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Shepelev N, Dontsova O, Rubtsova M. Post-Transcriptional and Post-Translational Modifications in Telomerase Biogenesis and Recruitment to Telomeres. Int J Mol Sci 2023; 24:5027. [PMID: 36902458 PMCID: PMC10003056 DOI: 10.3390/ijms24055027] [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: 02/02/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Telomere length is associated with the proliferative potential of cells. Telomerase is an enzyme that elongates telomeres throughout the entire lifespan of an organism in stem cells, germ cells, and cells of constantly renewed tissues. It is activated during cellular division, including regeneration and immune responses. The biogenesis of telomerase components and their assembly and functional localization to the telomere is a complex system regulated at multiple levels, where each step must be tuned to the cellular requirements. Any defect in the function or localization of the components of the telomerase biogenesis and functional system will affect the maintenance of telomere length, which is critical to the processes of regeneration, immune response, embryonic development, and cancer progression. An understanding of the regulatory mechanisms of telomerase biogenesis and activity is necessary for the development of approaches toward manipulating telomerase to influence these processes. The present review focuses on the molecular mechanisms involved in the major steps of telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
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Affiliation(s)
- Nikita Shepelev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Olga Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maria Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437, Russia
- Chemistry Department and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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2
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Abstract
The gene encoding the Pif1 helicase was first discovered in a Saccharomyces cerevisiae genetic screen as a mutant that reduces recombination between mitochondrial respiratory mutants and was subsequently rediscovered in a screen for genes affecting the telomere length in the nucleus. It is now known that Pif1 is involved in numerous aspects of DNA metabolism. All known functions of Pif1 rely on binding to DNA substrates followed by ATP hydrolysis, coupling the energy released to translocation along DNA to unwind duplex DNA or alternative DNA secondary structures. The interaction of Pif1 with higher-order DNA structures, like G-quadruplex DNA, as well as the length of single-stranded (ss)DNA necessary for Pif1 loading have been widely studied. Here, to test the effects of ssDNA length, sequence, and structure on Pif1's biochemical activities in vitro, we used a suite of oligonucleotide-based substrates to perform a basic characterization of Pif1 ssDNA binding, ATPase activity, and helicase activity. Using recombinant, untagged S. cerevisiae Pif1, we found that Pif1 preferentially binds to structured G-rich ssDNA, but the preferred binding substrates failed to maximally stimulate ATPase activity. In helicase assays, significant DNA unwinding activity was detected at Pif1 concentrations as low as 250 pM. Helicase assays also demonstrated that Pif1 most efficiently unwinds DNA fork substrates with unstructured ssDNA tails. As the chemical step size of Pif1 has been determined to be 1 ATP per translocation or unwinding event, this implies that the highly structured DNA inhibits conformational changes in Pif1 that couple ATP hydrolysis to DNA translocation and unwinding.
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Affiliation(s)
- David G Nickens
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Matthew L Bochman
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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3
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Zhou L, Zheng S, Rosas Bringas FR, Bakker B, Simon JE, Bakker PL, Kazemier HG, Schubert M, Roorda M, van Vugt MATM, Chang M, Foijer F. A synthetic lethal screen identifies HDAC4 as a potential target in MELK overexpressing cancers. G3 (BETHESDA, MD.) 2021; 11:jkab335. [PMID: 34550356 PMCID: PMC8664443 DOI: 10.1093/g3journal/jkab335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022]
Abstract
Maternal embryonic leucine zipper kinase (MELK) is frequently overexpressed in cancer, but the role of MELK in cancer is still poorly understood. MELK was shown to have roles in many cancer-associated processes including tumor growth, chemotherapy resistance, and tumor recurrence. To determine whether the frequent overexpression of MELK can be exploited in therapy, we performed a high-throughput screen using a library of Saccharomyces cerevisiae mutants to identify genes whose functions become essential when MELK is overexpressed. We identified two such genes: LAG2 and HDA3. LAG2 encodes an inhibitor of the Skp, Cullin, F-box containing (SCF) ubiquitin-ligase complex, while HDA3 encodes a subunit of the HDA1 histone deacetylase complex. We find that one of these synthetic lethal interactions is conserved in mammalian cells, as inhibition of a human homolog of HDA3 (Histone Deacetylase 4, HDAC4) is synthetically toxic in MELK overexpression cells. Altogether, our work identified a novel potential drug target for tumors that overexpress MELK.
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Affiliation(s)
- Lin Zhou
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Siqi Zheng
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Fernando R Rosas Bringas
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Judith E Simon
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Petra L Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Michael Schubert
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Maurits Roorda
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
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4
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Holland CL, Sanderson BA, Titus JK, Weis MF, Riojas AM, Malczewskyj E, Wasko BM, Lewis LK. Suppression of telomere capping defects of Saccharomyces cerevisiae yku70 and yku80 mutants by telomerase. G3-GENES GENOMES GENETICS 2021; 11:6395363. [PMID: 34718547 PMCID: PMC8664480 DOI: 10.1093/g3journal/jkab359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022]
Abstract
The Ku complex performs multiple functions inside eukaryotic cells, including protection of chromosomal DNA ends from degradation and fusion events, recruitment of telomerase, and repair of double-strand breaks (DSBs). Inactivation of Ku complex genes YKU70 or YKU80 in cells of the yeast Saccharomyces cerevisiae gives rise to mutants that exhibit shortened telomeres and temperature-sensitive growth. In this study, we have investigated the mechanism by which overexpression of telomerase suppresses the temperature sensitivity of yku mutants. Viability of yku cells was restored by overexpression of the Est2 reverse transcriptase and TLC1 RNA template subunits of telomerase, but not the Est1 or Est3 proteins. Overexpression of other telomerase- and telomere-associated proteins (Cdc13, Stn1, Ten1, Rif1, Rif2, Sir3, and Sir4) did not suppress the growth defects of yku70 cells. Mechanistic features of suppression were assessed using several TLC1 RNA deletion derivatives and Est2 enzyme mutants. Supraphysiological levels of three catalytically inactive reverse transcriptase mutants (Est2-D530A, Est2-D670A, and Est2-D671A) suppressed the loss of viability as efficiently as the wild-type Est2 protein, without inducing cell senescence. Roles of proteins regulating telomere length were also determined. The results support a model in which chromosomes in yku mutants are stabilized via a replication-independent mechanism involving structural reinforcement of protective telomere cap structures.
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Affiliation(s)
- Cory L Holland
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Brian A Sanderson
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - James K Titus
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Monica F Weis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Angelica M Riojas
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Eric Malczewskyj
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Brian M Wasko
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX, 77058, USA
| | - L Kevin Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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5
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Lin YY, Li MH, Chang YC, Fu PY, Ohniwa RL, Li HW, Lin JJ. Dynamic DNA Shortening by Telomere-Binding Protein Cdc13. J Am Chem Soc 2021; 143:5815-5825. [PMID: 33831300 DOI: 10.1021/jacs.1c00820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Telomeres are essential for chromosome maintenance. Cdc13 is a single-stranded telomeric DNA binding protein that caps telomeres and regulates telomerase function in yeast. Although specific binding of Cdc13 to telomeric DNA is critical for telomere protection, the detail mechanism how Cdc13-DNA complex protects telomere is unclear. Using two single-molecule methods, tethered particle motion and atomic force microscopy, we demonstrate that specific binding of Cdc13 on single-stranded telomeric DNA shortens duplex DNA into distinct states differed by ∼70-80 base pairs. DNA shortening by Cdc13 is dynamic and independent of duplex DNA sequences or length. Significantly, we found that Pif1 helicase is incapable of removing Cdc13 from the shortened DNA-Cdc13 complex, suggesting that Cdc13 forms structurally stable complex by shortening of the bound DNA. Together our data identified shortening of DNA by Cdc13 and provided an indication for efficient protection of telomere ends by the shortened DNA-Cdc13 complex.
