151
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Cesena D, Cassani C, Rizzo E, Lisby M, Bonetti D, Longhese MP. Regulation of telomere metabolism by the RNA processing protein Xrn1. Nucleic Acids Res 2017; 45:3860-3874. [PMID: 28160602 PMCID: PMC5397203 DOI: 10.1093/nar/gkx072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/19/2022] Open
Abstract
Telomeric DNA consists of repetitive G-rich sequences that terminate with a 3΄-ended single stranded overhang (G-tail), which is important for telomere extension by telomerase. Several proteins, including the CST complex, are necessary to maintain telomere structure and length in both yeast and mammals. Emerging evidence indicates that RNA processing factors play critical, yet poorly understood, roles in telomere metabolism. Here, we show that the lack of the RNA processing proteins Xrn1 or Rrp6 partially bypasses the requirement for the CST component Cdc13 in telomere protection by attenuating the activation of the DNA damage checkpoint. Xrn1 is necessary for checkpoint activation upon telomere uncapping because it promotes the generation of single-stranded DNA. Moreover, Xrn1 maintains telomere length by promoting the association of Cdc13 to telomeres independently of ssDNA generation and exerts this function by downregulating the transcript encoding the telomerase inhibitor Rif1. These findings reveal novel roles for RNA processing proteins in the regulation of telomere metabolism with implications for genome stability in eukaryotes.
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Affiliation(s)
- Daniele Cesena
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Emanuela Rizzo
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan 20126, Italy
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152
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Türkel S, Sarica S. Effects of stress activated protein kinases on the expression of EST3 gene that encodes telomerase subunit in Saccharomyces cerevisiae. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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153
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Abstract
Telomerase is the essential reverse transcriptase required for linear chromosome maintenance in most eukaryotes. Telomerase supplements the tandem array of simple-sequence repeats at chromosome ends to compensate for the DNA erosion inherent in genome replication. The template for telomerase reverse transcriptase is within the RNA subunit of the ribonucleoprotein complex, which in cells contains additional telomerase holoenzyme proteins that assemble the active ribonucleoprotein and promote its function at telomeres. Telomerase is distinct among polymerases in its reiterative reuse of an internal template. The template is precisely defined, processively copied, and regenerated by release of single-stranded product DNA. New specificities of nucleic acid handling that underlie the catalytic cycle of repeat synthesis derive from both active site specialization and new motif elaborations in protein and RNA subunits. Studies of telomerase provide unique insights into cellular requirements for genome stability, tissue renewal, and tumorigenesis as well as new perspectives on dynamic ribonucleoprotein machines.
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Affiliation(s)
- R Alex Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
| | - Jacob M Vogan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202; , , ,
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154
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Vasianovich Y, Wellinger RJ. Life and Death of Yeast Telomerase RNA. J Mol Biol 2017; 429:3242-3254. [PMID: 28115201 DOI: 10.1016/j.jmb.2017.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/10/2017] [Accepted: 01/14/2017] [Indexed: 12/20/2022]
Abstract
Telomerase reverse transcriptase elongates telomeres to overcome their natural attrition and allow unlimited cellular proliferation, a characteristic shared by stem cells and the majority of malignant cancerous cells. The telomerase holoenzyme comprises a core RNA molecule, a catalytic protein subunit, and other accessory proteins. Malfunction of certain telomerase components can cause serious genetic disorders including dyskeratosis congenita and aplastic anaemia. A hierarchy of tightly regulated steps constitutes the process of telomerase biogenesis, which, if interrupted or misregulated, can impede the production of a functional enzyme and severely affect telomere maintenance. Here, we take a closer look at the budding yeast telomerase RNA component, TLC1, in its long lifetime journey around the cell. We review the extensive knowledge on TLC1 transcription and processing. We focus on exciting recent studies on telomerase assembly, trafficking, and nuclear dynamics, which for the first time unveil striking similarities between the yeast and human telomerase ribonucleoproteins. Finally, we identify questions yet to be answered and new directions to be followed, which, in the future, might improve our knowledge of telomerase biology and trigger the development of new therapies against cancer and other telomerase-related diseases.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavillion, 3201 rue Jean-Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Applied Cancer Research Pavillion, 3201 rue Jean-Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
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155
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Tokuda N, Sasai M. Heterogeneous Spatial Distribution of Transcriptional Activity in Budding Yeast Nuclei. Biophys J 2016; 112:491-504. [PMID: 28040197 PMCID: PMC5300786 DOI: 10.1016/j.bpj.2016.11.3201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Recent microscopic and simulation studies have shown that the genome structure fluctuates dynamically in the nuclei of budding yeast Saccharomyces cerevisiae. This genome-wide movement should lead to the fluctuations of individual genes in their territorial regions. This raises an intriguing question of whether the resulting distribution of genes is correlated to their transcriptional activity. An effective method for examining this correlation is to analyze how the spatial distribution of genes and their transcriptional activity are modified by mutation. In this study, we analyzed the modification observed in a budding yeast mutant in which genes necessary for anchoring telomeres to the nuclear envelope, yku70 and esc1, are silenced. Taddei et al. reported that 60 genes are clearly misregulated by this mutation, with 28 and 32 genes downregulated and upregulated, respectively. We calculated the probability density maps of the misregulated genes using a model of dynamical movement of the yeast genome in both wild-type (WT) and yku70 esc1 mutant and showed that the density of downregulated genes is larger near the nucleolus, whereas the density of upregulated genes is larger at the opposite side of the nucleus. By comparing these genes with those highly (top 200 of transcriptome) and lowly (bottom 200) expressed, we showed that the simulated distribution of 28 downregulated (12 out of 32 upregulated) genes has a distinctly larger overlap with the distribution of lowly (highly) expressed genes in the mutant than in the WT. The remaining 20 upregulated genes are localized near the nuclear envelope both in the WT and in the mutant. These results showed that the transcriptional level of genes is affected by their spatial distribution, thus highlighting the importance of the structural regulation in the yeast genome.
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Affiliation(s)
- Naoko Tokuda
- Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan
| | - Masaki Sasai
- Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan; Department of Applied Physics, Nagoya University, Nagoya, Japan.
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156
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Larcher MV, Pasquier E, MacDonald RS, Wellinger RJ. Ku Binding on Telomeres Occurs at Sites Distal from the Physical Chromosome Ends. PLoS Genet 2016; 12:e1006479. [PMID: 27930670 PMCID: PMC5145143 DOI: 10.1371/journal.pgen.1006479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023] Open
Abstract
The Ku complex binds non-specifically to DNA breaks and ensures repair via NHEJ. However, Ku is also known to bind directly to telomeric DNA ends and its presence there is associated with telomere capping, but avoiding NHEJ. How the complex discriminates between a DNA break and a telomeric extremity remains unknown. Our results using a tagged Ku complex, or a chromosome end capturing method, in budding yeast show that yKu association with telomeres can occur at sites distant from the physical end, on sub-telomeric elements, as well as on interstitial telomeric repeats. Consistent with previous studies, our results also show that yKu associates with telomeres in two distinct and independent ways: either via protein-protein interactions between Yku80 and Sir4 or via direct DNA binding. Importantly, yKu associates with the new sites reported here via both modes. Therefore, in sir4Δ cells, telomere bound yKu molecules must have loaded from a DNA-end near the transition of non-telomeric to telomeric repeat sequences. Such ends may have been one sided DNA breaks that occur as a consequence of stalled replication forks on or near telomeric repeat DNA. Altogether, the results predict a new model for yKu function at telomeres that involves yKu binding at one-sided DNA breaks caused by replication stalling. On telomere proximal chromatin, this binding is not followed by initiation of non-homologous end-joining, but rather by break-induced replication or repeat elongation by telomerase. After repair, the yKu-distal portion of telomeres is bound by Rap1, which in turn reduces the potential for yKu to mediate NHEJ. These results thus propose a solution to a long-standing conundrum, namely how to accommodate the apparently conflicting functions of Ku on telomeres. The Ku complex binds to and mediates the rejoining of two DNA ends that were generated by a double-stranded DNA break in the genome. However, Ku is known to be present at telomeres as well. If it would induce end-to-end joining there, it would create chromosome end-fusions that inevitably will lead to gross chromosome rearrangements and genome instability, common hallmarks for cancer initiation. Our results here show that Ku actually is associated with sites on telomeric regions that are distant from the physical ends of the chromosomes. We propose that this association serves to rescue DNA replication that has difficulty passing through telomeric chromatin. If so called one-sided breaks occur near or in telomeric repeats, they will generate critically short telomeres that need to be elongated. The binding of Ku may thus either facilitate the establishment of a specialized end-copying mechanism, called break induced replication or aid in recruiting telomerase to the short ends. These findings thus propose ways to potential solutions for the major conceptual problem that arose with the finding that Ku is associated with telomeres.
