1
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Sosa Ponce ML, Remedios MH, Moradi-Fard S, Cobb JA, Zaremberg V. SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid. J Cell Biol 2023; 222:e202206061. [PMID: 37042812 PMCID: PMC10103788 DOI: 10.1083/jcb.202206061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/29/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
The nuclear envelope (NE) is important in maintaining genome organization. The role of lipids in communication between the NE and telomere regulation was investigated, including how changes in lipid composition impact gene expression and overall nuclear architecture. Yeast was treated with the non-metabolizable lysophosphatidylcholine analog edelfosine, known to accumulate at the perinuclear ER. Edelfosine induced NE deformation and disrupted telomere clustering but not anchoring. Additionally, the association of Sir4 at telomeres decreased. RNA-seq analysis showed altered expression of Sir-dependent genes located at sub-telomeric (0-10 kb) regions, consistent with Sir4 dispersion. Transcriptomic analysis revealed that two lipid metabolic circuits were activated in response to edelfosine, one mediated by the membrane sensing transcription factors, Spt23/Mga2, and the other by a transcriptional repressor, Opi1. Activation of these transcriptional programs resulted in higher levels of unsaturated fatty acids and the formation of nuclear lipid droplets. Interestingly, cells lacking Sir proteins displayed resistance to unsaturated-fatty acids and edelfosine, and this phenotype was connected to Rap1.
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Affiliation(s)
| | | | - Sarah Moradi-Fard
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
| | - Jennifer A. Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Calgary, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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2
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Smoak RA, Snyder LF, Fassler JS, He BZ. Parallel expansion and divergence of an adhesin family in pathogenic yeasts. Genetics 2023; 223:iyad024. [PMID: 36794645 PMCID: PMC10319987 DOI: 10.1093/genetics/iyad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Opportunistic yeast pathogens arose multiple times in the Saccharomycetes class, including the recently emerged, multidrug-resistant (MDR) Candida auris. We show that homologs of a known yeast adhesin family in Candida albicans, the Hyr/Iff-like (Hil) family, are enriched in distinct clades of Candida species as a result of multiple, independent expansions. Following gene duplication, the tandem repeat-rich region in these proteins diverged extremely rapidly and generated large variations in length and β-aggregation potential, both of which are known to directly affect adhesion. The conserved N-terminal effector domain was predicted to adopt a β-helical fold followed by an α-crystallin domain, making it structurally similar to a group of unrelated bacterial adhesins. Evolutionary analyses of the effector domain in C. auris revealed relaxed selective constraint combined with signatures of positive selection, suggesting functional diversification after gene duplication. Lastly, we found the Hil family genes to be enriched at chromosomal ends, which likely contributed to their expansion via ectopic recombination and break-induced replication. Combined, these results suggest that the expansion and diversification of adhesin families generate variation in adhesion and virulence within and between species and are a key step toward the emergence of fungal pathogens.
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Affiliation(s)
- Rachel A Smoak
- Civil and Environmental Engineering, The University of Iowa, Iowa City, IA 52242, USA
| | - Lindsey F Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Jan S Fassler
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Bin Z He
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
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3
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D’Angiolo M, Yue JX, De Chiara M, Barré BP, Giraud Panis MJ, Gilson E, Liti G. Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones. Genetics 2023; 223:iyac186. [PMID: 36563016 PMCID: PMC9991508 DOI: 10.1093/genetics/iyac186] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/02/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Telomeres are ribonucleoproteins that cap chromosome-ends and their DNA length is controlled by counteracting elongation and shortening processes. The budding yeast Saccharomyces cerevisiae has been a leading model to study telomere DNA length control and dynamics. Its telomeric DNA is maintained at a length that slightly varies between laboratory strains, but little is known about its variation at the species level. The recent publication of the genomes of over 1,000 S. cerevisiae strains enabled us to explore telomere DNA length variation at an unprecedented scale. Here, we developed a bioinformatic pipeline (YeaISTY) to estimate telomere DNA length from whole-genome sequences and applied it to the sequenced S. cerevisiae collection. Our results revealed broad natural telomere DNA length variation among the isolates. Notably, telomere DNA length is shorter in those derived from wild rather than domesticated environments. Moreover, telomere DNA length variation is associated with mitochondrial metabolism, and this association is driven by wild strains. Overall, these findings reveal broad variation in budding yeast's telomere DNA length regulation, which might be shaped by its different ecological life-styles.
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Affiliation(s)
- Melania D’Angiolo
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Jia-Xing Yue
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), 651 Dongfeng Road East, China
| | - Matteo De Chiara
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Benjamin P Barré
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Marie-Josèphe Giraud Panis
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
| | - Eric Gilson
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
- Department of Genetics, CHU, 06107 Nice, France
| | - Gianni Liti
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 28 Avenue de Valombrose, 06107 Nice, France
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4
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Mei Q, Yu Q, Li X, Chen J, Yu X. Regulation of telomere silencing by the core histones-autophagy-Sir2 axis. Life Sci Alliance 2023; 6:6/3/e202201614. [PMID: 36585257 PMCID: PMC9806677 DOI: 10.26508/lsa.202201614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022] Open
Abstract
Telomeres contain compacted heterochromatin, and genes adjacent to telomeres are subjected to transcription silencing. Maintaining telomere structure integrity and transcription silencing is important to prevent the occurrence of premature aging and aging-related diseases. How telomere silencing is regulated during aging is not well understood. Here, we find that the four core histones are reduced during yeast chronological aging, leading to compromised telomere silencing. Mechanistically, histone loss promotes the nuclear export of Sir2 and its degradation by autophagy. Meanwhile, reducing core histones enhances the autophagy pathway, which further accelerates autophagy-mediated Sir2 degradation. By screening the histone mutant library, we identify eight histone mutants and one histone modification (histone methyltransferase Set1-catalyzed H3K4 trimethylation) that regulate telomere silencing by modulating the core histones-autophagy-Sir2 axis. Overall, our findings reveal core histones and autophagy as causes of aging-coupled loss of telomere silencing and shed light on dynamic regulation of telomere structure during aging.
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Affiliation(s)
- Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Xin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Jianguo Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
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5
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Substrates of the MAPK Slt2: Shaping Yeast Cell Integrity. J Fungi (Basel) 2022; 8:jof8040368. [PMID: 35448599 PMCID: PMC9031059 DOI: 10.3390/jof8040368] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
The cell wall integrity (CWI) MAPK pathway of budding yeast Saccharomyces cerevisiae is specialized in responding to cell wall damage, but ongoing research shows that it participates in many other stressful conditions, suggesting that it has functional diversity. The output of this pathway is mainly driven by the activity of the MAPK Slt2, which regulates important processes for yeast physiology such as fine-tuning of signaling through the CWI and other pathways, transcriptional activation in response to cell wall damage, cell cycle, or determination of the fate of some organelles. To this end, Slt2 precisely phosphorylates protein substrates, modulating their activity, stability, protein interaction, and subcellular localization. Here, after recapitulating the methods that have been employed in the discovery of proteins phosphorylated by Slt2, we review the bona fide substrates of this MAPK and the growing set of candidates still to be confirmed. In the context of the complexity of MAPK signaling regulation, we discuss how Slt2 determines yeast cell integrity through phosphorylation of these substrates. Increasing data from large-scale analyses and the available methodological approaches pave the road to early identification of new Slt2 substrates and functions.