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Affiliation(s)
- Yi-Yun Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan
| | - Min-Hsuan Li
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan
| | - Yen-Chan Chang
- Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
| | - Peng-Yu Fu
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan
| | - Ryosuke L Ohniwa
- Faculty of Medicine, University of Tsukuba, Ibaraki 305-8577, Japan.,Center for Biotechnology, National Taiwan University, Taipei City 10617, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
| | - Jing-Jer Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei City 10617, Taiwan.,Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei City 112, Taiwan
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6
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Muellner J, Schmidt KH. Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family. Genes (Basel) 2020; 11:genes11020224. [PMID: 32093266 PMCID: PMC7073672 DOI: 10.3390/genes11020224] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/04/2022] Open
Abstract
The two PIF1 family helicases in Saccharomyces cerevisiae, Rrm3, and ScPif1, associate with thousands of sites throughout the genome where they perform overlapping and distinct roles in telomere length maintenance, replication through non-histone proteins and G4 structures, lagging strand replication, replication fork convergence, the repair of DNA double-strand break ends, and transposable element mobility. ScPif1 and its fission yeast homolog Pfh1 also localize to mitochondria where they protect mitochondrial genome integrity. In addition to yeast serving as a model system for the rapid functional evaluation of human Pif1 variants, yeast cells lacking Rrm3 have proven useful for elucidating the cellular response to replication fork pausing at endogenous sites. Here, we review the increasingly important cellular functions of the yeast PIF1 helicases in maintaining genome integrity, and highlight recent advances in our understanding of their roles in facilitating fork progression through replisome barriers, their functional interactions with DNA repair, and replication stress response pathways.
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Affiliation(s)
- Julius Muellner
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kristina H. Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA;
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
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Maestroni L, Audry J, Luciano P, Coulon S, Géli V, Corda Y. RPA and Pif1 cooperate to remove G-rich structures at both leading and lagging strand. Cell Stress 2020; 4:48-63. [PMID: 32190820 PMCID: PMC7063842 DOI: 10.15698/cst2020.03.214] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In Saccharomyces cerevisiae, the absence of Pif1 helicase induces the instability of G4-containing CEB1 minisatellite during leading strand but not lagging strand replication. We report that RPA and Pif1 cooperate to maintain CEB1 stability when the G4 forming strand is either on the leading or lagging strand templates. At the leading strand, RPA acts in the same pathway as Pif1 to maintain CEB1 stability. Consistent with this result, RPA co-precipitates with Pif1. This association between Pif1 and RPA is affected by the rfa1-D228Y mutation that lowers the affinity of RPA in particular for G-rich single-stranded DNA. At the lagging strand, in contrast to pif1Δ, the rfa1-D228Y mutation strongly increases the frequency of CEB1 rearrangements. We explain that Pif1 is dispensable at the lagging strand DNA by the ability of RPA by itself to prevent formation of stable G-rich secondary structures during lagging strand synthesis. Remarkably, overexpression of Pif1 rescues the instability of CEB1 at the lagging strand in the rfa1-D228Y mutant indicating that Pif1 can also act at the lagging strand. We show that the effects of the rfa1-D228Y (rpa1-D223Y in fission yeast) are conserved in Schizosaccharomyces pombe. Finally, we report that RNase H1 interacts in a DNA-dependent manner with RPA in budding yeast, however overexpression of RNase H1 does not rescue CEB1 instability observed in pif1Δ and rfa1-D228Y mutants. Collectively these results add new insights about the general role of RPA in preventing formation of DNA secondary structures and in coordinating the action of factors aimed at resolving them.
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Affiliation(s)
- Laetitia Maestroni
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Julien Audry
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Pierre Luciano
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Stéphane Coulon
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Vincent Géli
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Yves Corda
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
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8
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Dahan D, Tsirkas I, Dovrat D, Sparks MA, Singh SP, Galletto R, Aharoni A. Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures. Nucleic Acids Res 2019; 46:11847-11857. [PMID: 30395308 PMCID: PMC6294490 DOI: 10.1093/nar/gky1065] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/18/2018] [Indexed: 12/27/2022] Open
Abstract
Pif1 DNA helicase is a potent unwinder of G-quadruplex (G4) structures in vitro and functions to maintain genome stability at G4 sequences in Saccharomyces cerevisiae. Here, we developed and utilized a live-cell imaging approach to quantitatively measure the progression rates of single replication forks through different G4 containing sequences in individual yeast cells. We show that in the absence of Pif1, replication rates through specific lagging strand G4 sequences in vivo is significantly decreased. In contrast, we found that in the absence of Pif1, replication rates through the same G4s on the leading strand are not decreased relative to the respective WT strains, showing that Pif1 is essential only for efficient replication through lagging strand G4s. Additionally, we show that a canonical PIP sequence in Pif1 interacts with PCNA and that replication through G4 structures is significantly slower in the absence of this interaction in vitro and in vivo. Thus, Pif1–PCNA interaction is essential for optimal replisome progression through G4 sequences, highlighting the importance of coupling between Pif1 activity and replisome progression during yeast genome replication.
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Affiliation(s)
- Danielle Dahan
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Melanie A Sparks
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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9
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Belmonte FR, Dedousis N, Sipula I, Desai NA, Singhi AD, Chu Y, Zhang Y, Bannwarth S, Paquis-Flucklinger V, Harrington L, Shiva S, Jurczak MJ, O’Doherty RM, Kaufman BA. Petite Integration Factor 1 (PIF1) helicase deficiency increases weight gain in Western diet-fed female mice without increased inflammatory markers or decreased glucose clearance. PLoS One 2019; 14:e0203101. [PMID: 31136580 PMCID: PMC6538152 DOI: 10.1371/journal.pone.0203101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 05/09/2019] [Indexed: 11/19/2022] Open
Abstract
Petite Integration Factor 1 (PIF1) is a multifunctional helicase present in nuclei and mitochondria. PIF1 knock out (KO) mice exhibit accelerated weight gain and decreased wheel running on a normal chow diet. In the current study, we investigated whether Pif1 ablation alters whole body metabolism in response to weight gain. PIF1 KO and wild type (WT) C57BL/6J mice were fed a Western diet (WD) rich in fat and carbohydrates before evaluation of their metabolic phenotype. Compared with weight gain-resistant WT female mice, WD-fed PIF1 KO females, but not males, showed accelerated adipose deposition, decreased locomotor activity, and reduced whole-body energy expenditure without increased dietary intake. Surprisingly, PIF1 KO females did not show obesity-induced alterations in fasting blood glucose and glucose clearance. WD-fed PIF1 KO females developed mild hepatic steatosis and associated changes in liver gene expression that were absent in weight-matched, WD-fed female controls, linking hepatic steatosis to Pif1 ablation rather than increased body weight. WD-fed PIF1 KO females also showed decreased expression of inflammation-associated genes in adipose tissue. Collectively, these data separated weight gain from inflammation and impaired glucose homeostasis. They also support a role for Pif1 in weight gain resistance and liver metabolic dysregulation during nutrient stress.