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Affiliation(s)
- Mélanie V. Larcher
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Emeline Pasquier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - R. Stephen MacDonald
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail:
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157
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Kyriakou D, Stavrou E, Demosthenous P, Angelidou G, San Luis BJ, Boone C, Promponas VJ, Kirmizis A. Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae. BMC Biol 2016; 14:106. [PMID: 27927215 PMCID: PMC5142380 DOI: 10.1186/s12915-016-0325-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/09/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Transcriptome studies have revealed that many eukaryotic genomes are pervasively transcribed producing numerous long non-coding RNAs (lncRNAs). However, only a few lncRNAs have been ascribed a cellular role thus far, with most regulating the expression of adjacent genes. Even less lncRNAs have been annotated as essential hence implying that the majority may be functionally redundant. Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs). RESULTS Here, we employ synthetic genetic array (SGA) in Saccharomyces cerevisiae to identify GIs between long intergenic non-coding RNAs (lincRNAs) and protein-coding genes. We first validate this approach by demonstrating that the telomerase RNA TLC1 displays a GI network that corresponds to its well-described function in telomere length maintenance. We subsequently performed SGA screens on a set of uncharacterised lincRNAs and uncover their connection to diverse cellular processes. One of these lincRNAs, SUT457, exhibits a GI profile associating it to telomere organisation and we consistently demonstrate that SUT457 is required for telomeric overhang homeostasis through an Exo1-dependent pathway. Furthermore, the GI profile of SUT457 is distinct from that of its neighbouring genes suggesting a function independent to its genomic location. Accordingly, we show that ectopic expression of this lincRNA suppresses telomeric overhang accumulation in sut457Δ cells assigning a trans-acting role for SUT457 in telomere biology. CONCLUSIONS Overall, our work proposes that systematic application of this genetic approach could determine the functional significance of individual lncRNAs in yeast and other complex organisms.
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Affiliation(s)
- Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | | | - Georgia Angelidou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Vasilis J Promponas
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus.
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158
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Apte MS, Cooper JP. Life and cancer without telomerase: ALT and other strategies for making sure ends (don't) meet. Crit Rev Biochem Mol Biol 2016; 52:57-73. [PMID: 27892716 DOI: 10.1080/10409238.2016.1260090] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
While most cancer cells rely on telomerase expression/re-activation for linear chromosome maintenance and sustained proliferation, a significant population of cancers (10-15%) employs telomerase-independent strategies, collectively dubbed Alternative Lengthening of Telomeres (ALT). Most ALT cells relax the usual role of telomeres as inhibitors of local homologous recombination while maintaining the ability of telomeres to prohibit local non-homologous end joining reactions. Here we review current concepts surrounding how ALT telomeres achieve this new balance via alterations in chromatin landscape, DNA damage repair processes and handling of telomeric transcription. We also discuss telomerase independent end maintenance strategies utilized by other organisms, including fruitflies and yeasts, to draw parallels and contrasts and highlight additional modes, beyond ALT, that may be available to telomerase-minus cancers. We conclude by commenting on promises and challenges in the development of effective anti-ALT cancer therapies.
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Affiliation(s)
- Manasi S Apte
- a Laboratory of Biochemistry and Molecular Biology , Center for Cancer Research, National Cancer Institute, NIH , Bethesda , MD , USA
| | - Julia Promisel Cooper
- a Laboratory of Biochemistry and Molecular Biology , Center for Cancer Research, National Cancer Institute, NIH , Bethesda , MD , USA
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159
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Eugène S, Bourgeron T, Xu Z. Effects of initial telomere length distribution on senescence onset and heterogeneity. J Theor Biol 2016; 413:58-65. [PMID: 27864096 PMCID: PMC5177728 DOI: 10.1016/j.jtbi.2016.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/13/2016] [Accepted: 11/04/2016] [Indexed: 11/25/2022]
Abstract
Replicative senescence, induced by telomere shortening, exhibits considerable asynchrony and heterogeneity, the origins of which remain unclear. Here, we formally study how telomere shortening mechanisms impact on senescence kinetics and define two regimes of senescence, depending on the initial telomere length variance. We provide analytical solutions to the model, highlighting a non-linear relationship between senescence onset and initial telomere length distribution. This study reveals the complexity of the collective behavior of telomeres as they shorten, leading to senescence heterogeneity. New stochastic model of telomere shortening and elongation by telomerase. Analysis of the distribution of telomere length in the presence of telomerase. Senescence onset expressed as a function of the initial telomere length distribution. The initial telomere length distribution variance defines two senescence regimes.
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Affiliation(s)
- Sarah Eugène
- Sorbonne Universités, UPMC Université Pierre et Marie Curie, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France; INRIA Paris, 2 rue Simone Iff, F-75012 Paris, France.
| | - Thibault Bourgeron
- École Normale Supérieure de Lyon, UMR 5569, Unité de Mathématiques Pures et Appliquées, 69007 Lyon, France; INRIA Numed, 46 allée d'Italie, 69007 Lyon, France.
| | - Zhou Xu
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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160
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Bhattacharjee A, Stewart J, Chaiken M, Price CM. STN1 OB Fold Mutation Alters DNA Binding and Affects Selective Aspects of CST Function. PLoS Genet 2016; 12:e1006342. [PMID: 27690379 PMCID: PMC5045167 DOI: 10.1371/journal.pgen.1006342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/06/2016] [Indexed: 12/03/2022] Open
Abstract
Mammalian CST (CTC1-STN1-TEN1) participates in multiple aspects of telomere replication and genome-wide recovery from replication stress. CST resembles Replication Protein A (RPA) in that it binds ssDNA and STN1 and TEN1 are structurally similar to RPA2 and RPA3. Conservation between CTC1 and RPA1 is less apparent. Currently the mechanism underlying CST action is largely unknown. Here we address CST mechanism by using a DNA-binding mutant, (STN1 OB-fold mutant, STN1-OBM) to examine the relationship between DNA binding and CST function. In vivo, STN1-OBM affects resolution of endogenous replication stress and telomere duplex replication but telomeric C-strand fill-in and new origin firing after exogenous replication stress are unaffected. These selective effects indicate mechanistic differences in CST action during resolution of different replication problems. In vitro binding studies show that STN1 directly engages both short and long ssDNA oligonucleotides, however STN1-OBM preferentially destabilizes binding to short substrates. The finding that STN1-OBM affects binding to only certain substrates starts to explain the in vivo separation of function observed in STN1-OBM expressing cells. CST is expected to engage DNA substrates of varied length and structure as it acts to resolve different replication problems. Since STN1-OBM will alter CST binding to only some of these substrates, the mutant should affect resolution of only a subset of replication problems, as was observed in the STN1-OBM cells. The in vitro studies also provide insight into CST binding mechanism. Like RPA, CST likely contacts DNA via multiple OB folds. However, the importance of STN1 for binding short substrates indicates differences in the architecture of CST and RPA DNA-protein complexes. Based on our results, we propose a dynamic DNA binding model that provides a general mechanism for CST action at diverse forms of replication stress. Mammalian CST (CTC1/STN1/TEN1) is a three protein complex that aids in several steps during telomere replication and has genome-wide roles during recovery from replication fork stalling. Loss of CST leads to abnormalities in telomere structure, genomic instability and defects in chromosome segregation. Currently, we do not understand how CST acts to ensure the resolution of very diverse types of replication problem. We set out to address this question by studying a mutant form of CST that was predicted to alter DNA binding. The mutations are in the STN1 subunit. In vivo, the STN1 mutant (STN1-OBM) affects some aspects of CST function while others are normal. The effects of STN1-OBM do not align with the telomeric versus non-telomeric roles of CST but instead separate out different aspects of CST function at telomeres and genome-wide. In vitro binding studies indicate that STN1-OBM disrupts binding to only short DNA substrates. Since CST is likely to encounter DNA substrates of varied length and structure in vivo as it helps resolve different replication problems, this finding starts to explain why STN1-OBM affects only certain aspects of CST function. Our in vitro binding studies also shed light on how CST actually binds to DNA and they suggest a novel “dynamic binding model” that provides a mechanistic explanation for how CST helps resolve a diverse array of replication problems to preserve genome stability.
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Affiliation(s)
- Anukana Bhattacharjee
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Jason Stewart
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio, United States of America
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail: (JS); (CMP)
| | - Mary Chaiken
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Carolyn M. Price
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail: (JS); (CMP)
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161
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Lloyd NR, Dickey TH, Hom RA, Wuttke DS. Tying up the Ends: Plasticity in the Recognition of Single-Stranded DNA at Telomeres. Biochemistry 2016; 55:5326-40. [PMID: 27575340 PMCID: PMC5656232 DOI: 10.1021/acs.biochem.6b00496] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Telomeres terminate nearly exclusively in single-stranded DNA (ssDNA) overhangs comprised of the G-rich 3' end. This overhang varies widely in length from species to species, ranging from just a few bases to several hundred nucleotides. These overhangs are not merely a remnant of DNA replication but rather are the result of complex further processing. Proper management of the telomeric overhang is required both to deter the action of the DNA damage machinery and to present the ends properly to the replicative enzyme telomerase. This Current Topic addresses the biochemical and structural features used by the proteins that manage these variable telomeric overhangs. The Pot1 protein tightly binds the single-stranded overhang, preventing DNA damage sensors from binding. Pot1 also orchestrates the access of telomerase to that same substrate. The remarkable plasticity of the binding interface exhibited by the Schizosaccharomyces pombe Pot1 provides mechanistic insight into how these roles may be accomplished, and disease-associated mutations clustered around the DNA-binding interface in the hPOT1 highlight the importance of this function. The budding yeast Cdc13-Stn1-Ten1, a telomeric RPA complex closely associated with telomere function, also interacts with ssDNA in a fashion that allows degenerate sequences to be recognized. A related human complex composed of hCTC1, hSTN1, and hTEN1 has recently emerged with links to both telomere maintenance and general DNA replication and also exhibits mutations associated with telomere pathologies. Overall, these sequence-specific ssDNA binders exhibit a range of recognition properties that allow them to perform their unique biological functions.