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6
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Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast. Cell Rep 2021; 37:110149. [PMID: 34965436 DOI: 10.1016/j.celrep.2021.110149] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/19/2021] [Accepted: 11/30/2021] [Indexed: 01/18/2023] Open
Abstract
The eukaryotic TORC1 kinase assimilates diverse environmental cues, including growth factors and nutrients, to control growth by tuning anabolic and catabolic processes. In yeast, TORC1 stimulates protein synthesis in response to abundant nutrients primarily through its proximal effector kinase Sch9. Conversely, TORC1 inhibition following nutrient limitation unlocks various distally controlled kinases (e.g., Atg1, Gcn2, Npr1, Rim15, Slt2/Mpk1, and Yak1), which cooperate through poorly defined circuits to orchestrate the quiescence program. To better define the signaling landscape of the latter kinases, we use in vivo quantitative phosphoproteomics. Through pinpointing known and uncharted Npr1, Rim15, Slt2/Mpk1, and Yak1 effectors, our study examines the architecture of the distally controlled TORC1 kinase network. Accordingly, this is built on a combination of discrete, convergent, and multilayered feedback regulatory mechanisms, which likely ensure homeostatic control of and/or robust responses by TORC1 and its effector kinases under fluctuating nutritional conditions.
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7
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Jethmalani Y, Tran K, Negesse MY, Sun W, Ramos M, Jaiswal D, Jezek M, Amos S, Garcia EJ, Park D, Green EM. Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres. Life Sci Alliance 2021; 4:e202101126. [PMID: 34625508 PMCID: PMC8507492 DOI: 10.26508/lsa.202101126] [Citation(s) in RCA: 3] [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: 05/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
The yeast chromatin protein Set4 is a member of the Set3-subfamily of SET domain proteins which play critical roles in the regulation of gene expression in diverse developmental and environmental contexts. We previously reported that Set4 promotes survival during oxidative stress and regulates expression of stress response genes via stress-dependent chromatin localization. In this study, global gene expression analysis and investigation of histone modification status identified a role for Set4 in maintaining gene repressive mechanisms within yeast subtelomeres under both normal and stress conditions. We show that Set4 works in a partially overlapping pathway to the SIR complex and the histone deacetylase Rpd3 to maintain proper levels of histone acetylation and expression of stress response genes encoded in subtelomeres. This role for Set4 is particularly critical for cells under hypoxic conditions, where the loss of Set4 decreases cell fitness and cell wall integrity. These findings uncover a new regulator of subtelomeric chromatin that is key to stress defense pathways and demonstrate a function for Set4 in regulating repressive, heterochromatin-like environments.
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Affiliation(s)
- Yogita Jethmalani
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Khoa Tran
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Maraki Y Negesse
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Winny Sun
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Mark Ramos
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Deepika Jaiswal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Shandon Amos
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Eric Joshua Garcia
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - DoHwan Park
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
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8
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The Power of Stress: The Telo-Hormesis Hypothesis. Cells 2021; 10:cells10051156. [PMID: 34064566 PMCID: PMC8151059 DOI: 10.3390/cells10051156] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Adaptative response to stress is a strategy conserved across evolution to promote survival. In this context, the groundbreaking findings of Miroslav Radman on the adaptative value of changing mutation rates opened new avenues in our understanding of stress response. Inspired by this work, we explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress. We first summarize basic principles in telomere biology and then describe how various types of stress can alter telomere structure and functions. Finally, we discuss the hypothesis of stress-induced telomere signaling with hormetic effects.
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9
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Fredericks LR, Lee MD, Crabtree AM, Boyer JM, Kizer EA, Taggart NT, Roslund CR, Hunter SS, Kennedy CB, Willmore CG, Tebbe NM, Harris JS, Brocke SN, Rowley PA. The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina. PLoS Genet 2021; 17:e1009341. [PMID: 33539346 PMCID: PMC7888664 DOI: 10.1371/journal.pgen.1009341] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/17/2021] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, including Saccharomyces yeasts. Although many Saccharomyces killer toxins have been previously identified, their evolutionary origins remain uncertain given that many of these genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from the Saccharomyces genus has identified a novel killer toxin with a unique spectrum of activity produced by Saccharomyces paradoxus. The expression of this killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin from Saccharomyces cerevisiae and has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomyces yeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the genome. When ectopically expressed in S. cerevisiae from cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a family of biologically active K1-like killer toxins. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification. The phylogenetic relationship between K1L and its genomic homologs suggests a common ancestry and gene flow via dsRNAs and DNAs across taxonomic divisions. This appears to enable the acquisition of a diverse arsenal of killer toxins by different yeast species for potential use in niche competition.
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Affiliation(s)
- Lance R. Fredericks
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Mark D. Lee
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Angela M. Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Josephine M. Boyer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Emily A. Kizer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Nathan T. Taggart
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Cooper R. Roslund
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Samuel S. Hunter
- iBEST Genomics Core, University of Idaho, Moscow, Idaho, United States of America
| | - Courtney B. Kennedy
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Cody G. Willmore
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Nova M. Tebbe
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Jade S. Harris
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah N. Brocke
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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10
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Lei B, Capella M, Montgomery SA, Borg M, Osakabe A, Goiser M, Muhammad A, Braun S, Berger F. A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W. Curr Biol 2021; 31:182-191.e5. [PMID: 33096036 DOI: 10.1016/j.cub.2020.09.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.
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Affiliation(s)
- Bingkun Lei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Matías Capella
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Sean A Montgomery
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Abubakar Muhammad
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Planegg-Martinsried, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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11
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Bruhn C, Ajazi A, Ferrari E, Lanz MC, Batrin R, Choudhary R, Walvekar A, Laxman S, Longhese MP, Fabre E, Smolka MB, Foiani M. The Rad53 CHK1/CHK2-Spt21 NPAT and Tel1 ATM axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nat Commun 2020; 11:4154. [PMID: 32814778 PMCID: PMC7438486 DOI: 10.1038/s41467-020-17961-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
The DNA damage response (DDR) coordinates DNA metabolism with nuclear and non-nuclear processes. The DDR kinase Rad53CHK1/CHK2 controls histone degradation to assist DNA repair. However, Rad53 deficiency causes histone-dependent growth defects in the absence of DNA damage, pointing out unknown physiological functions of the Rad53-histone axis. Here we show that histone dosage control by Rad53 ensures metabolic homeostasis. Under physiological conditions, Rad53 regulates histone levels through inhibitory phosphorylation of the transcription factor Spt21NPAT on Ser276. Rad53-Spt21 mutants display severe glucose dependence, caused by excess histones through two separable mechanisms: dampening of acetyl-coenzyme A-dependent carbon metabolism through histone hyper-acetylation, and Sirtuin-mediated silencing of starvation-induced subtelomeric domains. We further demonstrate that repression of subtelomere silencing by physiological Tel1ATM and Rpd3HDAC activities coveys tolerance to glucose restriction. Our findings identify DDR mutations, histone imbalances and aberrant subtelomeric chromatin as interconnected causes of glucose dependence, implying that DDR kinases coordinate metabolism and epigenetic changes.
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Affiliation(s)
- Christopher Bruhn
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
| | - Arta Ajazi
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Elisa Ferrari
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Ramveer Choudhary
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Adhish Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Edificio U3, Piazza della Scienza 2, 20126, Milan, Italy
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Marcus Bustamente Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marco Foiani
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
- Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy.