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Affiliation(s)
- Frances R. Belmonte
- University of Pittsburgh School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, and Vascular Medicine Institute, Pittsburgh, PA, United States of America
| | - Nikolaos Dedousis
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Biomedical Science Tower, Pittsburgh, PA, United States of America
| | - Ian Sipula
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Biomedical Science Tower, Pittsburgh, PA, United States of America
| | - Nikita A. Desai
- University of Pittsburgh School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, and Vascular Medicine Institute, Pittsburgh, PA, United States of America
| | - Aatur D. Singhi
- Department of Pathology and Pittsburgh Liver Research Center, University of Pittsburgh, Scaife Hall, Pittsburgh, PA, United States of America
| | - Yanxia Chu
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, UPMC Montefiore Hospital, Pittsburgh, PA, United States of America
| | - Yingze Zhang
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, UPMC Montefiore Hospital, Pittsburgh, PA, United States of America
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, France
| | | | - Lea Harrington
- Université de Montréal, Institut de Recherche en Immunologie et en Cancérologie, Montréal, Québec, Canada
| | - Sruti Shiva
- University of Pittsburgh School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, and Vascular Medicine Institute, Pittsburgh, PA, United States of America
| | - Michael J. Jurczak
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Biomedical Science Tower, Pittsburgh, PA, United States of America
| | - Robert M. O’Doherty
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Biomedical Science Tower, Pittsburgh, PA, United States of America
| | - Brett A. Kaufman
- University of Pittsburgh School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, and Vascular Medicine Institute, Pittsburgh, PA, United States of America
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10
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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: 20] [Impact Index Per Article: 2.9] [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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11
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Structure and function of Pif1 helicase. Biochem Soc Trans 2017; 45:1159-1171. [PMID: 28900015 DOI: 10.1042/bst20170096] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/18/2022]
Abstract
Pif1 family helicases have multiple roles in the maintenance of nuclear and mitochondrial DNA in eukaryotes. Saccharomyces cerevisiae Pif1 is involved in replication through barriers to replication, such as G-quadruplexes and protein blocks, and reduces genetic instability at these sites. Another Pif1 family helicase in S. cerevisiae, Rrm3, assists in fork progression through replication fork barriers at the rDNA locus and tRNA genes. ScPif1 (Saccharomyces cerevisiae Pif1) also negatively regulates telomerase, facilitates Okazaki fragment processing, and acts with polymerase δ in break-induced repair. Recent crystal structures of bacterial Pif1 helicases and the helicase domain of human PIF1 combined with several biochemical and biological studies on the activities of Pif1 helicases have increased our understanding of the function of these proteins. This review article focuses on these structures and the mechanism(s) proposed for Pif1's various activities on DNA.
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12
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Tran PLT, Pohl TJ, Chen CF, Chan A, Pott S, Zakian VA. PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes. Nat Commun 2017; 8:15025. [PMID: 28429714 PMCID: PMC5413955 DOI: 10.1038/ncomms15025] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/17/2017] [Indexed: 01/21/2023] Open
Abstract
Saccharomyces cerevisiae encodes two Pif1 family DNA helicases, Pif1 and Rrm3. Rrm3 promotes DNA replication past stable protein complexes at tRNA genes (tDNAs). We identify a new role for the Pif1 helicase: promotion of replication and suppression of DNA damage at tDNAs. Pif1 binds multiple tDNAs, and this binding is higher in rrm3Δ cells. Accumulation of replication intermediates and DNA damage at tDNAs is higher in pif1Δ rrm3Δ than in rrm3Δ cells. DNA damage at tDNAs in the absence of these helicases is suppressed by destabilizing R-loops while Pif1 and Rrm3 binding to tDNAs is increased upon R-loop stabilization. We propose that Rrm3 and Pif1 promote genome stability at tDNAs by displacing the stable multi-protein transcription complex and by removing R-loops. Thus, we identify tDNAs as a new source of R-loop-mediated DNA damage. Given their large number and high transcription rate, tDNAs may be a potent source of genome instability. The budding yeast genome encodes two Pif1 family helicases, Pif1 and Rrm3, previously shown to have distinct functions in the maintenance of telomeres and other aspects of genome stability. Here the authors identify a role for Pif1 (and Rrm3) in promoting DNA replication and suppressing R-loop mediated DNA damage at tRNA genes.
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Affiliation(s)
- Phong Lan Thao Tran
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA
| | - Thomas J Pohl
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA
| | - Chi-Fu Chen
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, 920 E 58th St, Chicago, Illinois 60637, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA
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13
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McDonald KR, Guise AJ, Pourbozorgi-Langroudi P, Cristea IM, Zakian VA, Capra JA, Sabouri N. Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity. PLoS Genet 2016; 12:e1006238. [PMID: 27611590 PMCID: PMC5017727 DOI: 10.1371/journal.pgen.1006238] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 08/11/2016] [Indexed: 12/27/2022] Open
Abstract
Replicative DNA helicases expose the two strands of the double helix to the replication apparatus, but accessory helicases are often needed to help forks move past naturally occurring hard-to-replicate sites, such as tightly bound proteins, RNA/DNA hybrids, and DNA secondary structures. Although the Schizosaccharomyces pombe 5’-to-3’ DNA helicase Pfh1 is known to promote fork progression, its genomic targets, dynamics, and mechanisms of action are largely unknown. Here we address these questions by integrating genome-wide identification of Pfh1 binding sites, comprehensive analysis of the effects of Pfh1 depletion on replication and DNA damage, and proteomic analysis of Pfh1 interaction partners by immunoaffinity purification mass spectrometry. Of the 621 high confidence Pfh1-binding sites in wild type cells, about 40% were sites of fork slowing (as marked by high DNA polymerase occupancy) and/or DNA damage (as marked by high levels of phosphorylated H2A). The replication and integrity of tRNA and 5S rRNA genes, highly transcribed RNA polymerase II genes, and nucleosome depleted regions were particularly Pfh1-dependent. The association of Pfh1 with genomic integrity at highly transcribed genes was S phase dependent, and thus unlikely to be an artifact of high transcription rates. Although Pfh1 affected replication and suppressed DNA damage at discrete sites throughout the genome, Pfh1 and the replicative DNA polymerase bound to similar extents to both Pfh1-dependent and independent sites, suggesting that Pfh1 is proximal to the replication machinery during S phase. Consistent with this interpretation, Pfh1 co-purified with many key replisome components, including the hexameric MCM helicase, replicative DNA polymerases, RPA, and the processivity clamp PCNA in an S phase dependent manner. Thus, we conclude that Pfh1 is an accessory DNA helicase that interacts with the replisome and promotes replication and suppresses DNA damage at hard-to-replicate sites. These data provide insight into mechanisms by which this evolutionarily conserved helicase helps preserve genome integrity. Progression of the DNA replication machinery is challenged in every S phase by active transcription, tightly bound protein complexes, and formation of stable DNA secondary structures. Using genome-wide analyses, we show that the evolutionarily conserved fission yeast Pfh1 DNA helicase promotes fork progression and suppresses DNA damage at natural sites of fork pausing, which occur at “hard-to-replicate” sites. Our data suggest that Pfh1 interacts with the replication apparatus. First, mass spectrometry revealed that Pfh1 interacts with many components of the replication machinery. Second, Pfh1 and the leading strand DNA polymerase occupy many common regions genome-wide, not only hard-to-replicate sites, but also sites whose replication is not Pfh1-dependent. The human genome encodes a Pfh1 homolog, hPIF1, and contains all of the same hard-to-replicate features that make fission yeast DNA replication dependent upon Pfh1. Thus, human cells likely also require replicative accessory DNA helicases to facilitate replication at hard-to-replicate sites, and hPIF1 is a good candidate for this role.