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Affiliation(s)
- Neil R. Lloyd
- Department of Chemistry and Biochemistry, 596 UCB, University of Colorado Boulder, Boulder, CO 80309-0596, USADepartment of Chemistry and Biochemistry, 596 UCB, University of Colorado Boulder, Boulder, CO 80309, USA
| | | | - Robert A. Hom
- Department of Chemistry and Biochemistry, 596 UCB, University of Colorado Boulder, Boulder, CO 80309-0596, USADepartment of Chemistry and Biochemistry, 596 UCB, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Deborah S. Wuttke
- Department of Chemistry and Biochemistry, 596 UCB, University of Colorado Boulder, Boulder, CO 80309-0596, USADepartment of Chemistry and Biochemistry, 596 UCB, University of Colorado Boulder, Boulder, CO 80309, USA
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162
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Chen YF, Lu CY, Lin YC, Yu TY, Chang CP, Li JR, Li HW, Lin JJ. Modulation of yeast telomerase activity by Cdc13 and Est1 in vitro. Sci Rep 2016; 6:34104. [PMID: 27659693 PMCID: PMC5034320 DOI: 10.1038/srep34104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/08/2016] [Indexed: 01/08/2023] Open
Abstract
Telomerase is the enzyme involved in extending telomeric DNA. Control of telomerase activity by modulating its access to chromosome ends is one of the most important fundamental mechanisms. This study established an in vitro yeast telomerase reconstitution system that resembles telomere replication in vivo. In this system, a tailed-duplex DNA formed by telomeric DNA was employed to mimic the structure of telomeres. The core catalytic components of telomerase Est2/Tlc1 RNA were used as the telomeric DNA extension machinery. Using the reconstituted systems, this study found that binding of Cdc13 to telomeric DNA inhibited the access of telomerase to its substrate. The result was further confirmed by a single-molecule approach using the tethered-particle motion (TPM)-based telomerase assay. The findings also showed that the inhibitory effect can be relieved by telomerase-associated protein Est1, consistent with the role of Cdc13 and Est1 in regulating telomere extension in vivo. Significantly, this study found that the DNA binding property of Cdc13 was altered by Est1, providing the first mechanistic evidence of Est1 regulating the access of telomerase to its substrate. Thus, the roles of Cdc13 and Est1 in modulating telomerase activity were clearly defined using the in vitro reconstituted system.
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Affiliation(s)
- Yu-Fan Chen
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chia-Ying Lu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Yi-Chien Lin
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Tai-Yuan Yu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chun-Ping Chang
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Jing-Ru Li
- Department of Chemistry, National Taiwan University, Taipei 100, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei 100, Taiwan
| | - Jing-Jer Lin
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan.,Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 100, Taiwan
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163
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Zubko EI, Shackleton JL, Zubko MK. ATLAS: An advanced PCR-method for routine visualization of telomere length in Saccharomyces cerevisiae. Int J Biol Macromol 2016; 93:1285-1294. [PMID: 27645931 DOI: 10.1016/j.ijbiomac.2016.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/20/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
Abstract
Measuring telomere length is essential in telomere biology. Southern blot hybridization is the predominant method for measuring telomere length in the genetic model Saccharomyces cerevisiae. We have further developed and refined a telomere PCR approach, which was rarely used previously (mainly in specific telomeric projects), into a robust method allowing direct visualisation of telomere length differences in routine experiments with S. cerevisiae, and showing a strong correlation of results with data obtained by Southern blot hybridization. In this expanded method denoted as ATLAS (A-dvanced T-elomere L-ength A-nalysis in S. cerevisiae), we have introduced: 1) set of new primers annealing with high specificity to telomeric regions on five different chromosomes; 2) new approach for designing reverse telomere primers that is based on the ligation of an adaptor of a fixed size to telomeric ends. ATLAS can be used at the scale of individual assays and high-throughput approaches. This simple, time/cost-effective and reproducible methodology will complement Southern blot hybridization and facilitate further progress in telomere research.
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Affiliation(s)
- Elena I Zubko
- School of Healthcare Science, Faculty of Science & Engineering, Manchester Metropolitan University, John Dalton Building, Chester St., Manchester, M1 5GD, United Kingdom
| | - Jennifer L Shackleton
- School of Healthcare Science, Faculty of Science & Engineering, Manchester Metropolitan University, John Dalton Building, Chester St., Manchester, M1 5GD, United Kingdom
| | - Mikhajlo K Zubko
- School of Healthcare Science, Faculty of Science & Engineering, Manchester Metropolitan University, John Dalton Building, Chester St., Manchester, M1 5GD, United Kingdom.
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Moradi-Fard S, Sarthi J, Tittel-Elmer M, Lalonde M, Cusanelli E, Chartrand P, Cobb JA. Smc5/6 Is a Telomere-Associated Complex that Regulates Sir4 Binding and TPE. PLoS Genet 2016; 12:e1006268. [PMID: 27564449 PMCID: PMC5001636 DOI: 10.1371/journal.pgen.1006268] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/28/2016] [Indexed: 11/19/2022] Open
Abstract
SMC proteins constitute the core members of the Smc5/6, cohesin and condensin complexes. We demonstrate that Smc5/6 is present at telomeres throughout the cell cycle and its association with chromosome ends is dependent on Nse3, a subcomponent of the complex. Cells harboring a temperature sensitive mutant, nse3-1, are defective in Smc5/6 localization to telomeres and have slightly shorter telomeres. Nse3 interacts physically and genetically with two Rap1-binding factors, Rif2 and Sir4. Reduction in telomere-associated Smc5/6 leads to defects in telomere clustering, dispersion of the silencing factor, Sir4, and a loss in transcriptional repression for sub-telomeric genes and non-coding telomeric repeat-containing RNA (TERRA). SIR4 recovery at telomeres is reduced in cells lacking Smc5/6 functionality and vice versa. However, nse3-1/ sir4 Δ double mutants show additive defects for telomere shortening and TPE indicating the contribution of Smc5/6 to telomere homeostasis is only in partial overlap with SIR factor silencing. These findings support a role for Smc5/6 in telomere maintenance that is separate from its canonical role(s) in HR-mediated events during replication and telomere elongation.
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Affiliation(s)
- Sarah Moradi-Fard
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jessica Sarthi
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mireille Tittel-Elmer
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maxime Lalonde
- Département de Biochimie, Université de Montréal, Montréal, Quebec, Canada
| | - Emilio Cusanelli
- Département de Biochimie, Université de Montréal, Montréal, Quebec, Canada
| | - Pascal Chartrand
- Département de Biochimie, Université de Montréal, Montréal, Quebec, Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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165
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Gobbini E, Cassani C, Villa M, Bonetti D, Longhese MP. Functions and regulation of the MRX complex at DNA double-strand breaks. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 3:329-337. [PMID: 28357369 PMCID: PMC5349012 DOI: 10.15698/mic2016.08.517] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/03/2016] [Indexed: 12/22/2022]
Abstract
DNA double-strand breaks (DSBs) pose a serious threat to genome stability and cell survival. Cells possess mechanisms that recognize DSBs and promote their repair through either homologous recombination (HR) or non-homologous end joining (NHEJ). The evolutionarily conserved Mre11-Rad50-Xrs2 (MRX) complex plays a central role in the cellular response to DSBs, as it is implicated in controlling end resection and in maintaining the DSB ends tethered to each other. Furthermore, it is responsible for DSB signaling by activating the checkpoint kinase Tel1 that, in turn, supports MRX function in a positive feedback loop. The present review focuses mainly on recent works in the budding yeast Saccharomyces cerevisiae to highlight structure and regulation of MRX as well as its interplays with Tel1.
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Affiliation(s)
- Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Matteo Villa
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Diego Bonetti
- Institute of Molecular Biology gGmbH (IMB), 55128 Mainz, Germany
| | - Maria P. Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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166
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Duan YM, Zhou BO, Peng J, Tong XJ, Zhang QD, Zhou JQ. Molecular dynamics of de novo telomere heterochromatin formation in budding yeast. J Genet Genomics 2016; 43:451-65. [DOI: 10.1016/j.jgg.2016.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/09/2016] [Accepted: 03/17/2016] [Indexed: 11/26/2022]
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167
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Endogenous Hot Spots of De Novo Telomere Addition in the Yeast Genome Contain Proximal Enhancers That Bind Cdc13. Mol Cell Biol 2016; 36:1750-63. [PMID: 27044869 DOI: 10.1128/mcb.00095-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/31/2016] [Indexed: 12/17/2022] Open
Abstract
DNA double-strand breaks (DSBs) pose a threat to genome stability and are repaired through multiple mechanisms. Rarely, telomerase, the enzyme that maintains telomeres, acts upon a DSB in a mutagenic process termed telomere healing. The probability of telomere addition is increased at specific genomic sequences termed sites of repair-associated telomere addition (SiRTAs). By monitoring repair of an induced DSB, we show that SiRTAs on chromosomes V and IX share a bipartite structure in which a core sequence (Core) is directly targeted by telomerase, while a proximal sequence (Stim) enhances the probability of de novo telomere formation. The Stim and Core sequences are sufficient to confer a high frequency of telomere addition to an ectopic site. Cdc13, a single-stranded DNA binding protein that recruits telomerase to endogenous telomeres, is known to stimulate de novo telomere addition when artificially recruited to an induced DSB. Here we show that the ability of the Stim sequence to enhance de novo telomere addition correlates with its ability to bind Cdc13, indicating that natural sites at which telomere addition occurs at high frequency require binding by Cdc13 to a sequence 20 to 100 bp internal from the site at which telomerase acts to initiate de novo telomere addition.
