: PMC6144812 DOI: 10.1093/nar/gky654] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 01/14/2023] Open
Abstract
Pfh1, the sole member of the Pif1 helicases in Schizosaccharomyces pombe, is multifunctional and essential for maintenance of both the nuclear and mitochondrial genomes. However, we lack mechanistic insights into the functions of Pfh1 and its different motifs. This paper is specifically concerned with the importance of the Pif1 signature motif (SM), a 23 amino acids motif unique to Pif1 helicases, because a single amino acid substitution in this motif is associated with increased risk of breast cancer in humans and inviability in S. pombe. Here we show that the nuclear isoform of Pfh1 (nPfh1) unwound RNA/DNA hybrids more efficiently than DNA/DNA, suggesting that Pfh1 resolves RNA/DNA structures like R-loops in vivo. In addition, nPfh1 displaced proteins from DNA and possessed strand-annealing activity. The unwinding and protein displacement activities were dependent on the SM because nPfh1 without a large portion of this motif (nPfh1-Δ21) or with the disease/inviability-linked mutation (nPfh1-L430P) lost these properties. Unexpectedly, both nPfh1-L430P and nPfh1-Δ21 still displayed binding to G-quadruplex DNA and demonstrated strand-annealing activity. Misregulated strand annealing and binding of nPfh1-L430P without unwinding are perhaps the reasons that cells expressing this allele are inviable.
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Affiliation(s)
- Jani B Mohammad
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | - Marcus Wallgren
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
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