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Affiliation(s)
- Karin R. McDonald
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Amanda J. Guise
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | | | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - John A. Capra
- Department of Biological Sciences, Vanderbilt Genetics Institute, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (JAC); (NS)
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- * E-mail: (JAC); (NS)
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14
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Silva S, Altmannova V, Luke-Glaser S, Henriksen P, Gallina I, Yang X, Choudhary C, Luke B, Krejci L, Lisby M. Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. Genes Dev 2016; 30:700-17. [PMID: 26966248 PMCID: PMC4803055 DOI: 10.1101/gad.276204.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/17/2016] [Indexed: 11/25/2022]
Abstract
Mph1 is a member of the conserved FANCM family of DNA motor proteins that play key roles in genome maintenance processes underlying Fanconi anemia, a cancer predisposition syndrome in humans. Here, we identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. In vitro, Mte1 (Mph1-associated telomere maintenance protein 1) binds directly to DNA with a preference for branched molecules such as D loops and fork structures. In addition, Mte1 stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Deletion of MTE1 reduces crossover recombination and suppresses the sensitivity of mph1Δ mutant cells to replication stress. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres, and MTE1 deletion results in elongated telomeres. Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance.
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Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | | | - Peter Henriksen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Irene Gallina
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Xuejiao Yang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Brian Luke
- Institute of Molecular Biology gGmbH (IMB), 55128 Mainz, Germany
| | - Lumir Krejci
- Department of Biology, Masaryk University, CZ-62500 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, CZ-62500 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic; Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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15
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Marcomini I, Gasser SM. Nuclear organization in DNA end processing: Telomeres vs double-strand breaks. DNA Repair (Amst) 2015; 32:134-140. [PMID: 26004856 DOI: 10.1016/j.dnarep.2015.04.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Many proteins ligands are shared between double-strand breaks and natural chromosomal ends or telomeres. The structural similarity of the 3' overhang, and the efficiency of cellular DNA end degradation machineries, highlight the need for mechanisms that resect selectively to promote or restrict recombination events. Here we examine the means used by eukaryotic cells to suppress resection at telomeres, target telomerase to short telomeres, and process broken ends for appropriate repair. Not only molecular ligands, but the spatial sequestration of telomeres and damage likely ensure that these two very similar structures have very distinct outcomes with respect to the DNA damage response and repair.
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Affiliation(s)
- Isabella Marcomini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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16
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Li JR, Yu TY, Chien IC, Lu CY, Lin JJ, Li HW. Pif1 regulates telomere length by preferentially removing telomerase from long telomere ends. Nucleic Acids Res 2014; 42:8527-36. [PMID: 24981509 PMCID: PMC4117769 DOI: 10.1093/nar/gku541] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Telomerase, a ribonucleoprotein complex, is responsible for maintaining the telomere length at chromosome ends. Using its RNA component as a template, telomerase uses its reverse transcriptase activity to extend the 3'-end single-stranded, repetitive telomeric DNA sequence. Pif1, a 5'-to-3' helicase, has been suggested to regulate telomerase activity. We used single-molecule experiments to directly show that Pif1 helicase regulates telomerase activity by removing telomerase from telomere ends, allowing the cycling of the telomerase for additional extension processes. This telomerase removal efficiency increases at longer ssDNA gaps and at higher Pif1 concentrations. The enhanced telomerase removal efficiency by Pif1 at the longer single-stranded telomeric DNA suggests a way of how Pif1 regulates telomerase activity and maintains telomere length.
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Affiliation(s)
- Jing-Ru Li
- Department of Chemistry, National Taiwan University, Taiwan
| | - Tai-Yuan Yu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taiwan
| | - I-Chieh Chien
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taiwan
| | - Chia-Ying Lu
- Institute of Biochemistry and Molecular Biology, National Taiwan University, Taiwan
| | - Jing-Jer Lin
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taiwan Institute of Biochemistry and Molecular Biology, National Taiwan University, Taiwan Institute of Biochemistry and Molecular Biology, National Taiwan University, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taiwan
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17
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18
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Chung WH. To peep into Pif1 helicase: multifaceted all the way from genome stability to repair-associated DNA synthesis. J Microbiol 2014; 52:89-98. [PMID: 24500472 DOI: 10.1007/s12275-014-3524-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/29/2013] [Indexed: 01/05/2023]
Abstract
Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.
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Affiliation(s)
- Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul, 132-714, Republic of Korea,
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19
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Abstract
The mechanisms that maintain the stability of chromosome ends have broad impact on genome integrity in all eukaryotes. Budding yeast is a premier organism for telomere studies. Many fundamental concepts of telomere and telomerase function were first established in yeast and then extended to other organisms. We present a comprehensive review of yeast telomere biology that covers capping, replication, recombination, and transcription. We think of it as yeast telomeres—soup to nuts.
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20
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Xu J, McEachern MJ. Maintenance of very long telomeres by recombination in the Kluyveromyces lactis stn1-M1 mutant involves extreme telomeric turnover, telomeric circles, and concerted telomeric amplification. Mol Cell Biol 2012; 32:2992-3008. [PMID: 22645309 PMCID: PMC3434524 DOI: 10.1128/mcb.00430-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/09/2012] [Indexed: 01/26/2023] Open
Abstract
Some cancers utilize the recombination-dependent process of alternative lengthening of telomeres (ALT) to maintain long heterogeneous telomeres. Here, we studied the recombinational telomere elongation (RTE) of the Kluyveromyces lactis stn1-M1 mutant. We found that the total amount of the abundant telomeric DNA in stn1-M1 cells is subject to rapid variation and that it is likely to be primarily extrachromosomal. Rad50 and Rad51, known to be required for different RTE pathways in Saccharomyces cerevisiae, were not essential for the production of either long telomeres or telomeric circles in stn1-M1 cells. Circles of DNA containing telomeric repeats (t-circles) either present at the point of establishment of long telomeres or introduced later into stn1-M1 cells each led to the formation of long tandem arrays of the t-circle's sequence, which were incorporated at multiple telomeres. These tandem arrays were extraordinarily unstable and showed evidence of repeated rounds of concerted amplification. Our results suggest that the maintenance of telomeres in the stn1-M1 mutant involves extreme turnover of telomeric sequences from processes including both large deletions and the copying of t-circles.