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168
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Geronimo CL, Zakian VA. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst) 2016; 44:151-158. [PMID: 27233114 DOI: 10.1016/j.dnarep.2016.05.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is widely appreciated that the ends of linear DNA molecules cannot be fully replicated by the conventional replication apparatus. Less well known is that semi-conservative replication of telomeric DNA also presents problems for DNA replication. These problems likely arise from the atypical chromatin structure of telomeres, the GC-richness of telomeric DNA that makes it prone to forming DNA secondary structures, and from RNA-DNA hybrids, formed by transcripts of one or both DNA strands. Given the different aspects of telomeres that complicate their replication, it is not surprising that multiple DNA helicases promote replication of telomeric DNA. This review focuses on one such class of DNA helicases, the Pif1 family of 5'-3' DNA helicases. In budding and fission yeasts, Pif1 family helicases impact both telomerase-mediated and semi-conservative replication of telomeric DNA as well as recombination-mediated telomere lengthening.
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Affiliation(s)
- Carly L Geronimo
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.
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169
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Churikov D, Charifi F, Eckert-Boulet N, Silva S, Simon MN, Lisby M, Géli V. SUMO-Dependent Relocalization of Eroded Telomeres to Nuclear Pore Complexes Controls Telomere Recombination. Cell Rep 2016; 15:1242-53. [PMID: 27134164 DOI: 10.1016/j.celrep.2016.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/14/2016] [Accepted: 03/28/2016] [Indexed: 02/05/2023] Open
Abstract
In budding yeast, inactivation of telomerase and ensuing telomere erosion cause relocalization of telomeres to nuclear pore complexes (NPCs). However, neither the mechanism of such relocalization nor its significance are understood. We report that proteins bound to eroded telomeres are recognized by the SUMO (small ubiquitin-like modifier)-targeted ubiquitin ligase (STUbL) Slx5-Slx8 and become increasingly SUMOylated. Recruitment of Slx5-Slx8 to eroded telomeres facilitates telomere relocalization to NPCs and type II telomere recombination, a counterpart of mammalian alternative lengthening of telomeres (ALT). Moreover, artificial tethering of a telomere to a NPC promotes type II telomere recombination but cannot bypass the lack of Slx5-Slx8 in this process. Together, our results indicate that SUMOylation positively contributes to telomere relocalization to the NPC, where poly-SUMOylated proteins that accumulated over time have to be removed. We propose that STUbL-dependent relocalization of telomeres to NPCs constitutes a pathway in which excessively SUMOylated proteins are removed from "congested" intermediates to ensure unconventional recombination.
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Affiliation(s)
- Dmitri Churikov
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France
| | - Ferose Charifi
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France
| | | | - Sonia Silva
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marie-Noelle Simon
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France.
| | - Michael Lisby
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 INSERM, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes (Equipe labellisée Ligue), Marseille 13009, France.
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170
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Laporte D, Courtout F, Tollis S, Sagot I. Quiescent Saccharomyces cerevisiae forms telomere hyperclusters at the nuclear membrane vicinity through a multifaceted mechanism involving Esc1, the Sir complex, and chromatin condensation. Mol Biol Cell 2016; 27:1875-84. [PMID: 27122604 PMCID: PMC4907721 DOI: 10.1091/mbc.e16-01-0069] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/20/2016] [Indexed: 01/09/2023] Open
Abstract
Upon quiescence entry, yeast cells assemble telomere hyperclusters. These structures localize to the nuclear membrane in an Esc1-dependent manner and assemble through the combined action of the Sir complex, deacetylation of H4K16, the binding of the linker histone H1, and condensin. Like other eukaryotes, Saccharomyces cerevisiae spatially organizes its chromosomes within the nucleus. In G1 phase, the yeast’s 32 telomeres are clustered into 6–10 foci that dynamically interact with the nuclear membrane. Here we show that, when cells leave the division cycle and enter quiescence, telomeres gather into two to three hyperclusters at the nuclear membrane vicinity. This localization depends on Esc1 but not on the Ku proteins. Telomere hypercluster formation requires the Sir complex but is independent of the nuclear microtubule bundle that specifically assembles in quiescent cells. Importantly, mutants deleted for the linker histone H1 Hho1 or defective in condensin activity or affected for histone H4 Lys-16 deacetylation are impaired, at least in part, for telomere hypercluster formation in quiescence, suggesting that this process involves chromosome condensation. Finally, we establish that telomere hypercluster formation is not necessary for quiescence establishment, maintenance, and exit, raising the question of the physiological raison d’être of this nuclear reorganization.
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Affiliation(s)
- Damien Laporte
- Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France CNRS-UMR5095 Bordeaux, 33077 Bordeaux cedex, France
| | - Fabien Courtout
- Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France CNRS-UMR5095 Bordeaux, 33077 Bordeaux cedex, France
| | - Sylvain Tollis
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH93BF, United Kingdom
| | - Isabelle Sagot
- Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, 33000 Bordeaux, France CNRS-UMR5095 Bordeaux, 33077 Bordeaux cedex, France
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171
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DNA Replication Stress Phosphoproteome Profiles Reveal Novel Functional Phosphorylation Sites on Xrs2 in Saccharomyces cerevisiae. Genetics 2016; 203:353-68. [PMID: 27017623 DOI: 10.1534/genetics.115.185231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/21/2016] [Indexed: 01/11/2023] Open
Abstract
In response to replication stress, a phospho-signaling cascade is activated and required for coordination of DNA repair and replication of damaged templates (intra-S-phase checkpoint) . How phospho-signaling coordinates the DNA replication stress response is largely unknown. We employed state-of-the-art liquid chromatography tandem-mass spectrometry (LC-MS/MS) approaches to generate high-coverage and quantitative proteomic and phospho-proteomic profiles during replication stress in yeast, induced by continuous exposure to the DNA alkylating agent methyl methanesulfonate (MMS) . We identified 32,057 unique peptides representing the products of 4296 genes and 22,061 unique phosphopeptides representing the products of 3183 genes. A total of 542 phosphopeptides (mapping to 339 genes) demonstrated an abundance change of greater than or equal to twofold in response to MMS. The screen enabled detection of nearly all of the proteins known to be involved in the DNA damage response, as well as many novel MMS-induced phosphorylations. We assessed the functional importance of a subset of key phosphosites by engineering a panel of phosphosite mutants in which an amino acid substitution prevents phosphorylation. In total, we successfully mutated 15 MMS-responsive phosphorylation sites in seven representative genes including APN1 (base excision repair); CTF4 and TOF1 (checkpoint and sister-chromatid cohesion); MPH1 (resolution of homologous recombination intermediates); RAD50 and XRS2 (MRX complex); and RAD18 (PRR). All of these phosphorylation site mutants exhibited MMS sensitivity, indicating an important role in protecting cells from DNA damage. In particular, we identified MMS-induced phosphorylation sites on Xrs2 that are required for MMS resistance in the absence of the MRX activator, Sae2, and that affect telomere maintenance.
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172
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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: 2.8] [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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173
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van Mourik PM, de Jong J, Agpalo D, Claussin C, Rothstein R, Chang M. Recombination-Mediated Telomere Maintenance in Saccharomyces cerevisiae Is Not Dependent on the Shu Complex. PLoS One 2016; 11:e0151314. [PMID: 26974669 PMCID: PMC4790948 DOI: 10.1371/journal.pone.0151314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/28/2016] [Indexed: 12/22/2022] Open
Abstract
In cells lacking telomerase, telomeres shorten progressively during each cell division due to incomplete end-replication. When the telomeres become very short, cells enter a state that blocks cell division, termed senescence. A subset of these cells can overcome senescence and maintain their telomeres using telomerase-independent mechanisms. In Saccharomyces cerevisiae, these cells are called ‘survivors’ and are dependent on Rad52-dependent homologous recombination and Pol32-dependent break-induced replication. There are two main types of survivors: type I and type II. The type I survivors require Rad51 and maintain telomeres by amplification of subtelomeric elements, while the type II survivors are Rad51-independent, but require the MRX complex and Sgs1 to amplify the C1–3A/TG1–3 telomeric sequences. Rad52, Pol32, Rad51, and Sgs1 are also important to prevent accelerated senescence, indicating that recombination processes are important at telomeres even before the formation of survivors. The Shu complex, which consists of Shu1, Shu2, Psy3, and Csm2, promotes Rad51-dependent homologous recombination and has been suggested to be important for break-induced replication. It also promotes the formation of recombination intermediates that are processed by the Sgs1-Top3-Rmi1 complex, as mutations in the SHU genes can suppress various sgs1, top3, and rmi1 mutant phenotypes. Given the importance of recombination processes during senescence and survivor formation, and the involvement of the Shu complex in many of the same processes during DNA repair, we hypothesized that the Shu complex may also have functions at telomeres. Surprisingly, we find that this is not the case: the Shu complex does not affect the rate of senescence, does not influence survivor formation, and deletion of SHU1 does not suppress the rapid senescence and type II survivor formation defect of a telomerase-negative sgs1 mutant. Altogether, our data suggest that the Shu complex is not important for recombination processes at telomeres.