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12
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Devia J, Bastías C, Kessi-Pérez EI, Villarroel CA, De Chiara M, Cubillos FA, Liti G, Martínez C, Salinas F. Transcriptional Activity and Protein Levels of Horizontally Acquired Genes in Yeast Reveal Hallmarks of Adaptation to Fermentative Environments. Front Genet 2020; 11:293. [PMID: 32425968 PMCID: PMC7212421 DOI: 10.3389/fgene.2020.00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/11/2020] [Indexed: 12/02/2022] Open
Abstract
In the past decade, the sequencing of large cohorts of Saccharomyces cerevisiae strains has revealed a landscape of genomic regions acquired by Horizontal Gene Transfer (HGT). The genes acquired by HGT play important roles in yeast adaptation to the fermentation process, improving nitrogen and carbon source utilization. However, the functional characterization of these genes at the molecular level has been poorly attended. In this work, we carried out a systematic analysis of the promoter activity and protein level of 30 genes contained in three horizontally acquired regions commonly known as regions A, B, and C. In three strains (one for each region), we used the luciferase reporter gene and the mCherry fluorescent protein to quantify the transcriptional and translational activity of these genes, respectively. We assayed the strains generated in four different culture conditions; all showed low levels of transcriptional and translational activity across these environments. However, we observed an increase in protein levels under low nitrogen culture conditions, suggesting a possible role of the horizontally acquired genes in the adaptation to nitrogen-limited environments. Furthermore, since the strains carrying the luciferase reporter gene are null mutants for the horizontally acquired genes, we assayed growth parameters (latency time, growth rate, and efficiency) and the fermentation kinetics in this set of deletion strains. The results showed that single deletion of 20 horizontally acquired genes modified the growth parameters, whereas the deletion of five of them altered the maximal CO2 production rate (Vmax). Interestingly, we observed a correlation between growth parameters and Vmax for an ORF within region A, encoding an ortholog to a thiamine (vitamin B1) transporter whose deletion decreased the growth rate, growth efficiency, and CO2 production. Altogether, our results provided molecular and phenotypic evidence highlighting the importance of horizontally acquired genes in yeast adaptation to fermentative environments.
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Affiliation(s)
- Joaquín Devia
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Camila Bastías
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Carlos A Villarroel
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | | | - Francisco A Cubillos
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia, Chile
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13
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Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Sci Rep 2020; 10:6055. [PMID: 32269268 PMCID: PMC7142091 DOI: 10.1038/s41598-020-63209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/26/2020] [Indexed: 01/24/2023] Open
Abstract
Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
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14
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Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis. Microorganisms 2020; 8:microorganisms8030321. [PMID: 32110897 PMCID: PMC7143498 DOI: 10.3390/microorganisms8030321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/02/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022] Open
Abstract
The growing global population and developing world has put a strain on non-renewable natural resources, such as fuels. The shift to renewable sources will, thus, help meet demands, often through the modification of existing biosynthetic pathways or the introduction of novel pathways into non-native species. There are several useful biosynthetic pathways endogenous to organisms that are not conducive for the scale-up necessary for industrial use. The use of genetic and synthetic biological approaches to engineer these pathways in non-native organisms can help ameliorate these challenges. The budding yeast Saccharomyces cerevisiae offers several advantages for genetic engineering for this purpose due to its widespread use as a model system studied by many researchers. The focus of this review is to present a primer on understanding genomic considerations prior to genetic modification and manipulation of S. cerevisiae. The choice of a site for genetic manipulation can have broad implications on transcription throughout a region and this review will present the current understanding of position effects on transcription.
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15
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Gvozdenov Z, Bendix LD, Kolhe J, Freeman BC. The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility. J Mol Biol 2019; 431:4993-5003. [PMID: 31628945 PMCID: PMC6983977 DOI: 10.1016/j.jmb.2019.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/29/2019] [Accepted: 09/11/2019] [Indexed: 01/02/2023]
Abstract
Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure. Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function, whereas prolonged Hsp90 inactivation led to a significant decrease in the steady-state transcription factor protein levels. Intriguingly, despite the broad chaperone impact on a variety of transcription factors, the operational influence of Hsp90 was at the level of chromatin with only a mild effect on gene regulation. Thus, Hsp90 selectively governs the transcription factor process overseeing local chromatin structure.
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Affiliation(s)
- Zlata Gvozdenov
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Lindsey D Bendix
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Janhavi Kolhe
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Brian C Freeman
- University of Illinois, Urbana-Champaign, Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA.
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16
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Garcia EJ, de Jonge JJ, Liao PC, Stivison E, Sing CN, Higuchi-Sanabria R, Boldogh IR, Pon LA. Reciprocal interactions between mtDNA and lifespan control in budding yeast. Mol Biol Cell 2019; 30:2943-2952. [PMID: 31599702 PMCID: PMC6857569 DOI: 10.1091/mbc.e18-06-0356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 01/01/2023] Open
Abstract
Loss of mitochondrial DNA (mtDNA) results in loss of mitochondrial respiratory activity, checkpoint-regulated inhibition of cell cycle progression, defects in growth, and nuclear genome instability. However, after several generations, yeast cells can adapt to the loss of mtDNA. During this adaptation, rho0 cells, which have no mtDNA, exhibit increased growth rates and nuclear genome stabilization. Here, we report that an immediate response to loss of mtDNA is a decrease in replicative lifespan (RLS). Moreover, we find that adapted rho0 cells bypass the mtDNA inheritance checkpoint, exhibit increased mitochondrial function, and undergo an increase in RLS as they adapt to the loss of mtDNA. Transcriptome analysis reveals that metabolic reprogramming to compensate for defects in mitochondrial function is an early event during adaptation and that up-regulation of stress response genes occurs later in the adaptation process. We also find that specific subtelomeric genes are silenced during adaptation to loss of mtDNA. Moreover, we find that deletion of SIR3, a subtelomeric gene silencing protein, inhibits silencing of subtelomeric genes associated with adaptation to loss of mtDNA, as well as adaptation-associated increases in mitochondrial function and RLS extension.
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Affiliation(s)
- Enrique J. Garcia
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Janeska J. de Jonge
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Elizabeth Stivison
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Cierra N. Sing
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Istvan R. Boldogh
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Liza A. Pon
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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17
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Kothiwal D, Laloraya S. A SIR-independent role for cohesin in subtelomeric silencing and organization. Proc Natl Acad Sci U S A 2019; 116:5659-5664. [PMID: 30842278 PMCID: PMC6431164 DOI: 10.1073/pnas.1816582116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Cohesin is a key determinant of chromosome architecture due to its DNA binding and tethering ability. Cohesin binds near centromeres and chromosome arms and also close to telomeres, but its role near telomeres remains elusive. In budding yeast, transcription within 20 kb of telomeres is repressed, in part by the histone-modifying silent information regulator (SIR) complex. However, extensive subtelomeric repressed domains lie outside the SIR-binding region, but the mechanism of silencing in these regions remains poorly understood. Here, we report a role for cohesin in subtelomeric silencing that extends even beyond the zone of SIR binding. Clusters of subtelomeric genes were preferentially derepressed in a cohesin mutant, whereas SIR binding was unaltered. Genetic interactions with known telomere silencing factors indicate that cohesin operates independent of the SIR-mediated pathway for telomeric silencing. Mutant cells exhibited Mpk1-dependent Sir3 hyperphosphorylation that contributes to subtelomeric derepression to a limited extent. Compaction of subtelomeric domains and tethering to the nuclear envelope were impaired in mutant cells. Our findings provide evidence for a unique SIR-independent mechanism of subtelomeric repression mediated by cohesin.