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Affiliation(s)
- Jianing Xu
- Department of Genetics, Fred Davison Life Science Complex, University of Georgia, Athens, Georgia
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21
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Dewar JM, Lydall D. Similarities and differences between "uncapped" telomeres and DNA double-strand breaks. Chromosoma 2011; 121:117-30. [PMID: 22203190 DOI: 10.1007/s00412-011-0357-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 12/08/2011] [Indexed: 11/25/2022]
Abstract
Telomeric DNA is present at the ends of eukaryotic chromosomes and is bound by telomere "capping" proteins, which are the (Cdc13-Stn1-Ten1) CST complex, Ku (Yku70-Yku80), and Rap1-Rif1-Rif2 in budding yeast. Inactivation of any of these complexes causes telomere "uncapping," stimulating a DNA damage response (DDR) that frequently involves resection of telomeric DNA and stimulates cell cycle arrest. This is presumed to occur because telomeres resemble one half of a DNA double-strand break (DSB). In this review, we outline the DDR that occurs at DSBs and compare it to the DDR occurring at uncapped telomeres, in both budding yeast and metazoans. We give particular attention to the resection of DSBs in budding yeast by Mre11-Xrs2-Rad50 (MRX), Sgs1/Dna2, and Exo1 and compare their roles at DSBs and uncapped telomeres. We also discuss how resection uncapped telomeres in budding yeast is promoted by the by 9-1-1 complex (Rad17-Mec3-Ddc1), to illustrate how analysis of uncapped telomeres can serve as a model for the DDR elsewhere in the genome. Finally, we discuss the role of the helicase Pif1 and its requirement for resection of uncapped telomeres, but not DSBs. Pif1 has roles in DNA replication and mammalian and plant CST complexes have been identified and have roles in global genome replication. Based on these observations, we suggest that while the DDR at uncapped telomeres is partially due to their resemblance to a DSB, it may also be partially due to defective DNA replication. Specifically, we propose that the budding yeast CST complex has dual roles to inhibit a DSB-like DDR initiated by Exo1 and a replication-associated DDR initiated by Pif1. If true, this would suggest that the mammalian CST complex inhibits a Pif1-dependent DDR.
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Affiliation(s)
- James M Dewar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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22
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Bah A, Gilson E, Wellinger RJ. Telomerase is required to protect chromosomes with vertebrate-type T2AG3 3' ends in Saccharomyces cerevisiae. J Biol Chem 2011; 286:27132-8. [PMID: 21676873 DOI: 10.1074/jbc.m111.220186] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Telomeres containing vertebrate-type DNA repeats can be stably maintained in Saccharomyces cerevisiae cells. We show here that telomerase is required for growth of yeast cells containing these vertebrate-type telomeres. When present at the chromosome termini, these heterologous repeats elicit a DNA damage response and a certain deprotection of telomeres. The data also show that these phenotypes are due only to the terminal localization of the vertebrate repeats because if they are sandwiched between native yeast repeats, no phenotype is observed. Indeed and quite surprisingly, in this latter situation, telomeres are of virtually normal lengths, despite the presence of up to 50% of heterologous repeats. Furthermore, the presence of the distal vertebrate-type repeats can cause increased problems of the replication fork. These results show that in budding yeast the integrity of the 3' overhang is required for proper termination of telomere replication as well as protection.
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Affiliation(s)
- Amadou Bah
- Département de Microbiologie et d'Infectiologie, Groupe ARN/RNA Group, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Ave. Nord, Sherbrooke, Quebec J1H 5N4, Canada
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23
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Paeschke K, Capra JA, Zakian VA. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell 2011; 145:678-91. [PMID: 21620135 PMCID: PMC3129610 DOI: 10.1016/j.cell.2011.04.015] [Citation(s) in RCA: 461] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 02/10/2011] [Accepted: 03/23/2011] [Indexed: 11/28/2022]
Abstract
G-quadruplex (G4) DNA structures are extremely stable four-stranded secondary structures held together by noncanonical G-G base pairs. Genome-wide chromatin immunoprecipitation was used to determine the in vivo binding sites of the multifunctional Saccharomyces cerevisiae Pif1 DNA helicase, a potent unwinder of G4 structures in vitro. G4 motifs were a significant subset of the high-confidence Pif1-binding sites. Replication slowed in the vicinity of these motifs, and they were prone to breakage in Pif1-deficient cells, whereas non-G4 Pif1-binding sites did not show this behavior. Introducing many copies of G4 motifs caused slow growth in replication-stressed Pif1-deficient cells, which was relieved by spontaneous mutations that eliminated their ability to form G4 structures, bind Pif1, slow DNA replication, and stimulate DNA breakage. These data suggest that G4 structures form in vivo and that they are resolved by Pif1 to prevent replication fork stalling and DNA breakage.
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Affiliation(s)
- Katrin Paeschke
- Department of Molecular Biology, Princeton University Princeton, NJ 08544-1014
| | - John A. Capra
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University Princeton, NJ 08544-1014
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24
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Abstract
In the budding yeast Saccharomyces cerevisiae, the structure and function of telomeres are maintained by binding proteins, such as Cdc13-Stn1-Ten1 (CST), Yku, and the telomerase complex. Like CST and Yku, telomerase also plays a role in telomere protection or capping. Unlike CST and Yku, however, the underlying molecular mechanism of telomerase-mediated telomere protection remains unclear. In this study, we employed both the CDC13-EST1 fusion gene and the separation-of-function allele est1-D514A to elucidate that Est1 provided a telomere protection pathway that was independent of both the CST and Yku pathways. Est1's ability to convert single-stranded telomeric DNA into a G quadruplex was required for telomerase-mediated telomere protection function. Additionally, Est1 maintained the integrity of telomeres by suppressing the recombination of subtelomeric Y' elements. Our results demonstrate that one major functional role that Est1 brings to the telomerase complex is the capping or protection of telomeres.
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25
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Dewar JM, Lydall D. Pif1- and Exo1-dependent nucleases coordinate checkpoint activation following telomere uncapping. EMBO J 2010; 29:4020-34. [PMID: 21045806 PMCID: PMC3020640 DOI: 10.1038/emboj.2010.267] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 09/29/2010] [Indexed: 11/16/2022] Open
Abstract
Essential telomere 'capping' proteins act as a safeguard against ageing and cancer by inhibiting the DNA damage response (DDR) and regulating telomerase recruitment, thus distinguishing telomeres from double-strand breaks (DSBs). Uncapped telomeres and unrepaired DSBs can both stimulate a potent DDR, leading to cell cycle arrest and cell death. Using the cdc13-1 mutation to conditionally 'uncap' telomeres in budding yeast, we show that the telomere capping protein Cdc13 protects telomeres from the activity of the helicase Pif1 and the exonuclease Exo1. Our data support a two-stage model for the DDR at uncapped telomeres; Pif1 and Exo1 resect telomeric DNA <5 kb from the chromosome end, stimulating weak checkpoint activation; resection is extended >5 kb by Exo1 and full checkpoint activation occurs. Cdc13 is also crucial for telomerase recruitment. However, cells lacking Cdc13, Pif1 and Exo1, do not senesce and maintain their telomeres in a manner dependent upon telomerase, Ku and homologous recombination. Thus, attenuation of the DDR at uncapped telomeres can circumvent the need for otherwise-essential telomere capping proteins.