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Affiliation(s)
- Paula M. van Mourik
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jannie de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Danielle Agpalo
- Department of Genetics and Development, Columbia University Medical Center, New York, United States of America
| | - Clémence Claussin
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, United States of America
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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174
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Termolino P, Cremona G, Consiglio MF, Conicella C. Insights into epigenetic landscape of recombination-free regions. Chromosoma 2016; 125:301-8. [PMID: 26801812 PMCID: PMC4830869 DOI: 10.1007/s00412-016-0574-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 11/29/2022]
Abstract
Genome architecture is shaped by gene-rich and repeat-rich regions also known as euchromatin and heterochromatin, respectively. Under normal conditions, the repeat-containing regions undergo little or no meiotic crossover (CO) recombination. COs within repeats are risky for the genome integrity. Indeed, they can promote non-allelic homologous recombination (NAHR) resulting in deleterious genomic rearrangements associated with diseases in humans. The assembly of heterochromatin is driven by the combinatorial action of many factors including histones, their modifications, and DNA methylation. In this review, we discuss current knowledge dealing with the epigenetic signatures of the major repeat regions where COs are suppressed. Then we describe mutants for epiregulators of heterochromatin in different organisms to find out how chromatin structure influences the CO rate and distribution.
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Affiliation(s)
- Pasquale Termolino
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Gaetana Cremona
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Maria Federica Consiglio
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Clara Conicella
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy.
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175
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Lin KW, Zakian VA. 21st Century Genetics: Mass Spectrometry of Yeast Telomerase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:111-6. [PMID: 26763982 PMCID: PMC5441543 DOI: 10.1101/sqb.2015.80.027656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Telomerase is a specialized reverse transcriptase that maintains the ends of chromosomes in almost all eukaryotes. The core of telomerase consists of telomerase RNA and the reverse transcriptase that uses a short segment without the RNA to template the addition of telomeric repeats. In addition, one or more accessory proteins are required for telomerase action in vivo. The best-studied accessory protein is Est1, which is conserved from yeasts to humans. In budding yeast, Est1 has two critical in vivo functions: By interaction with Cdc13, a telomere-binding protein, it recruits telomerase to telomeres, and it also increases telomerase activity. Although budding yeast telomerase is highly regulated by the cell cycle, Est1 is the only telomerase subunit whose abundance is cell cycle-regulated. Close to 400 yeast genes are reported to affect telomere length, although the specific function of most of them is unknown. With the goal of identifying novel telomerase regulators by mass spectrometry, we developed methods for purifying yeast telomerase and its associated proteins. We summarize the methods we used and describe the experiments that show that four telomerase-associated proteins identified by mass spectrometry, none of which had been linked previously to telomeres, affect telomere length and cell cycle regulation of telomerase by controlling Est1 abundance.
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Affiliation(s)
- Kah Wai Lin
- Department of Molecular Biology, Lewis Thomas Labs, Princeton University, Princeton, New Jersey 08544
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Labs, Princeton University, Princeton, New Jersey 08544
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176
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Procházková Schrumpfová P, Schořová Š, Fajkus J. Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. FRONTIERS IN PLANT SCIENCE 2016; 7:851. [PMID: 27446102 PMCID: PMC4924339 DOI: 10.3389/fpls.2016.00851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 05/31/2016] [Indexed: 05/20/2023]
Abstract
Telomeres, as physical ends of linear chromosomes, are targets of a number of specific proteins, including primarily telomerase reverse transcriptase. Access of proteins to the telomere may be affected by a number of diverse factors, e.g., protein interaction partners, local DNA or chromatin structures, subcellular localization/trafficking, or simply protein modification. Knowledge of composition of the functional nucleoprotein complex of plant telomeres is only fragmentary. Moreover, the plant telomeric repeat binding proteins that were characterized recently appear to also be involved in non-telomeric processes, e.g., ribosome biogenesis. This interesting finding was not totally unexpected since non-telomeric functions of yeast or animal telomeric proteins, as well as of telomerase subunits, have been reported for almost a decade. Here we summarize known facts about the architecture of plant telomeres and compare them with the well-described composition of telomeres in other organisms.
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Affiliation(s)
- Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- *Correspondence: Petra Procházková Schrumpfová,
| | - Šárka Schořová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.Brno, Czech Republic
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177
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Aksenova AY, Han G, Shishkin AA, Volkov KV, Mirkin SM. Expansion of Interstitial Telomeric Sequences in Yeast. Cell Rep 2015; 13:1545-51. [PMID: 26586439 DOI: 10.1016/j.celrep.2015.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/07/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022] Open
Abstract
Telomeric repeats located within chromosomes are called interstitial telomeric sequences (ITSs). They are polymorphic in length and are likely hotspots for initiation of chromosomal rearrangements that have been linked to human disease. Using our S. cerevisiae system to study repeat-mediated genome instability, we have previously shown that yeast telomeric (Ytel) repeats induce various gross chromosomal rearrangements (GCR) when their G-rich strands serve as the lagging strand template for replication (G orientation). Here, we show that interstitial Ytel repeats in the opposite C orientation prefer to expand rather than cause GCR. A tract of eight Ytel repeats expands at a rate of 4 × 10(-4) per replication, ranking them among the most expansion-prone DNA microsatellites. A candidate-based genetic analysis implicates both post-replication repair and homologous recombination pathways in the expansion process. We propose a model for Ytel repeat expansions and discuss its applications for genome instability and alternative telomere lengthening (ALT).
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Affiliation(s)
- Anna Y Aksenova
- Department of Biology, Tufts University, Medford, MA 02155, USA; Department of Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gil Han
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Kirill V Volkov
- Department of Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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178
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Jiang J, Chan H, Cash DD, Miracco EJ, Ogorzalek Loo RR, Upton HE, Cascio D, O'Brien Johnson R, Collins K, Loo JA, Zhou ZH, Feigon J. Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactions. Science 2015; 350:aab4070. [PMID: 26472759 DOI: 10.1126/science.aab4070] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/01/2015] [Indexed: 12/17/2022]
Abstract
Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the cryo-electron microscopy structure of Tetrahymena telomerase at ~9 angstrom resolution. In addition to seven known holoenzyme proteins, we identify two additional proteins that form a complex (TEB) with single-stranded telomere DNA-binding protein Teb1, paralogous to heterotrimeric replication protein A (RPA). The p75-p45-p19 subcomplex is identified as another RPA-related complex, CST (CTC1-STN1-TEN1). This study reveals the paths of TER in the TERT-TER-p65 catalytic core and single-stranded DNA exit; extensive subunit interactions of the TERT essential N-terminal domain, p50, and TEB; and other subunit identities and structures, including p19 and p45C crystal structures. Our findings provide structural and mechanistic insights into telomerase holoenzyme function.
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Affiliation(s)
- Jiansen Jiang
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA. California Nanosystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Henry Chan
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Darian D Cash
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Edward J Miracco
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | | | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA
| | - Reid O'Brien Johnson
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. Department of Biological Chemistry, UCLA, Los Angeles, CA 90095, USA. UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA. California Nanosystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. California Nanosystems Institute, UCLA, Los Angeles, CA 90095, USA. UCLA-U.S. Department of Energy (DOE) Institute of Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA.
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179
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Mersaoui SY, Gravel S, Karpov V, Wellinger RJ. DNA damage checkpoint adaptation genes are required for division of cells harbouring eroded telomeres. MICROBIAL CELL 2015; 2:394-405. [PMID: 28357265 PMCID: PMC5354583 DOI: 10.15698/mic2015.10.229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In budding yeast, telomerase and the Cdc13p protein are two key players acting to ensure telomere stability. In the absence of telomerase, cells eventually enter a growth arrest which only few can overcome via a conserved process; such cells are called survivors. Survivors rely on homologous recombination-dependent mechanisms for telomeric repeat addition. Previously, we showed that such survivor cells also manage to bypass the loss of the essential Cdc13p protein to give rise to Cdc13-independent (or cap-independent) strains. Here we show that Cdc13-independent cells grow with persistently recognized DNA damage, which does not however result in a checkpoint activation; thus no defect in cell cycle progression is detectable. The absence of checkpoint signalling rather is due to the accumulation of mutations in checkpoint genes such as RAD24 or MEC1. Importantly, our results also show that cells that have lost the ability to adapt to persistent DNA damage, also are very much impaired in generating cap-independent cells. Altogether, these results show that while the capping process can be flexible, it takes a very specific genetic setup to allow a change from canonical capping to alternative capping. We hypothesize that in the alternative capping mode, genome integrity mechanisms are abrogated, which could cause increased mutation frequencies. These results from yeast have clear parallels in transformed human cancer cells and offer deeper insights into processes operating in pre-cancerous human cells that harbour eroded telomeres.
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Affiliation(s)
- Sofiane Y Mersaoui
- Dept of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, J1E 4K8, Canada
| | - Serge Gravel
- Dept of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, J1E 4K8, Canada
| | - Victor Karpov
- Dept of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, J1E 4K8, Canada
| | - Raymund J Wellinger
- Dept of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, J1E 4K8, Canada
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180
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Lin KW, McDonald KR, Guise AJ, Chan A, Cristea IM, Zakian VA. Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length. Nat Commun 2015; 6:8290. [PMID: 26365526 PMCID: PMC4579843 DOI: 10.1038/ncomms9290] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/06/2015] [Indexed: 12/20/2022] Open
Abstract
Almost 400 genes affect yeast telomere length, including Est1, which is critical for recruitment and activation of telomerase. Here we use mass spectrometry to identify novel telomerase regulators by their co-purification with the telomerase holoenzyme. In addition to all known subunits, over 100 proteins are telomerase associated, including all three subunits of the essential Cdc48-Npl4-Ufd1 complex as well as three E3 ubiquitin ligases. The Cdc48 complex is evolutionarily conserved and targets ubiquitinated proteins for degradation. Est1 levels are ∼40-fold higher in cells with reduced Cdc48, yet, paradoxically, telomeres are shorter. Furthermore, Est1 is ubiquitinated and its cell cycle-regulated abundance is lost in Cdc48-deficient cells. Deletion of the telomerase-associated E3 ligase, Ufd4, in cdc48-3 cells further increases Est1 abundance but suppresses the telomere length phenotype of the single mutant. These data argue that, in concert with Ufd4, the Cdc48 complex regulates telomerase by controlling the level and activity of Est1.