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Affiliation(s)
- Deepash Kothiwal
- Department of Biochemistry, Indian Institute of Science, 560012 Bangalore, India
| | - Shikha Laloraya
- Department of Biochemistry, Indian Institute of Science, 560012 Bangalore, India
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18
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Laberthonnière C, Magdinier F, Robin JD. Bring It to an End: Does Telomeres Size Matter? Cells 2019; 8:E30. [PMID: 30626097 PMCID: PMC6356554 DOI: 10.3390/cells8010030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/01/2019] [Accepted: 01/04/2019] [Indexed: 12/22/2022] Open
Abstract
Telomeres are unique nucleoprotein structures. Found at the edge of each chromosome, their main purpose is to mask DNA ends from the DNA-repair machinery by formation of protective loops. Through life and cell divisions, telomeres shorten and bring cells closer to either cell proliferation crisis or senescence. Beyond this mitotic clock role attributed to the need for telomere to be maintained over a critical length, the very tip of our DNA has been shown to impact transcription by position effect. TPE and a long-reach counterpart, TPE-OLD, are mechanisms recently described in human biology. Still in infancy, the mechanism of action of these processes and their respective genome wide impact remain to be resolved. In this review, we will discuss recent findings on telomere dynamics, TPE, TPE-OLD, and lessons learnt from model organisms.
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Affiliation(s)
| | - Frédérique Magdinier
- Aix Marseille Univ, MMG, Marseille Medical Genetics U1251, 13385 Marseille, France.
| | - Jérôme D Robin
- Aix Marseille Univ, MMG, Marseille Medical Genetics U1251, 13385 Marseille, France.
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19
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Luo J, Sun X, Cormack BP, Boeke JD. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature 2018; 560:392-396. [PMID: 30069047 DOI: 10.1038/s41586-018-0374-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 06/25/2018] [Indexed: 11/09/2022]
Abstract
Extant species have wildly different numbers of chromosomes, even among taxa with relatively similar genome sizes (for example, insects)1,2. This is likely to reflect accidents of genome history, such as telomere-telomere fusions and genome duplication events3-5. Humans have 23 pairs of chromosomes, whereas other apes have 24. One human chromosome is a fusion product of the ancestral state6. This raises the question: how well can species tolerate a change in chromosome numbers without substantial changes to genome content? Many tools are used in chromosome engineering in Saccharomyces cerevisiae7-10, but CRISPR-Cas9-mediated genome editing facilitates the most aggressive engineering strategies. Here we successfully fused yeast chromosomes using CRISPR-Cas9, generating a near-isogenic series of strains with progressively fewer chromosomes ranging from sixteen to two. A strain carrying only two chromosomes of about six megabases each exhibited modest transcriptomic changes and grew without major defects. When we crossed a sixteen-chromosome strain with strains with fewer chromosomes, we noted two trends. As the number of chromosomes dropped below sixteen, spore viability decreased markedly, reaching less than 10% for twelve chromosomes. As the number of chromosomes decreased further, yeast sporulation was arrested: a cross between a sixteen-chromosome strain and an eight-chromosome strain showed greatly reduced full tetrad formation and less than 1% sporulation, from which no viable spores could be recovered. However, homotypic crosses between pairs of strains with eight, four or two chromosomes produced excellent sporulation and spore viability. These results indicate that eight chromosome-chromosome fusion events suffice to isolate strains reproductively. Overall, budding yeast tolerates a reduction in chromosome number unexpectedly well, providing a striking example of the robustness of genomes to change.
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Affiliation(s)
- Jingchuan Luo
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.,Department of Molecular Biology & Genetics, JHU School of Medicine, Baltimore, MD, USA
| | - Xiaoji Sun
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Brendan P Cormack
- Department of Molecular Biology & Genetics, JHU School of Medicine, Baltimore, MD, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
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20
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Vps74 Connects the Golgi Apparatus and Telomeres in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:1807-1816. [PMID: 29593073 PMCID: PMC5940170 DOI: 10.1534/g3.118.200172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In mammalian cell culture, the Golgi apparatus fragment upon DNA damage. GOLPH3, a Golgi component, is a phosphorylation target of DNA-PK after DNA damage and contributes to Golgi fragmentation. The function of the yeast (Saccharomyces cerevisiae) ortholog of GOLPH3, Vps74, in the DNA damage response has been little studied, although genome-wide screens suggested a role at telomeres. In this study we investigated the role of Vps74 at telomeres and in the DNA damage response. We show that Vps74 decreases the fitness of telomere defective cdc13-1 cells and contributes to the fitness of yku70Δ cells. Importantly, loss of Vps74 in yku70Δ cells exacerbates the temperature dependent growth defects of these cells in a Chk1 and Mec1-dependent manner. Furthermore, Exo1 reduces the fitness of vps74Δ yku70Δ cells suggesting that ssDNA contributes to the fitness defects of vps74Δ yku70Δ cells. Systematic genetic interaction analysis of vps74Δ, yku70Δ and yku70Δ vps74Δ cells suggests that vps74Δ causes a milder but similar defect to that seen in yku70Δ cells. vps74Δ cells have slightly shorter telomeres and loss of VPS74 in yku70Δ or mre11Δ cells further shortens the telomeres of these cells. Interestingly, loss of Vps74 leads to increased levels of Stn1, a partner of Cdc13 in the CST telomere capping complex. Overexpression of Stn1 was previously shown to cause telomere shortening, suppression of cdc13-1 and enhancement of yku70Δ growth defects, suggesting that increased levels of Stn1 may be the route by which Vps74 affects telomere function. These results establish Vps74 as a novel regulator of telomere biology.
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21
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The PHR Family: The Role of Extracellular Transglycosylases in Shaping Candida albicans Cells. J Fungi (Basel) 2017; 3:jof3040059. [PMID: 29371575 PMCID: PMC5753161 DOI: 10.3390/jof3040059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 01/25/2023] Open
Abstract
Candida albicans is an opportunistic microorganism that can become a pathogen causing mild superficial mycosis or more severe invasive infections that can be life-threatening for debilitated patients. In the etiology of invasive infections, key factors are the adaptability of C. albicans to the different niches of the human body and the transition from a yeast form to hypha. Hyphal morphology confers high adhesiveness to the host cells, as well as the ability to penetrate into organs. The cell wall plays a crucial role in the morphological changes C. albicans undergoes in response to specific environmental cues. Among the different categories of enzymes involved in the formation of the fungal cell wall, the GH72 family of transglycosylases plays an important assembly role. These enzymes cut and religate β-(1,3)-glucan, the major determinant of cell shape. In C. albicans, the PHR family encodes GH72 enzymes, some of which work in specific environmental conditions. In this review, we will summarize the work from the initial discovery of PHR genes to the study of the pH-dependent expression of PHR1 and PHR2, from the characterization of the gene products to the recent findings concerning the stress response generated by the lack of GH72 activity in C. albicans hyphae.
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22
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The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae. Genetics 2017; 203:1563-99. [PMID: 27516616 DOI: 10.1534/genetics.112.145243] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/30/2016] [Indexed: 12/31/2022] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae occurs at several genomic sites including the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA) tandem array. Epigenetic silencing at each of these domains is characterized by the absence of nearly all histone modifications, including most prominently the lack of histone H4 lysine 16 acetylation. In all cases, silencing requires Sir2, a highly-conserved NAD(+)-dependent histone deacetylase. At locations other than the rDNA, silencing also requires additional Sir proteins, Sir1, Sir3, and Sir4 that together form a repressive heterochromatin-like structure termed silent chromatin. The mechanisms of silent chromatin establishment, maintenance, and inheritance have been investigated extensively over the last 25 years, and these studies have revealed numerous paradigms for transcriptional repression, chromatin organization, and epigenetic gene regulation. Studies of Sir2-dependent silencing at the rDNA have also contributed to understanding the mechanisms for maintaining the stability of repetitive DNA and regulating replicative cell aging. The goal of this comprehensive review is to distill a wide array of biochemical, molecular genetic, cell biological, and genomics studies down to the "nuts and bolts" of silent chromatin and the processes that yield transcriptional silencing.