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Affiliation(s)
- James M Dewar
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle upon Tyne, Tyne-and-Wear, UK
| | - David Lydall
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle upon Tyne, Tyne-and-Wear, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, Tyne-and-Wear, UK
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26
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Paeschke K, McDonald KR, Zakian VA. Telomeres: structures in need of unwinding. FEBS Lett 2010; 584:3760-72. [PMID: 20637196 PMCID: PMC2954063 DOI: 10.1016/j.febslet.2010.07.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 06/25/2010] [Accepted: 07/02/2010] [Indexed: 11/26/2022]
Abstract
Telomeres protect the ends of eukaryotic chromosomes from being recognized and processed as double strand breaks. In most organisms, telomeric DNA is highly repetitive with a high GC-content. Moreover, the G residues are concentrated in the strand running 3'-5' from the end of the chromosome towards its center. This G-rich strand is extended to form a 3' single-stranded tail that can form unusual secondary structures such as T-loops and G-quadruplex DNA. Both the duplex repeats and the single-stranded G-tail are assembled into stable protein-DNA complexes. The unique architecture, high GC content, and multi-protein association create particularly stable protein-DNA complexes that are a challenge for replication, recombination, and transcription. Helicases utilize the energy of nucleotide hydrolysis to unwind base paired nucleic acids and, in some cases, to displace proteins from them. The telomeric functions of helicases from the RecQ, Pifl, FANCJ, and DNA2 families are reviewed in this article. We summarize data showing that perturbation of their telomere activities can lead to telomere dysfunction and genome instability and in some cases human disease.
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Affiliation(s)
| | | | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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27
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Human Pif1 helicase is a G-quadruplex DNA-binding protein with G-quadruplex DNA-unwinding activity. Biochem J 2010; 430:119-28. [PMID: 20524933 DOI: 10.1042/bj20100612] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pif1 proteins are helicases that in yeast are implicated in the maintenance of genome stability. One activity of Saccharomyces cerevisiae Pif1 is to stabilize DNA sequences that could otherwise form deleterious G4 (G-quadruplex) structures by acting as a G4 resolvase. The present study shows that human Pif1 (hPif1, nuclear form) is a G4 DNA-binding and resolvase protein and that these activities are properties of the conserved helicase domain (amino acids 206-620 of 641, hPifHD). hPif1 preferentially bound synthetic G4 DNA relative to ssDNA (single-stranded DNA), dsDNA (double-stranded DNA) and a partially single-stranded duplex DNA helicase substrate. G4 DNA unwinding, but not binding, required an extended (>10 nucleotide) 5' ssDNA tail, and in competition assays, G4 DNA was an ineffective suppressor of helicase activity compared with ssDNA. These results suggest a distinction between the determinants of G4 DNA binding and the ssDNA interactions required for helicase action and that hPif1 may act on G4 substrates by binding alone or as a resolvase. Human Pif1 could therefore have a role in processing G4 structures that arise in the single-stranded nucleic acid intermediates formed during DNA replication and gene expression.
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28
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Telomere capping in non-dividing yeast cells requires Yku and Rap1. EMBO J 2010; 29:3007-19. [PMID: 20628356 DOI: 10.1038/emboj.2010.155] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 06/18/2010] [Indexed: 01/13/2023] Open
Abstract
The assembly of a protective cap onto the telomeres of eukaryotic chromosomes suppresses genomic instability through inhibition of DNA repair activities that normally process accidental DNA breaks. We show here that the essential Cdc13-Stn1-Ten1 complex is entirely dispensable for telomere protection in non-dividing cells. However, Yku and Rap1 become crucially important for this function in these cells. After inactivation of Yku70 in G1-arrested cells, moderate but significant telomere degradation occurs. As the activity of cyclin-dependent kinases (CDK) promotes degradation, these results suggest that Yku stabilizes G1 telomeres by blocking the access of CDK1-independent nucleases to telomeres. The results indeed show that both Exo1 and the Mre11/Rad50/Xrs2 complex are required for telomeric resection after Yku loss in non-dividing cells. Unexpectedly, both asynchronously growing and quiescent G0 cells lacking Rap1 display readily detectable telomere degradation, suggesting an earlier unanticipated function for this protein in suppression of nuclease activities at telomeres. Together, our results show a high flexibility of the telomeric cap and suggest that distinct configurations may provide for efficient capping in dividing versus non-dividing cells.
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Abstract
Helicases are ubiquitous enzymes found in all organisms that are necessary for all (or virtually all) aspects of nucleic acid metabolism. The Pif1 helicase family is a group of 5'-->3' directed, ATP-dependent, super family IB helicases found in nearly all eukaryotes. Here, we review the discovery, evolution, and what is currently known about these enzymes in Saccharomyces cerevisiae (ScPif1 and ScRrm3), Schizosaccharomyces pombe (SpPfh1), Trypanosoma brucei (TbPIF1, 2, 5, and 8), mice (mPif1), and humans (hPif1). Pif1 helicases variously affect telomeric, ribosomal, and mitochondrial DNA replication, as well as Okazaki fragment maturation, and in at least some cases affect these processes by using their helicase activity to disrupt stable nucleoprotein complexes. While the functions of these enzymes vary within and between organisms, it is evident that Pif1 family helicases are crucial for both nuclear and mitochondrial genome maintenance.
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Affiliation(s)
- Matthew L Bochman
- Department of Molecular Biology, Princeton University, 101 Lewis Thomas Laboratory, Washington Rd., Princeton, NJ 08544, USA
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Deletion of Ogg1 DNA glycosylase results in telomere base damage and length alteration in yeast. EMBO J 2009; 29:398-409. [PMID: 19942858 DOI: 10.1038/emboj.2009.355] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 11/04/2009] [Indexed: 12/20/2022] Open
Abstract
Telomeres consist of short guanine-rich repeats. Guanine can be oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). 8-oxoguanine DNA glycosylase (Ogg1) repairs these oxidative guanine lesions through the base excision repair (BER) pathway. Here we show that in Saccharomyces cerevisiae ablation of Ogg1p leads to an increase in oxidized guanine level in telomeric DNA. The ogg1 deletion (ogg1Delta) strain shows telomere lengthening that is dependent on telomerase and/or Rad52p-mediated homologous recombination. 8-oxoG in telomeric repeats attenuates the binding of the telomere binding protein, Rap1p, to telomeric DNA in vitro. Moreover, the amount of telomere-bound Rap1p and Rif2p is reduced in ogg1Delta strain. These results suggest that oxidized guanines may perturb telomere length equilibrium by attenuating telomere protein complex to function in telomeres, which in turn impedes their regulation of pathways engaged in telomere length maintenance. We propose that Ogg1p is critical in maintaining telomere length homoeostasis through telomere guanine damage repair, and that interfering with telomere length homoeostasis may be one of the mechanism(s) by which oxidative DNA damage inflicts the genome.
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Abstract
Telomere binding proteins protect chromosome ends from degradation and mask chromosome termini from checkpoint surveillance. In Saccharomyces cerevisiae, Cdc13 binds single-stranded G-rich telomere repeats, maintaining telomere integrity and length. Two additional proteins, Ten1 and Stn1, interact with Cdc13 but their contributions to telomere integrity are not well defined. Ten1 is known to prevent accumulation of aberrant single-stranded telomere DNA; whether this results from defective end protection or defective telomere replication is unclear. Here we report our analysis of a new group of ten1 temperature-sensitive (ts) mutants. At permissive temperatures, ten1-ts strains display greatly elongated telomeres. After shift to nonpermissive conditions, however, ten1-ts mutants accumulate extensive telomeric single-stranded DNA. Cdk1 activity is required to generate these single-stranded regions, and deleting the EXO1 nuclease partially suppresses ten1-ts growth defects. This is similar to cdc13-1 mutants, suggesting ten1-ts strains are defective for end protection. Moreover, like Cdc13, our analysis reveals Ten1 promotes de novo telomere addition. Interestingly, in ten1-ts strains at high temperatures, telomeric single-stranded DNA and Rad52-YFP repair foci are strongly induced despite Cdc13 remaining associated with telomeres, revealing Cdc13 telomere binding is not sufficient for end protection. Finally, unlike cdc13-1 mutants, ten1-ts strains display strong synthetic interactions with mutations in the POLalpha complex. These results emphasize that Cdc13 relies on Ten1 to execute its essential function, but leave open the possibility that Ten1 has a Cdc13-independent role in DNA replication.