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Affiliation(s)
- Kah-Wai Lin
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Karin R McDonald
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Amanda J Guise
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Washington Road, 08544 Princeton, New Jersey, USA
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181
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Regulation of Telomere Length Requires a Conserved N-Terminal Domain of Rif2 in Saccharomyces cerevisiae. Genetics 2015; 201:573-86. [PMID: 26294668 PMCID: PMC4596670 DOI: 10.1534/genetics.115.177899] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/19/2015] [Indexed: 12/26/2022] Open
Abstract
The regulation of telomere length equilibrium is essential for cell growth and survival since critically short telomeres signal DNA damage and cell cycle arrest. While the broad principles of length regulation are well established, the molecular mechanism of how these steps occur is not fully understood. We mutagenized the RIF2 gene in Saccharomyces cerevisiae to understand how this protein blocks excess telomere elongation. We identified an N-terminal domain in Rif2 that is essential for length regulation, which we have termed BAT domain for Blocks Addition of Telomeres. Tethering this BAT domain to Rap1 blocked telomere elongation not only in rif2Δ mutants but also in rif1Δ and rap1C-terminal deletion mutants. Mutation of a single amino acid in the BAT domain, phenylalanine at position 8 to alanine, recapitulated the rif2Δ mutant phenotype. Substitution of F8 with tryptophan mimicked the wild-type phenylalanine, suggesting the aromatic amino acid represents a protein interaction site that is essential for telomere length regulation.
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182
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Goto GH, Zencir S, Hirano Y, Ogi H, Ivessa A, Sugimoto K. Binding of Multiple Rap1 Proteins Stimulates Chromosome Breakage Induction during DNA Replication. PLoS Genet 2015; 11:e1005283. [PMID: 26263073 PMCID: PMC4532487 DOI: 10.1371/journal.pgen.1005283] [Citation(s) in RCA: 11] [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: 11/16/2014] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
Telomeres, the ends of linear eukaryotic chromosomes, have a specialized chromatin structure that provides a stable chromosomal terminus. In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomere length. Here we show that binding of multiple Rap1 proteins stimulates DNA double-stranded break (DSB) induction at both telomeric and non-telomeric regions. Consistent with the role of DSB induction, Rap1 stimulates nearby recombination events in a dosage-dependent manner. Rap1 recruits Rif1 and Rif2 to telomeres, but neither Rif1 nor Rif2 is required for DSB induction. Rap1-mediated DSB induction involves replication fork progression but inactivation of checkpoint kinase Mec1 does not affect DSB induction. Rap1 tethering shortens artificially elongated telomeres in parallel with telomerase inhibition, and this telomere shortening does not require homologous recombination. These results suggest that Rap1 contributes to telomere homeostasis by promoting chromosome breakage. Telomere length is maintained primarily through equilibrium between telomerase-mediated lengthening and the loss of telomeric sequence through the end-replication problem. In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomerase recruitment in a dosage-dependent manner. In this paper we provide evidence suggesting an alternative Rap1-dependent telomere shortening mechanism in which binding of multiple Rap1 proteins mediates DNA break induction during DNA replication. This process does not involve recombination events; therefore, it is distinct from loop-mediated telomere trimming.
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Affiliation(s)
- Greicy H. Goto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Sevil Zencir
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Yukinori Hirano
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Hiroo Ogi
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Andreas Ivessa
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- * E-mail:
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183
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Greetham M, Skordalakes E, Lydall D, Connolly BA. The Telomere Binding Protein Cdc13 and the Single-Stranded DNA Binding Protein RPA Protect Telomeric DNA from Resection by Exonucleases. J Mol Biol 2015; 427:3023-30. [PMID: 26264873 PMCID: PMC4580210 DOI: 10.1016/j.jmb.2015.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/30/2015] [Accepted: 08/04/2015] [Indexed: 11/30/2022]
Abstract
The telomere is present at the ends of all eukaryotic chromosomes and usually consists of repetitive TG-rich DNA that terminates in a single-stranded 3' TG extension and a 5' CA-rich recessed strand. A biochemical assay that allows the in vitro observation of exonuclease-catalyzed degradation (resection) of telomeres has been developed. The approach uses an oligodeoxynucleotide that folds to a stem-loop with a TG-rich double-stranded region and a 3' single-stranded extension, typical of telomeres. Cdc13, the major component of the telomere-specific CST complex, strongly protects the recessed strand from the 5'→3' exonuclease activity of the model exonuclease from bacteriophage λ. The isolated DNA binding domain of Cdc13 is less effective at shielding telomeres. Protection is specific, not being observed in control DNA lacking the specific TG-rich telomere sequence. RPA, the eukaryotic single-stranded DNA binding protein, also inhibits telomere resection. However, this protein is non-specific, equally hindering the degradation of non-telomere controls.
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Affiliation(s)
- Matthew Greetham
- Institute for Cell and Molecular Biology, The University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - David Lydall
- Institute for Cell and Molecular Biology, The University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Bernard A Connolly
- Institute for Cell and Molecular Biology, The University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom.
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184
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Ogi H, Goto GH, Ghosh A, Zencir S, Henry E, Sugimoto K. Requirement of the FATC domain of protein kinase Tel1 for localization to DNA ends and target protein recognition. Mol Biol Cell 2015; 26:3480-8. [PMID: 26246601 PMCID: PMC4591692 DOI: 10.1091/mbc.e15-05-0259] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/29/2015] [Indexed: 02/04/2023] Open
Abstract
Two large phosphatidylinositol 3-kinase-related protein kinases (PIKKs), ATM and ATR, play a central role in the DNA damage response pathway. PIKKs contain a highly conserved extreme C-terminus called the FRAP-ATM-TRRAP-C-terminal (FATC) domain. In budding yeast, ATM and ATR correspond to Tel1 and Mec1, respectively. In this study, we characterized functions of the FATC domain of Tel1 by introducing substitution or truncation mutations. One substitution mutation, termed tel1-21, and a truncation mutation, called tel1-ΔC, did not significantly affect the expression level. The tel1-21 mutation impaired the cellular response to DNA damage and conferred moderate telomere maintenance defect. In contrast, the tel1-ΔC mutation behaved like a null mutation, conferring defects in both DNA damage response and telomere maintenance. Tel1-21 protein localized to DNA ends as effectively as wild-type Tel1 protein, whereas Tel1-ΔC protein failed. Introduction of a hyperactive TEL1-hy mutation suppressed the tel1-21 mutation but not the tel1-ΔC mutation. In vitro analyses revealed that both Tel1-21 and Tel1-ΔC proteins undergo efficient autophosphorylation but exhibit decreased kinase activities toward the exogenous substrate protein, Rad53. Our results show that the FATC domain of Tel1 mediates localization to DNA ends and contributes to phosphorylation of target proteins.
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Affiliation(s)
- Hiroo Ogi
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103
| | - Greicy H Goto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103
| | - Avik Ghosh
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103
| | - Sevil Zencir
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103
| | - Everett Henry
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103 )
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185
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Abstract
Structure-prone DNA repeats are common components of genomic DNA in all kingdoms of life. In humans, these repeats are linked to genomic instabilities that result in various hereditary disorders, including many cancers. It has long been known that DNA repeats are not only highly polymorphic in length but can also cause chromosomal fragility and stimulate gross chromosomal rearrangements, i.e., deletions, duplications, inversions, translocations and more complex shuffles. More recently, it has become clear that inherently unstable DNA repeats dramatically elevate mutation rates in surrounding DNA segments and that these mutations can occur up to ten kilobases away from the repetitive tract, a phenomenon we call repeat-induced mutagenesis (RIM). This review describes experimental data that led to the discovery and characterization of RIM and discusses the molecular mechanisms that could account for this phenomenon.
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Affiliation(s)
- Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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186
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Vogan JM, Collins K. Dynamics of Human Telomerase Holoenzyme Assembly and Subunit Exchange across the Cell Cycle. J Biol Chem 2015; 290:21320-35. [PMID: 26170453 DOI: 10.1074/jbc.m115.659359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 01/04/2023] Open
Abstract
Human telomerase acts on telomeres during the genome synthesis phase of the cell cycle, accompanied by its concentration in Cajal bodies and transient colocalization with telomeres. Whether the regulation of human telomerase holoenzyme assembly contributes to the cell cycle restriction of telomerase function is unknown. We investigated the steady-state levels, assembly, and exchange dynamics of human telomerase subunits with quantitative in vivo cross-linking and other methods. We determined the physical association of telomerase subunits in cells blocked or progressing through the cell cycle as synchronized by multiple protocols. The total level of human telomerase RNA (hTR) was invariant across the cell cycle. In vivo snapshots of telomerase holoenzyme composition established that hTR remains bound to human telomerase reverse transcriptase (hTERT) throughout all phases of the cell cycle, and subunit competition assays suggested that hTERT-hTR interaction is not readily exchangeable. In contrast, the telomerase holoenzyme Cajal body-associated protein, TCAB1, was released from hTR in mitotic cells coincident with TCAB1 delocalization from Cajal bodies. This telomerase holoenzyme disassembly was reversible with cell cycle progression without any change in total TCAB1 protein level. Consistent with differential cell cycle regulation of hTERT-hTR and TCAB1-hTR protein-RNA interactions, overexpression of hTERT or TCAB1 had limited if any influence on hTR assembly of the other subunit. Overall, these findings revealed a cell cycle regulation that disables human telomerase association with telomeres while preserving the co-folded hTERT-hTR ribonucleoprotein catalytic core. Studies here, integrated with previous work, led to a unifying model for telomerase subunit assembly and trafficking in human cells.