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Nutritional Control of Chronological Aging and Heterochromatin in Saccharomyces cerevisiae. Genetics 2017; 205:1179-1193. [PMID: 28064165 DOI: 10.1534/genetics.116.196485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/22/2016] [Indexed: 12/22/2022] Open
Abstract
Calorie restriction extends life span in organisms as diverse as yeast and mammals through incompletely understood mechanisms.The role of NAD+-dependent deacetylases known as Sirtuins in this process, particularly in the yeast Saccharomyces cerevisiae, is controversial. We measured chronological life span of wild-type and sir2Δ strains over a higher glucose range than typically used for studying yeast calorie restriction. sir2Δ extended life span in high glucose complete minimal medium and had little effect in low glucose medium, revealing a partial role for Sir2 in the calorie-restriction response under these conditions. Experiments performed on cells grown in rich medium with a newly developed genetic strategy revealed that sir2Δ shortened life span in low glucose while having little effect in high glucose, again revealing a partial role for Sir2 In complete minimal media, Sir2 shortened life span as glucose levels increased; whereas in rich media, Sir2 extended life span as glucose levels decreased. Using a genetic strategy to measure the strength of gene silencing at HML, we determined increasing glucose stabilized Sir2-based silencing during growth on complete minimal media. Conversely, increasing glucose destabilized Sir-based silencing during growth on rich media, specifically during late cell divisions. In rich medium, silencing was far less stable in high glucose than in low glucose during stationary phase. Therefore, Sir2 was involved in a response to nutrient cues including glucose that regulates chronological aging, possibly through Sir2-dependent modification of chromatin or deacetylation of a nonhistone protein.
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24
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Peguero-Sanchez E, Pardo-Lopez L, Merino E. IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association. BMC Genomics 2015; 16:1059. [PMID: 26666532 PMCID: PMC4678720 DOI: 10.1186/s12864-015-2266-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023] Open
Abstract
Background The initiation of translation via cellular internal ribosome entry sites plays an important role in the stress response and certain physiological conditions in which canonical cap-dependent translation initiation is compromised. Currently, only a limited number of these regulatory elements have been experimentally identified. Notably, cellular internal ribosome entry sites lack conservation of both the primary sequence and mRNA secondary structure, rendering their identification difficult. Despite their biological importance, the currently available computational strategies to predict them have had limited success. We developed a bioinformatic method based on a support vector machine for the prediction of internal ribosome entry sites in fungi using the 5’-UTR sequences of 20 non-redundant fungal organisms. Additionally, we performed a comparative analysis and characterization of the functional relationships among the gene products predicted to be translated by this cap-independent mechanism. Results Using our method, we predicted 6,532 internal ribosome entry sites in 20 non-redundant fungal organisms. Some orthologous groups were enriched with our positive predictions. This is the case of the HSP70 chaperone family, which remarkably has two verified internal ribosome entry sites, one in humans and the other in flies. A second example is the orthologous group of the eIF4G repression protein Sbp1p, which has two homologous genes known to be translated by this cap-independent mechanism, one in mice and the other in yeast. These examples emphasize the wide conservation of these regulatory elements as a result of selective pressure. In addition, we performed a protein-protein interaction network characterization of the gene products of our positive predictions using Saccharomyces cerevisiae as a model, which revealed a highly connected and modular topology, suggesting a functional association. A remarkable example of this functional association is our prediction of internal ribosome entry sites elements in three components of the RNA polymerase II mediator complex. Conclusions We developed a method for the prediction of cellular internal ribosome entry sites that may guide experimental and bioinformatic analyses to increase our understanding of protein translation regulation. Our analysis suggests that fungi show evolutionary conservation and functional association of proteins translated by this cap-independent mechanism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2266-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Esteban Peguero-Sanchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP 62210, Mexico.
| | - Liliana Pardo-Lopez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP 62210, Mexico.
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Cuernavaca, Morelos, CP 62210, Mexico.
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25
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Fulnečková J, Ševčíková T, Lukešová A, Sýkorová E. Transitions between the Arabidopsis-type and the human-type telomere sequence in green algae (clade Caudivolvoxa, Chlamydomonadales). Chromosoma 2015; 125:437-51. [PMID: 26596989 DOI: 10.1007/s00412-015-0557-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022]
Abstract
Telomeres are nucleoprotein structures that distinguish native chromosomal ends from double-stranded breaks. They are maintained by telomerase that adds short G-rich telomeric repeats at chromosomal ends in most eukaryotes and determines the TnAmGo sequence of canonical telomeres. We employed an experimental approach that was based on detection of repeats added by telomerase to identify the telomere sequence type forming the very ends of chromosomes. Our previous studies that focused on the algal order Chlamydomonadales revealed several changes in telomere motifs that were consistent with the phylogeny and supported the concept of the Arabidopsis-type sequence being the ancestral telomeric motif for green algae. In addition to previously described independent transitions to the Chlamydomonas-type sequence, we report that the ancestral telomeric motif was replaced by the human-type sequence in the majority of algal species grouped within a higher order clade, Caudivolvoxa. The Arabidopsis-type sequence was apparently retained in the Polytominia clade. Regarding the telomere sequence, the Chlorogonia clade within Caudivolvoxa bifurcates into two groups, one with the human-type sequence and the other group with the Arabidopsis-type sequence that is solely formed by the Chlorogonium species. This suggests that reversion to the Arabidopsis-type telomeric motif occurred in the common ancestral Chlorogonium species. The human-type sequence is also synthesized by telomerases of algal strains from Arenicolinia, Dunaliellinia and Stephanosphaerinia, except a distinct subclade within Stephanosphaerinia, where telomerase activity was not detected and a change to an unidentified telomeric motif might arise. We discuss plausible reasons why changes in telomeric motifs were tolerated during evolution of green algae.