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Abstract
Pif1, an evolutionarily conserved helicase, negatively regulates telomere length by removing telomerase from chromosome ends. Pif1 has also been implicated in DNA replication processes such as Okazaki fragment maturation and replication fork pausing. We find that overexpression of Saccharomyces cervisiae PIF1 results in dose-dependent growth inhibition. Strong overexpression causes relocalization of the DNA damage response factors Rfa1 and Mre11 into nuclear foci and activation of the Rad53 DNA damage checkpoint kinase, indicating that the toxicity is caused by accumulation of DNA damage. We screened the complete set of approximately 4800 haploid gene deletion mutants and found that moderate overexpression of PIF1, which is only mildly toxic on its own, causes growth defects in strains with mutations in genes involved in DNA replication and the DNA damage response. Interestingly, we find that telomerase-deficient strains are also sensitive to PIF1 overexpression. Our data are consistent with a model whereby increased levels of Pif1 interfere with DNA replication, causing collapsed replication forks. At chromosome ends, collapsed forks result in truncated telomeres that must be rapidly elongated by telomerase to maintain viability.
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Ribeyre C, Lopes J, Boulé JB, Piazza A, Guédin A, Zakian VA, Mergny JL, Nicolas A. The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo. PLoS Genet 2009; 5:e1000475. [PMID: 19424434 PMCID: PMC2673046 DOI: 10.1371/journal.pgen.1000475] [Citation(s) in RCA: 295] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 04/08/2009] [Indexed: 12/02/2022] Open
Abstract
In budding yeast, the Pif1 DNA helicase is involved in the maintenance of both nuclear and mitochondrial genomes, but its role in these processes is still poorly understood. Here, we provide evidence for a new Pif1 function by demonstrating that its absence promotes genetic instability of alleles of the G-rich human minisatellite CEB1 inserted in the Saccharomyces cerevisiae genome, but not of other tandem repeats. Inactivation of other DNA helicases, including Sgs1, had no effect on CEB1 stability. In vitro, we show that CEB1 repeats formed stable G-quadruplex (G4) secondary structures and the Pif1 protein unwinds these structures more efficiently than regular B-DNA. Finally, synthetic CEB1 arrays in which we mutated the potential G4-forming sequences were no longer destabilized in pif1Δ cells. Hence, we conclude that CEB1 instability in pif1Δ cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences. Changes in the primary DNA sequence are a major source of pathologies and cancers. The hereditary information also resides in secondary DNA structures, a layer of genetic information that remains poorly understood. Biophysical and structural studies have long established that, in vitro, the DNA molecule can adopt diverse structures different from the canonical Watson-Crick conformations. However, for a long time their existence in vivo has been regarded with a certain skepticism and their functional role elusive. One example is the G-quadruplex structure, which involves G-quartets that form between four DNA strands. Here, using in vitro and in vivo assays in the yeast S. cerevisiae, we reveal the unexpected role of the Pif1 helicase in maintaining the stability of the human CEB1 G-rich tandem repeat array. By site-directed mutagenesis, we show that the genomic instability of CEB1 repeats in absence of Pif1 and is directly dependent on the ability of CEB1 to form G-quadruplex structures. We show that Pif1 is very efficient in vitro in processing G-quadruplex structures formed by CEB1. We propose that Pif1 maintains CEB1 repeats by its ability to resolve G-quadruplex structures, thus providing circumstantial evidence of their formation in vivo.
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Affiliation(s)
- Cyril Ribeyre
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Judith Lopes
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Jean-Baptiste Boulé
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Aurèle Piazza
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Aurore Guédin
- Laboratoire de Biophysique, Museum National d'Histoire Naturelle USM 503, INSERM U565, CNRS UMR5153, Paris, France
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jean-Louis Mergny
- Laboratoire de Biophysique, Museum National d'Histoire Naturelle USM 503, INSERM U565, CNRS UMR5153, Paris, France
| | - Alain Nicolas
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
- * E-mail:
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Chavez A, Tsou AM, Johnson FB. Telomeres do the (un)twist: helicase actions at chromosome termini. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1792:329-40. [PMID: 19245831 PMCID: PMC2670356 DOI: 10.1016/j.bbadis.2009.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 02/12/2009] [Accepted: 02/12/2009] [Indexed: 12/17/2022]
Abstract
Telomeres play critical roles in protecting genome stability, and their dysfunction contributes to cancer and age-related degenerative diseases. The precise architecture of telomeres, including their single-stranded 3' overhangs, bound proteins, and ability to form unusual secondary structures such as t-loops, is central to their function and thus requires careful processing by diverse factors. Furthermore, telomeres provide unique challenges to the DNA replication and recombination machinery, and are particularly suited for extension by the telomerase reverse transcriptase. Helicases use the energy from NTP hydrolysis to track along DNA and disrupt base pairing. Here we review current findings concerning how helicases modulate several aspects of telomere form and function.
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Affiliation(s)
- Alejandro Chavez
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
- Cell and Molecular Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA
- Medical Scientist Training Program, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Amy M. Tsou
- Cell and Molecular Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA
- Medical Scientist Training Program, University of Pennsylvania School of Medicine, Philadelphia, PA
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - F. Brad Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA
- Institute on Aging, University of Pennsylvania School of Medicine, Philadelphia, PA
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Chan A, Boulé JB, Zakian VA. Two pathways recruit telomerase to Saccharomyces cerevisiae telomeres. PLoS Genet 2008; 4:e1000236. [PMID: 18949040 PMCID: PMC2567097 DOI: 10.1371/journal.pgen.1000236] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 09/22/2008] [Indexed: 11/19/2022] Open
Abstract
The catalytic subunit of yeast telomerase, Est2p, is a telomere associated throughout most of the cell cycle, while the Est1p subunit binds only in late S/G2 phase, the time of telomerase action. Est2p binding in G1/early S phase requires a specific interaction between telomerase RNA (TLC1) and Ku80p. Here, we show that in four telomerase-deficient strains (cdc13-2, est1Ä, tlc1-SD, and tlc1-BD), Est2p telomere binding was normal in G1/early S phase but reduced to about 40–50% of wild type levels in late S/G2 phase. Est1p telomere association was low in all four strains. Wild type levels of Est2p telomere binding in late S/G2 phase was Est1p-dependent and required that Est1p be both telomere-bound and associated with a stem-bulge region in TLC1 RNA. In three telomerase-deficient strains in which Est1p is not Est2p-associated (tlc1-SD, tlc1-BD, and est2Ä), Est1p was present at normal levels but its telomere binding was very low. When the G1/early S phase and the late S/G2 phase telomerase recruitment pathways were both disrupted, neither Est2p nor Est1p was telomere-associated. We conclude that reduced levels of Est2p and low Est1p telomere binding in late S/G2 phase correlated with an est phenotype, while a WT level of Est2p binding in G1 was not sufficient to maintain telomeres. In addition, even though Cdc13p and Est1p interact by two hybrid, biochemical and genetic criteria, this interaction did not occur unless Est1p was Est2p-associated, suggesting that Est1p comes to the telomere only as part of the holoenzyme. Finally, the G1 and late S/G2 phase pathways for telomerase recruitment are distinct and are likely the only ones that bring telomerase to telomeres in wild-type cells. Duplication of linear DNA is complicated by the fact that conventional DNA polymerases cannot copy their ends. From yeasts to humans, replication of DNA ends, called telomeres, is accomplished by a telomere-dedicated reverse transcriptase called telomerase that uses its RNA subunit as a template. We show that there are two genetically distinct pathways that recruit yeast telomerase, Est2p, to telomeres in a cell cycle–dependent manner. Only one of the two pathways, the pathway operating late in the cell cycle, is required for telomere maintenance. In telomerase-deficient strains, the amount of Est2p that is telomere-bound late in the cell cycle is about 50% of wild type levels. Maintenance of functional levels of Est2p late in the cell cycle requires that Est1p, another telomerase subunit, be telomere-bound. In addition, Est1p must be associated with Est2p via an interaction between it and telomerase RNA. Human telomerase is not active in most somatic cells, but is critical for stem cell longevity. Even a modest reduction in telomerase has a serious impact on human health. The sensitivity of yeast to reduced levels of telomere-associated telomerase may help us understand why human stem cells require high levels of telomerase for their survival.