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Affiliation(s)
- Jacob M Vogan
- From the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720
| | - Kathleen Collins
- From the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720
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187
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Bajon E, Laterreur N, Wellinger RJ. A Single Templating RNA in Yeast Telomerase. Cell Rep 2015; 12:441-8. [PMID: 26166570 DOI: 10.1016/j.celrep.2015.06.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/04/2015] [Accepted: 06/13/2015] [Indexed: 12/31/2022] Open
Abstract
The number of essential telomerase components in the active ribonucleoprotein (RNP) has important implications for its mechanism of action yet is by and large unknown. We report that two differentially tagged TLC1 RNAs endogenously expressed in a heterozygous diploid and simultaneously detected via multi-color fluorescence in situ hybridization (FISH) experiments do not co-localize. Probabilistic calculations combined with direct quantification of FISH signals demonstrate that the TLC1 RNA indeed occurs as a single molecule in these RNPs. In addition, two differentially tagged reverse-transcriptase subunits could not be co-immunoprecipitated. These results therefore show that, in yeast cells, telomerase is assembled and matured and occurs as a monomer when not on telomeres. Finally, combining these findings with previous evidence leads us to propose that the enzyme also acts as a monomer when elongating telomeres.
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Affiliation(s)
- Emmanuel Bajon
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, Université de Sherbrooke, 3201, rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Nancy Laterreur
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, Université de Sherbrooke, 3201, rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine, Université de Sherbrooke, 3201, rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada.
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188
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Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
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189
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Steakley DL, Rine J. On the Mechanism of Gene Silencing in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2015; 5:1751-63. [PMID: 26082137 PMCID: PMC4528331 DOI: 10.1534/g3.115.018515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/15/2015] [Indexed: 11/18/2022]
Abstract
Multiple mechanisms have been proposed for gene silencing in Saccharomyces cerevisiae, ranging from steric occlusion of DNA binding proteins from their recognition sequences in silenced chromatin to a specific block in the formation of the preinitiation complex to a block in transcriptional elongation. This study provided strong support for the steric occlusion mechanism by the discovery that RNA polymerase of bacteriophage T7 could be substantially blocked from transcribing from its cognate promoter when embedded in silenced chromatin. Moreover, unlike previous suggestions, we found no evidence for stalled RNA polymerase II within silenced chromatin. The effectiveness of the Sir protein-based silencing mechanism to block transcription activated by Gal4 at promoters in the domain of silenced chromatin was marginal, yet it improved when tested against mutant forms of the Gal4 protein, highlighting a role for specific activators in their sensitivity to gene silencing.
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Affiliation(s)
- David Lee Steakley
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, Stanley Hall, University of California Berkeley, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, Stanley Hall, University of California Berkeley, Berkeley, California 94720
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190
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Ikeda A, Muneoka T, Murakami S, Hirota A, Yabuki Y, Karashima T, Nakazono K, Tsuruno M, Pichler H, Shirahige K, Kodama Y, Shimamoto T, Mizuta K, Funato K. Sphingolipids regulate telomere clustering by affecting the transcription of genes involved in telomere homeostasis. J Cell Sci 2015; 128:2454-67. [PMID: 26045446 DOI: 10.1242/jcs.164160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 05/20/2015] [Indexed: 12/14/2022] Open
Abstract
In eukaryotic organisms, including mammals, nematodes and yeasts, the ends of chromosomes, telomeres are clustered at the nuclear periphery. Telomere clustering is assumed to be functionally important because proper organization of chromosomes is necessary for proper genome function and stability. However, the mechanisms and physiological roles of telomere clustering remain poorly understood. In this study, we demonstrate a role for sphingolipids in telomere clustering in the budding yeast Saccharomyces cerevisiae. Because abnormal sphingolipid metabolism causes downregulation of expression levels of genes involved in telomere organization, sphingolipids appear to control telomere clustering at the transcriptional level. In addition, the data presented here provide evidence that telomere clustering is required to protect chromosome ends from DNA-damage checkpoint signaling. As sphingolipids are found in all eukaryotes, we speculate that sphingolipid-based regulation of telomere clustering and the protective role of telomere clusters in maintaining genome stability might be conserved in eukaryotes.
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Affiliation(s)
- Atsuko Ikeda
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Tetsuya Muneoka
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Suguru Murakami
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Ayaka Hirota
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Yukari Yabuki
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Takefumi Karashima
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Kota Nakazono
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Masahiro Tsuruno
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Harald Pichler
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/2, Graz 8010, Austria
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo 113-0032, Japan
| | | | - Toshi Shimamoto
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Keiko Mizuta
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
| | - Kouichi Funato
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, Hiroshima 739-8528, Japan
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191
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Ellahi A, Thurtle DM, Rine J. The Chromatin and Transcriptional Landscape of Native Saccharomyces cerevisiae Telomeres and Subtelomeric Domains. Genetics 2015; 200:505-21. [PMID: 25823445 PMCID: PMC4492376 DOI: 10.1534/genetics.115.175711] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/22/2015] [Indexed: 12/18/2022] Open
Abstract
Saccharomyces cerevisiae telomeres have been a paradigm for studying telomere position effects on gene expression. Telomere position effect was first described in yeast by its effect on the expression of reporter genes inserted adjacent to truncated telomeres. The reporter genes showed variable silencing that depended on the Sir2/3/4 complex. Later studies examining subtelomeric reporter genes inserted at natural telomeres hinted that telomere position effects were less pervasive than previously thought. Additionally, more recent data using the sensitive technology of chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) revealed a discrete and noncontinuous pattern of coenrichment for all three Sir proteins at a few telomeres, calling the generality of these conclusions into question. Here we combined the ChIP-Seq of the Sir proteins with RNA sequencing (RNA-Seq) of messenger RNAs (mRNAs) in wild-type and in SIR2, SIR3, and SIR4 deletion mutants to characterize the chromatin and transcriptional landscape of all native S. cerevisiae telomeres at the highest achievable resolution. Most S. cerevisiae chromosomes had subtelomeric genes that were expressed, with only ∼6% of subtelomeric genes silenced in a SIR-dependent manner. In addition, we uncovered 29 genes with previously unknown cell-type-specific patterns of expression. These detailed data provided a comprehensive assessment of the chromatin and transcriptional landscape of the subtelomeric domains of a eukaryotic genome.
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Affiliation(s)
- Aisha Ellahi
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
| | - Deborah M Thurtle
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720
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192
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Hsieh MH, Tsai CH, Lin CC, Li TK, Hung TW, Chang LT, Hsin LW, Teng SC. Topoisomerase II inhibition suppresses the proliferation of telomerase-negative cancers. Cell Mol Life Sci 2015; 72:1825-37. [PMID: 25430478 PMCID: PMC11113807 DOI: 10.1007/s00018-014-1783-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
Telomere maintenance is required for chromosome stability, and telomeres are typically elongated by telomerase following DNA replication. In both tumor and yeast cells that lack telomerase, telomeres are maintained via an alternative recombination mechanism. Previous studies have indicated that yeast Sgs1 and Top3 may work together to remove highly negative supercoils that are generated from recombination. However, the mechanism by which cells eradicate highly positive supercoils during recombination remains unclear. In the present study, we demonstrate that TOP2 is involved in telomere-telomere recombination. Disturbance of telomeric structure by RIF1 or RIF2 deletion alleviates the requirement for TOP2 in telomere-telomere recombination. In human telomerase-negative alternative lengthening of telomere (ALT) cells, TOP2α or TOP2β knockdown decreases ALT-associated PML bodies, increases telomere dysfunction-induced foci and triggers telomere shortening. Similar results were observed when ALT cells were treated with ICRF-193, a TOP2 inhibitor. Importantly, ICRF-193 treatment blocks ALT-associated phenotypes in vitro, causes telomere shortening, and inhibits ALT cell proliferation in mice. Taken together, these findings imply that TOP2 is involved in the ALT pathway, perhaps by resolving the highly positive supercoil structure at the front of the helicase. Inhibition of topoisomerase II may be a promising therapeutic approach that can be used to prevent cell proliferation in ALT-type cancer cells.