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Affiliation(s)
- Jana Fulnečková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic.,Faculty of Science, and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Life Science Research Centre & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, CZ-71000, Ostrava, Czech Republic
| | - Alena Lukešová
- Institute of Soil Biology, Biology Centre Academy of Sciences of the Czech Republic, v.vi., Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-61265, Brno, Czech Republic. .,Faculty of Science, and CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
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Larin ML, Harding K, Williams EC, Lianga N, Doré C, Pilon S, Langis É, Yanofsky C, Rudner AD. Competition between Heterochromatic Loci Allows the Abundance of the Silencing Protein, Sir4, to Regulate de novo Assembly of Heterochromatin. PLoS Genet 2015; 11:e1005425. [PMID: 26587833 PMCID: PMC4654584 DOI: 10.1371/journal.pgen.1005425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 07/06/2015] [Indexed: 12/24/2022] Open
Abstract
Changes in the locations and boundaries of heterochromatin are critical during development, and de novo assembly of silent chromatin in budding yeast is a well-studied model for how new sites of heterochromatin assemble. De novo assembly cannot occur in the G1 phase of the cell cycle and one to two divisions are needed for complete silent chromatin assembly and transcriptional repression. Mutation of DOT1, the histone H3 lysine 79 (K79) methyltransferase, and SET1, the histone H3 lysine 4 (K4) methyltransferase, speed de novo assembly. These observations have led to the model that regulated demethylation of histones may be a mechanism for how cells control the establishment of heterochromatin. We find that the abundance of Sir4, a protein required for the assembly of silent chromatin, decreases dramatically during a G1 arrest and therefore tested if changing the levels of Sir4 would also alter the speed of de novo establishment. Halving the level of Sir4 slows heterochromatin establishment, while increasing Sir4 speeds establishment. yku70Δ and ubp10Δ cells also speed de novo assembly, and like dot1Δ cells have defects in subtelomeric silencing, suggesting that these mutants may indirectly speed de novo establishment by liberating Sir4 from telomeres. Deleting RIF1 and RIF2, which suppresses the subtelomeric silencing defects in these mutants, rescues the advanced de novo establishment in yku70Δ and ubp10Δ cells, but not in dot1Δ cells, suggesting that YKU70 and UBP10 regulate Sir4 availability by modulating subtelomeric silencing, while DOT1 functions directly to regulate establishment. Our data support a model whereby the demethylation of histone H3 K79 and changes in Sir4 abundance and availability define two rate-limiting steps that regulate de novo assembly of heterochromatin.
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Affiliation(s)
- Michelle L. Larin
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Katherine Harding
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Elizabeth C. Williams
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Noel Lianga
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Carole Doré
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sophie Pilon
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Éric Langis
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Corey Yanofsky
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adam D. Rudner
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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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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The response to inositol: regulation of glycerolipid metabolism and stress response signaling in yeast. Chem Phys Lipids 2014; 180:23-43. [PMID: 24418527 DOI: 10.1016/j.chemphyslip.2013.12.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 12/26/2013] [Indexed: 12/13/2022]
Abstract
This article focuses on discoveries of the mechanisms governing the regulation of glycerolipid metabolism and stress response signaling in response to the phospholipid precursor, inositol. The regulation of glycerolipid lipid metabolism in yeast in response to inositol is highly complex, but increasingly well understood, and the roles of individual lipids in stress response are also increasingly well characterized. Discoveries that have emerged over several decades of genetic, molecular and biochemical analyses of metabolic, regulatory and signaling responses of yeast cells, both mutant and wild type, to the availability of the phospholipid precursor, inositol are discussed.
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Oppikofer M, Kueng S, Gasser SM. SIR–nucleosome interactions: Structure–function relationships in yeast silent chromatin. Gene 2013; 527:10-25. [DOI: 10.1016/j.gene.2013.05.088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 01/09/2023]
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Lee S, Gaspar ML, Aregullin MA, Jesch SA, Henry SA. Activation of protein kinase C-mitogen-activated protein kinase signaling in response to inositol starvation triggers Sir2p-dependent telomeric silencing in yeast. J Biol Chem 2013; 288:27861-71. [PMID: 23943620 DOI: 10.1074/jbc.m113.493072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Depriving wild type yeast of inositol, a soluble precursor for phospholipid, phosphoinositide, and complex sphingolipid synthesis, activates the protein kinase C (PKC)-MAPK signaling pathway, which plays a key role in the activation of NAD(+)-dependent telomeric silencing. We now report that triggering PKC-MAPK signaling by inositol deprivation or by blocking inositol-containing sphingolipid synthesis with aureobasidin A results in increased telomeric silencing regulated by the MAPK, Slt2p, and the NAD(+)-dependent deacetylase, Sir2p. Consistent with the dependence on NAD(+) in Sir2p-regulated silencing, we found that inositol depletion induces the expression of BNA2, which is required for the de novo synthesis of NAD(+). Moreover, telomeric silencing is greatly reduced in bna2Δ and npt1Δ mutants, which are defective in de novo and salvage pathways for NAD(+) synthesis, respectively. Surprisingly, however, omitting nicotinic acid from the growth medium, which reduces cellular NAD(+) levels, leads to increased telomeric silencing in the absence of inositol and/or at high temperature. This increase in telomeric silencing in response to inositol starvation is correlated to chronological life span extension but is Sir2p-independent. We conclude that activation of the PKC-MAPK signaling by interruption of inositol sphingolipid synthesis leads to increased Sir2p-dependent silencing and is dependent upon the de novo and salvage pathways for NAD(+) synthesis but is not correlated with cellular NAD(+) levels.
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Affiliation(s)
- Sojin Lee
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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Grunstein M, Gasser SM. Epigenetics in Saccharomyces cerevisiae. Cold Spring Harb Perspect Biol 2013; 5:cshperspect.a017491. [PMID: 23818500 DOI: 10.1101/cshperspect.a017491] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Saccharomyces cerevisiae provides a well-studied model system for heritable silent chromatin, in which a nonhistone protein complex--the SIR complex--represses genes by spreading in a sequence-independent manner, much like heterochromatin in higher eukaryotes. The ability to study mutations in histones and to screen genome-wide for mutations that impair silencing has yielded an unparalleled depth of detail about this system. Recent advances in the biochemistry and structural biology of the SIR-chromatin complex bring us much closer to a molecular understanding of how Sir3 selectively recognizes the deacetylated histone H4 tail and demethylated histone H3 core. The existence of appropriate mutants has also shown how components of the silencing machinery affect physiological processes beyond transcriptional repression.
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Affiliation(s)
- Michael Grunstein
- University of California, Los Angeles, Los Angeles, California 90095, USA
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Abstract
Budding yeast, like other eukaryotes, carries its genetic information on chromosomes that are sequestered from other cellular constituents by a double membrane, which forms the nucleus. An elaborate molecular machinery forms large pores that span the double membrane and regulate the traffic of macromolecules into and out of the nucleus. In multicellular eukaryotes, an intermediate filament meshwork formed of lamin proteins bridges from pore to pore and helps the nucleus reform after mitosis. Yeast, however, lacks lamins, and the nuclear envelope is not disrupted during yeast mitosis. The mitotic spindle nucleates from the nucleoplasmic face of the spindle pole body, which is embedded in the nuclear envelope. Surprisingly, the kinetochores remain attached to short microtubules throughout interphase, influencing the position of centromeres in the interphase nucleus, and telomeres are found clustered in foci at the nuclear periphery. In addition to this chromosomal organization, the yeast nucleus is functionally compartmentalized to allow efficient gene expression, repression, RNA processing, genomic replication, and repair. The formation of functional subcompartments is achieved in the nucleus without intranuclear membranes and depends instead on sequence elements, protein-protein interactions, specific anchorage sites at the nuclear envelope or at pores, and long-range contacts between specific chromosomal loci, such as telomeres. Here we review the spatial organization of the budding yeast nucleus, the proteins involved in forming nuclear subcompartments, and evidence suggesting that the spatial organization of the nucleus is important for nuclear function.
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Abstract
The mechanisms that maintain the stability of chromosome ends have broad impact on genome integrity in all eukaryotes. Budding yeast is a premier organism for telomere studies. Many fundamental concepts of telomere and telomerase function were first established in yeast and then extended to other organisms. We present a comprehensive review of yeast telomere biology that covers capping, replication, recombination, and transcription. We think of it as yeast telomeres—soup to nuts.