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Affiliation(s)
- Angela Chan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jean-Baptiste Boulé
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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Morin I, Ngo HP, Greenall A, Zubko MK, Morrice N, Lydall D. Checkpoint-dependent phosphorylation of Exo1 modulates the DNA damage response. EMBO J 2008; 27:2400-10. [PMID: 18756267 PMCID: PMC2532783 DOI: 10.1038/emboj.2008.171] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 07/30/2008] [Indexed: 11/09/2022] Open
Abstract
Exo1 is a nuclease involved in mismatch repair, DSB repair, stalled replication fork processing and in the DNA damage response triggered by dysfunctional telomeres. In budding yeast and mice, Exo1 creates single-stranded DNA (ssDNA) at uncapped telomeres. This ssDNA accumulation activates the checkpoint response resulting in cell cycle arrest. Here, we demonstrate that Exo1 is phosphorylated when telomeres are uncapped in cdc13-1 and yku70Delta yeast cells, and in response to the induction of DNA damage. After telomere uncapping, Exo1 phosphorylation depends on components of the checkpoint machinery such as Rad24, Rad17, Rad9, Rad53 and Mec1, but is largely independent of Chk1, Tel1 and Dun1. Serines S372, S567, S587 and S692 of Exo1 were identified as targets for phosphorylation. Furthermore, mutation of these Exo1 residues altered the DNA damage response to uncapped telomeres and camptothecin treatment, in a manner that suggests Exo1 phosphorylation inhibits its activity. We propose that Rad53-dependent Exo1 phosphorylation is involved in a negative feedback loop to limit ssDNA accumulation and DNA damage checkpoint activation.
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Affiliation(s)
- Isabelle Morin
- Institute for Ageing and Health, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Hien-Ping Ngo
- Institute for Ageing and Health, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Amanda Greenall
- Institute for Ageing and Health, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
- Centre for Integrated Systems Biology of Ageing and Nutrition, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Mikhajlo K Zubko
- Institute for Ageing and Health, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
- Division of Biology, School of Biology, Chemistry & Health Science, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Nick Morrice
- MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - David Lydall
- Institute for Ageing and Health, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
- Centre for Integrated Systems Biology of Ageing and Nutrition, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
- Institute for Cell and Molecular Biosciences, Henry Wellcome Laboratory for Biogerontology Research, Newcastle University, Newcastle Upon Tyne, UK
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Bianchi A, Shore D. How telomerase reaches its end: mechanism of telomerase regulation by the telomeric complex. Mol Cell 2008; 31:153-65. [PMID: 18657499 DOI: 10.1016/j.molcel.2008.06.013] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Indexed: 10/21/2022]
Abstract
The telomerase enzyme, which synthesizes telomeric DNA repeats, is regulated in cis at individual chromosome ends by the telomeric protein/DNA complex in a manner dependent on telomere repeat-array length. A dynamic interplay between telomerase-inhibiting factors bound at duplex DNA repeats and telomerase-promoting ones bound at single-stranded terminal DNA overhangs appears to modulate telomerase activity and to be directly related to the transient deprotection of telomeres. We discuss recent advances on the mechanism of telomerase regulation at chromosome ends in both yeast and mammalian systems.
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Affiliation(s)
- Alessandro Bianchi
- Department of Molecular Biology and NCCR Frontiers in Genetics Program, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Geneva, Switzerland
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Abstract
The temperature-sensitive phenotypes of yku70Delta and yku80Delta have provided a useful tool for understanding telomere homeostasis. Mutating the helicase domain of the telomerase inhibitor Pif1 resulted in the inactivation of cell cycle checkpoints and the subsequent rescue of temperature sensitivity of the yku70Delta strain. The inactivation of Pif1 in yku70Delta increased overall telomere length. However, the long G-rich, single-stranded overhangs at the telomeres, which are the major cause of temperature sensitivity, were slightly increased. Interestingly, the rescue of temperature sensitivity in strains having both pif1-m2 and yku70Delta mutations depended on the homologous recombination pathway. Furthermore, the BLM/WRN helicase yeast homolog Sgs1 exacerbated the temperature sensitivity of the yku70Delta strain. Therefore, the yKu70-80 heterodimer and telomerase maintain telomere size, and the helicase activity of Pif1 likely also helps to balance the overall size of telomeres and G-rich, single-stranded overhangs in wild-type cells by regulating telomere protein homeostasis. However, the absence of yKu70 may provide other proteins such as those involved in homologous recombination, Sgs1, or Pif1 additional access to G-rich, single-stranded DNA and may determine telomere size, cell cycle checkpoint activation, and, ultimately, temperature sensitivity.
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Sabourin M, Tuzon CT, Zakian VA. Telomerase and Tel1p preferentially associate with short telomeres in S. cerevisiae. Mol Cell 2007; 27:550-61. [PMID: 17656141 PMCID: PMC2650483 DOI: 10.1016/j.molcel.2007.07.016] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 06/21/2007] [Accepted: 07/17/2007] [Indexed: 11/27/2022]
Abstract
In diverse organisms, telomerase preferentially elongates short telomeres. We generated a single short telomere in otherwise wild-type (WT) S. cerevisiae cells. The binding of the positive regulators Ku and Cdc13p was similar at short and WT-length telomeres. The negative regulators Rif1p and Rif2p were present at the short telomere, although Rif2p levels were reduced. Two telomerase holoenzyme components, Est1p and Est2p, were preferentially enriched at short telomeres in late S/G2 phase, the time of telomerase action. Tel1p, the yeast ATM-like checkpoint kinase, was highly enriched at short telomeres from early S through G2 phase and even into the next cell cycle. Nonetheless, induction of a single short telomere did not elicit a cell-cycle arrest. Tel1p binding was dependent on Xrs2p and required for preferential binding of telomerase to short telomeres. These data suggest that Tel1p targets telomerase to the DNA ends most in need of extension.
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Affiliation(s)
- Michelle Sabourin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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