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Affiliation(s)
- Meng-Hsun Hsieh
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Road, Taipei, 100, Taiwan,
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193
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Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PLoS One 2015; 10:e0125201. [PMID: 25923330 PMCID: PMC4414351 DOI: 10.1371/journal.pone.0125201] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 03/06/2015] [Indexed: 11/19/2022] Open
Abstract
Telomeres are the ends of eukaryotic chromosomes, consisting of consecutive short repeats that protect chromosome ends from degradation. Telomeres shorten with each cell division, leading to replicative cell senescence. Deregulation of telomere length homeostasis is associated with the development of various age-related diseases and cancers. A number of experimental techniques exist for telomere length measurement; however, until recently, the absence of tools for extracting telomere lengths from high-throughput sequencing data has significantly obscured the association of telomere length with molecular processes in normal and diseased conditions. We have developed Computel, a program in R for computing mean telomere length from whole-genome next-generation sequencing data. Computel is open source, and is freely available at https://github.com/lilit-nersisyan/computel. It utilizes a short-read alignment-based approach and integrates various popular tools for sequencing data analysis. We validated it with synthetic and experimental data, and compared its performance with the previously available software. The results have shown that Computel outperforms existing software in accuracy, independence of results from sequencing conditions, stability against inherent sequencing errors, and better ability to distinguish pure telomeric sequences from interstitial telomeric repeats. By providing a highly reliable methodology for determining telomere lengths from whole-genome sequencing data, Computel should help to elucidate the role of telomeres in cellular health and disease.
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194
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Cusanelli E, Chartrand P. Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity. Front Genet 2015; 6:143. [PMID: 25926849 PMCID: PMC4396414 DOI: 10.3389/fgene.2015.00143] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/25/2015] [Indexed: 12/15/2022] Open
Abstract
Telomeres are dynamic nucleoprotein structures that protect the ends of chromosomes from degradation and activation of DNA damage response. For this reason, telomeres are essential to genome integrity. Chromosome ends are enriched in heterochromatic marks and proper organization of telomeric chromatin is important to telomere stability. Despite their heterochromatic state, telomeres are transcribed giving rise to long noncoding RNAs (lncRNA) called TERRA (telomeric repeat-containing RNA). TERRA molecules play critical roles in telomere biology, including regulation of telomerase activity and heterochromatin formation at chromosome ends. Emerging evidence indicate that TERRA transcripts form DNA-RNA hybrids at chromosome ends which can promote homologous recombination among telomeres, delaying cellular senescence and sustaining genome instability. Intriguingly, TERRA RNA-telomeric DNA hybrids are involved in telomere length homeostasis of telomerase-negative cancer cells. Furthermore, TERRA transcripts play a role in the DNA damage response (DDR) triggered by dysfunctional telomeres. We discuss here recent developments on TERRA's role in telomere biology and genome integrity, and its implication in cancer.
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Affiliation(s)
- Emilio Cusanelli
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna Vienna, Austria
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal Montréal, QC, Canada
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195
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Abstract
Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology.
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196
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Inhibition of telomere recombination by inactivation of KEOPS subunit Cgi121 promotes cell longevity. PLoS Genet 2015; 11:e1005071. [PMID: 25822194 PMCID: PMC4378880 DOI: 10.1371/journal.pgen.1005071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
DNA double strand break (DSB) is one of the major damages that cause genome instability and cellular aging. The homologous recombination (HR)-mediated repair of DSBs plays an essential role in assurance of genome stability and cell longevity. Telomeres resemble DSBs and are competent for HR. Here we show that in budding yeast Saccharomyces cerevisiae telomere recombination elicits genome instability and accelerates cellular aging. Inactivation of KEOPS subunit Cgi121 specifically inhibits telomere recombination, and significantly extends cell longevity in both telomerase-positive and pre-senescing telomerase-negative cells. Deletion of CGI121 in the short-lived yku80tel mutant restores lifespan to cgi121Δ level, supporting the function of Cgi121 in telomeric single-stranded DNA generation and thus in promotion of telomere recombination. Strikingly, inhibition of telomere recombination is able to further slow down the aging process in long-lived fob1Δ cells, in which rDNA recombination is restrained. Our study indicates that HR activity at telomeres interferes with telomerase to pose a negative impact on cellular longevity. Aging is a general biological process among the living organisms which is affected by environmental stimuli but also genetically controlled. Genome instability is one of the aging hallmarks and has long been implicated as one of the main causal factors in aging. DNA double strand breaks (DSBs) are the most deleterious DNA damages that cause genome instability. To counteract DNA damage of DSBs and maintain high level of genome integrity, cells have evolved powerful repair systems such as homologous recombination (HR). HR is crucial for DNA repair and genome integrity maintenance, and is generally believed to be essential for assurance of cell longevity. Telomeres, the physical ends of eukaryotic linear chromosomes, are preferentially elongated by telomerase, a specialized reverse transcriptase, in most cases. However, due to the resemblance of telomeres to DSBs, HR can not be eliminated but rather readily takes place on telomeres, even in the presence of telomerase. Here we show that HR at yeast telomeres elicits genome instability and accelerates cellular aging. Inactivation of the evolutionarily conserved KEOPS complex subunit Cgi121 specifically inhibits telomere HR and results in extremely long lifespan, indicating a dark side of HR in longevity regulation.
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197
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Si T, Luo Y, Bao Z, Zhao H. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth Biol 2015; 4:283-91. [PMID: 24758359 DOI: 10.1021/sb500074a] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A fundamental challenge in basic and applied biology is to reprogram cells with improved or novel traits on a genomic scale. However, the current ability to reprogram a cell on the genome scale is limited to bacterial cells. Here, we report RNA interference (RNAi)-assisted genome evolution (RAGE) as a generally applicable method for genome-scale engineering in the yeast Saccharomyces cerevisiae. Through iterative cycles of creating a library of RNAi induced reduction-of-function mutants coupled with high throughput screening or selection, RAGE can continuously improve target trait(s) by accumulating multiplex beneficial genetic modifications in an evolving yeast genome. To validate the RNAi library constructed with yeast genomic DNA and convergent-promoter expression cassette, we demonstrated RNAi screening in Saccharomyces cerevisiae for the first time by identifying two known and three novel suppressors of a telomerase-deficient mutation yku70Δ. We then showed the application of RAGE for improved acetic acid tolerance, a key trait for microbial production of chemicals and fuels. Three rounds of iterative RNAi screening led to the identification of three gene knockdown targets that acted synergistically to confer an engineered yeast strain with substantially improved acetic acid tolerance. RAGE should greatly accelerate the design and evolution of organisms with desired traits and provide new insights on genome structure, function, and evolution.
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Affiliation(s)
- Tong Si
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yunzi Luo
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Zehua Bao
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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198
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Abstract
The budding yeast Saccharomyces cerevisiae is a powerful model organism for studying fundamental aspects of eukaryotic cell biology. This Primer article presents a brief historical perspective on the emergence of this organism as a premier experimental system over the course of the past century. An overview of the central features of the S. cerevisiae genome, including the nature of its genetic elements and general organization, is also provided. Some of the most common experimental tools and resources available to yeast geneticists are presented in a way designed to engage and challenge undergraduate and graduate students eager to learn more about the experimental amenability of budding yeast. Finally, a discussion of several major discoveries derived from yeast studies highlights the far-reaching impact that the yeast system has had and will continue to have on our understanding of a variety of cellular processes relevant to all eukaryotes, including humans.
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199
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Feldmann EA, Galletto R. The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes. Biochemistry 2014; 53:7471-83. [PMID: 25382181 PMCID: PMC4263426 DOI: 10.1021/bi501049b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Saccharomyces cerevisiae repressor-activator protein
1 (Rap1) is an essential protein involved in multiple steps of DNA
regulation, as an activator in transcription, as a repressor at silencer
elements, and as a major component of the shelterin-like complex at
telomeres. All the known functions of Rap1 require the known high-affinity
and specific interaction of the DNA-binding domain with its recognition
sequences. In this work, we focus on the interaction of the DNA-binding
domain of Rap1 (Rap1DBD) with double-stranded DNA substrates.
Unexpectedly, we found that while Rap1DBD forms a high-affinity
1:1 complex with its DNA recognition site, it can also form lower-affinity
complexes with higher stoichiometries on DNA. These lower-affinity
interactions are independent of the presence of the recognition sequence,
and we propose they originate from the ability of Rap1DBD to bind to DNA in two different binding modes. In one high-affinity
binding mode, Rap1DBD likely binds in the conformation
observed in the available crystal structures. In the other alternative
lower-affinity binding mode, we propose that a single Myb-like domain
of the Rap1DBD makes interactions with DNA, allowing for
more than one protein molecule to bind to the DNA substrates. Our
findings suggest that the Rap1DBD does not simply target
the protein to its recognition sequence but rather it might be a possible
point of regulation.
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Affiliation(s)
- Erik A Feldmann
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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200
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PP2A and Aurora differentially modify Cdc13 to promote telomerase release from telomeres at G2/M phase. Nat Commun 2014; 5:5312. [PMID: 25387524 DOI: 10.1038/ncomms6312] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
In yeast, the initiation of telomere replication at the late S phase involves in combined actions of kinases on Cdc13, the telomere binding protein. Cdc13 recruits telomerase to telomeres through its interaction with Est1, a component of telomerase. However, how cells terminate the function of telomerase at G2/M is still elusive. Here we show that the protein phosphatase 2A (PP2A) subunit Pph22 and the yeast Aurora kinase homologue Ipl1 coordinately inhibit telomerase at G2/M by dephosphorylating and phosphorylating the telomerase recruitment domain of Cdc13, respectively. While Pph22 removes Tel1/Mec1-mediated Cdc13 phosphorylation to reduce Cdc13-Est1 interaction, Ipl1-dependent Cdc13 phosphorylation elicits dissociation of Est1-TLC1, the template RNA component of telomerase. Failure of these regulations prevents telomerase from departing telomeres, causing perturbed telomere lengthening and prolonged M phase. Together our results demonstrate that differential and additive actions of PP2A and Aurora on Cdc13 limit telomerase action by removing active telomerase from telomeres at G2/M phase.
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