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Kueng S, Tsai-Pflugfelder M, Oppikofer M, Ferreira HC, Roberts E, Tsai C, Roloff TC, Sack R, Gasser SM. Regulating repression: roles for the sir4 N-terminus in linker DNA protection and stabilization of epigenetic states. PLoS Genet 2012; 8:e1002727. [PMID: 22654676 PMCID: PMC3359979 DOI: 10.1371/journal.pgen.1002727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 04/11/2012] [Indexed: 01/19/2023] Open
Abstract
Silent information regulator proteins Sir2, Sir3, and Sir4 form a heterotrimeric complex that represses transcription at subtelomeric regions and homothallic mating type (HM) loci in budding yeast. We have performed a detailed biochemical and genetic analysis of the largest Sir protein, Sir4. The N-terminal half of Sir4 is dispensable for SIR–mediated repression of HM loci in vivo, except in strains that lack Yku70 or have weak silencer elements. For HM silencing in these cells, the C-terminal domain (Sir4C, residues 747–1,358) must be complemented with an N-terminal domain (Sir4N; residues 1–270), expressed either independently or as a fusion with Sir4C. Nonetheless, recombinant Sir4C can form a complex with Sir2 and Sir3 in vitro, is catalytically active, and has sedimentation properties similar to a full-length Sir4-containing SIR complex. Sir4C-containing SIR complexes bind nucleosomal arrays and protect linker DNA from nucleolytic digestion, but less effectively than wild-type SIR complexes. Consistently, full-length Sir4 is required for the complete repression of subtelomeric genes. Supporting the notion that the Sir4 N-terminus is a regulatory domain, we find it extensively phosphorylated on cyclin-dependent kinase consensus sites, some being hyperphosphorylated during mitosis. Mutation of two major phosphoacceptor sites (S63 and S84) derepresses natural subtelomeric genes when combined with a serendipitous mutation (P2A), which alone can enhance the stability of either the repressed or active state. The triple mutation confers resistance to rapamycin-induced stress and a loss of subtelomeric repression. We conclude that the Sir4 N-terminus plays two roles in SIR–mediated silencing: it contributes to epigenetic repression by stabilizing the SIR–mediated protection of linker DNA; and, as a target of phosphorylation, it can destabilize silencing in a regulated manner. Three Silent Information Regulator (SIR) proteins Sir2, Sir3, and Sir4 are involved in the epigenetic gene silencing of the homothallic mating (HM) loci and of telomere-proximal genes in budding yeast. They bind as a heterotrimeric complex to chromatin, repressing the underlying genes. Sir2 has an essential histone deacetylase activity, and Sir3 binds nucleosomes, with a high specificity for unmodified histones. We explored Sir4, whose role had largely remained a mystery. We report here that Sir4 N- and C-terminal domains have distinct functions: The Sir4 C-terminus binds all proteins essential for SIR–mediated silencing and is sufficient to repress HM loci, but surprisingly it is not sufficient to efficiently repress at telomeres. The Sir4 N-terminus binds DNA, which strengthens the SIR–chromatin interaction and helps target Sir4 to telomeric loci. In addition the Sir4 N-terminus binds sequence-specific factors that recruit Sir4 to sites of repression. We find that the Sir4 N-terminus is a target of mitotic phosphorylation. Mutation of the phosphoacceptor sites indicates that they help fine-tune subtelomeric repression. We propose therefore that phosphorylation of the Sir4 N-terminal domain modulates epigenetic repression at telomeres in response to cell cycle and/or stress situations.
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Affiliation(s)
- Stephanie Kueng
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Mariano Oppikofer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Helder C. Ferreira
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Emma Roberts
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Chinyen Tsai
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, Basel, Switzerland
- * E-mail:
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A framework for mapping, visualisation and automatic model creation of signal-transduction networks. Mol Syst Biol 2012; 8:578. [PMID: 22531118 PMCID: PMC3361003 DOI: 10.1038/msb.2012.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An intuitive formalism for reconstructing cellular networks from empirical data is presented, and used to build a comprehensive yeast MAP kinase network. The accompanying rxncon software tool can convert networks to a range of standard graphical formats and mathematical models. ![]()
Network mapping at the granularity of empirical data that largely avoids combinatorial complexity Automatic visualisation and model generation with the rxncon open source software tool Visualisation in a range of formats, including all three SBGN formats, as well as contingency matrix or regulatory graph Comprehensive and completely references map of the yeast MAP kinase network in the rxncon format
Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.
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Loewith R, Hall MN. Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics 2011; 189:1177-201. [PMID: 22174183 PMCID: PMC3241408 DOI: 10.1534/genetics.111.133363] [Citation(s) in RCA: 623] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/12/2011] [Indexed: 12/16/2022] Open
Abstract
TOR (Target Of Rapamycin) is a highly conserved protein kinase that is important in both fundamental and clinical biology. In fundamental biology, TOR is a nutrient-sensitive, central controller of cell growth and aging. In clinical biology, TOR is implicated in many diseases and is the target of the drug rapamycin used in three different therapeutic areas. The yeast Saccharomyces cerevisiae has played a prominent role in both the discovery of TOR and the elucidation of its function. Here we review the TOR signaling network in S. cerevisiae.
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Affiliation(s)
- Robbie Loewith
- Department of Molecular Biology and National Centers of Competence in Research and Frontiers in Genetics and Chemical Biology, University of Geneva, Geneva, CH-1211, Switzerland
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Ruault M, De Meyer A, Loïodice I, Taddei A. Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast. ACTA ACUST UNITED AC 2011; 192:417-31. [PMID: 21300849 PMCID: PMC3101097 DOI: 10.1083/jcb.201008007] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A general feature of the nucleus is the organization of repetitive deoxyribonucleic acid sequences in clusters concentrating silencing factors. In budding yeast, we investigated how telomeres cluster in perinuclear foci associated with the silencing complex Sir2-Sir3-Sir4 and found that Sir3 is limiting for telomere clustering. Sir3 overexpression triggers the grouping of telomeric foci into larger foci that relocalize to the nuclear interior and correlate with more stable silencing in subtelomeric regions. Furthermore, we show that Sir3's ability to mediate telomere clustering can be separated from its role in silencing. Indeed, nonacetylable Sir3, which is unable to spread into subtelomeric regions, can mediate telomere clustering independently of Sir2-Sir4 as long as it is targeted to telomeres by the Rap1 protein. Thus, arrays of Sir3 binding sites at telomeres appeared as the sole requirement to promote trans-interactions between telomeres. We propose that similar mechanisms involving proteins able to oligomerize account for long-range interactions that impact genomic functions in many organisms.
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Affiliation(s)
- Myriam Ruault
- Unité Mixte de Recherche 218, Centre National de la Recherche Scientifique, F-75248 Paris, Cedex 05, France
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Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol 2011; 7:455. [PMID: 21206489 PMCID: PMC3049408 DOI: 10.1038/msb.2010.110] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 11/24/2010] [Indexed: 01/11/2023] Open
Abstract
Chromosome position analysis of ChIP-chip data revealed that several carbon source and stress-responsive yeast transcription factors conditionally bind subtelomeric X elements. Integration of several microarray gene expression data sets showed that, in this context, the factors conditionally control the boundaries and strength of subtelomeric silencing. Regulation of silencing by a fatty acid-responsive factor was found to be dependent on Sir2p and independent of Hda1p. These findings provide a critical link for establishing the mechanisms by which telomere biology is coordinated with other cellular processes including responses to environmental stimuli, aging and adaptation.
It is well established that environmental conditions modulate gene expression through local binding of a variety of conditionally active transcription factors, each responsive to specific environmental cues. However, another prevalent mechanism of gene regulation in eukaryotic cells is the long-range control of groups of genes by chromatin modifications or other position-dependent mechanisms. One such phenomenon, gene silencing, is an important and evolutionarily conserved mode of regulation that controls expression of subtelomeric genes. These genes are enriched for stress response and metabolic genes and their regulation is controlled by the spreading of silencing molecules from chromosome ends (telomeres) into subtelomeric regions. Levels of subtelomeric silencing have been linked to cellular lifespan, and study of the regulation of silencing is fundamental to our understanding of human aging. The spread of silencing in subtelomeric regions is discontinuous, and is controlled by various genomic elements that can either relay and enhance silencing from telomeres (proto-silencing) or create boundaries that protect some genomic regions from silencing. In yeast, every subtelomeric region contains an X element that proto-silences centromere-proximal genes, and also insulates telomere-proximal genes from silencing. In this paper, we identify a regulatory mechanism to control X element-mediated proto-silencing and insulating activities in response to environmental cues. The mechanism was identified using chromosome position analysis of microarray-based chromatin immunoprecipitation (ChIP-chip) data for environment-responsive TFs and genome-wide gene expression data under the same conditions. The mechanism involves the conditional association of environment-responsive transcription factors to X elements. The binding at X elements results in regulation of proto-silencing of centromere-proximal genes, or insulation of telomere-proximal genes (depending on the factor) in response to environmental stimuli related to stress response and metabolism. One example is shown below (Figure 4B). Transcription factor, Oaf1p, conditionally binds X elements in the presence of fatty acids and enhances proto-silencing specifically under this condition. Oaf1p and several other factors implicated here are known to control adjacent genes at intrachromosomal positions, suggesting their dual functionality in both gene-specific transcriptional regulation, and long-range position-dependent mechanism. Investigation of this mechanism during the response to fatty acid exposure showed that conditional proto-silencing activity is dependent on Sir2p, a molecule known to be involved in subtelomeric silencing related to aging. This study reveals a path cells can use to coordinate subtelomeric silencing related to aging with cellular environment, and with the activities of other cellular processes. Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of stress response pathways and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing or to protect chromosomal regions from spreading epigenetic control. In this study, analysis of genome-wide chromatin immunoprecipitation and expression data, suggests that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements. In this context, Oaf1p, Rox1p, Gzf1p and Phd1p control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others, including Adr1p, Yap5p and Msn4p, appear to influence boundaries of silencing, regulating telomere-proximal genes in Y′ elements. The factors implicated here are known to control adjacent genes at intrachromosomal positions, suggesting their dual functionality. This study reveals a path for the coordination of subtelomeric silencing with cellular environment, and with activities of other cellular processes.
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The Hog1 mitogen-activated protein kinase mediates a hypoxic response in Saccharomyces cerevisiae. Genetics 2011; 188:325-38. [PMID: 21467572 DOI: 10.1534/genetics.111.128322] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have studied hypoxic induction of transcription by studying the seripauperin (PAU) genes of Saccharomyces cerevisiae. Previous studies showed that PAU induction requires the depletion of heme and is dependent upon the transcription factor Upc2. We have now identified additional factors required for PAU induction during hypoxia, including Hog1, a mitogen-activated protein kinase (MAPK) whose signaling pathway originates at the membrane. Our results have led to a model in which heme and ergosterol depletion alters membrane fluidity, thereby activating Hog1 for hypoxic induction. Hypoxic activation of Hog1 is distinct from its previously characterized response to osmotic stress, as the two conditions cause different transcriptional consequences. Furthermore, Hog1-dependent hypoxic activation is independent of the S. cerevisiae general stress response. In addition to Hog1, specific components of the SAGA coactivator complex, including Spt20 and Sgf73, are also required for PAU induction. Interestingly, the mammalian ortholog of Spt20, p38IP, has been previously shown to interact with the mammalian ortholog of Hog1, p38. Taken together, our results have uncovered a previously unknown hypoxic-response pathway that may be conserved throughout eukaryotes.
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Radman-Livaja M, Ruben G, Weiner A, Friedman N, Kamakaka R, Rando OJ. Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization. EMBO J 2011; 30:1012-26. [PMID: 21336256 DOI: 10.1038/emboj.2011.30] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 01/20/2011] [Indexed: 11/10/2022] Open
Abstract
Chromatin domains are believed to spread via a polymerization-like mechanism in which modification of a given nucleosome recruits a modifying complex, which can then modify the next nucleosome in the polymer. In this study, we carry out genome-wide mapping of the Sir3 component of the Sir silencing complex in budding yeast during a time course of establishment of heterochromatin. Sir3 localization patterns do not support a straightforward model for nucleation and polymerization, instead showing strong but spatially delimited binding to silencers, and weaker and more variable Ume6-dependent binding to novel secondary recruitment sites at the seripauperin (PAU) genes. Genome-wide nucleosome mapping revealed that Sir binding to subtelomeric regions was associated with overpackaging of subtelomeric promoters. Sir3 also bound to a surprising number of euchromatic sites, largely at genes expressed at high levels, and was dynamically recruited to GAL genes upon galactose induction. Together, our results indicate that heterochromatin complex localization cannot simply be explained by nucleation and linear polymerization, and show that heterochromatin complexes associate with highly expressed euchromatic genes in many different organisms.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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42
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Genetic approaches to aging in budding and fission yeasts: new connections and new opportunities. Subcell Biochem 2011; 57:291-314. [PMID: 22094427 DOI: 10.1007/978-94-007-2561-4_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Yeasts are powerful model systems to examine the evolutionarily conserved aspects of eukaryotic aging because they maintain many of the same core cellular signaling pathways and essential organelles as human cells. We constructed a strain of the budding yeast Saccharomyces cerevisiae that could monitor the distribution of proteins involved in heterochromatic silencing and aging, and isolated mutants that alter this distribution. The largest class of such mutants cause defects in mitochondrial function, and appear to cause changes in nuclear silencing separate from the well-known Rtg2p-dependent pathway that alters nuclear transcription in response to the loss of the mitochondrial genome. Mutants that inactivate the ATP2 gene, which encodes the ATPase subunit of the mitochondrial F(1)F(0)-ATPase, were isolated twice in our screen and identify a lifespan extending pathway in a gene that is conserved in both prokaryotes and eukaryotes. The budding yeast S. cerevisiae S. cerevisiae has been used with great success to identify other lifespan-extending pathways in screens using surrogate phenotypes such as stress resistance or silencing to identify random mutants, or in high throughput screens that utilize the deletion strain set resource. However, the direct selection of long-lived mutants from a pool of random mutants is more challenging. We have established a new chronological aging assay for the evolutionarily distant fission yeast Schizosaccharomyces pombe that recapitulates aspects of aging conserved in all eukaryotes. We have constructed a novel S. pombe S. pombe DNA insertion mutant bank, and used it to show that we can directly select for a long-lived mutant. The use of both the budding and fission yeast systems should continue to facilitate the identification and validation of lifespan extending pathways that are conserved in humans.
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43
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Abstract
The budding yeast nucleus, like those of other eukaryotic species, is highly organized with respect to both chromosomal sequences and enzymatic activities. At the nuclear periphery interactions of nuclear pores with chromatin, mRNA, and transport factors promote efficient gene expression, whereas centromeres, telomeres, and silent chromatin are clustered and anchored away from pores. Internal nuclear organization appears to be function-dependent, reflecting localized sites for tRNA transcription, rDNA transcription, ribosome assembly, and DNA repair. Recent advances have identified new proteins involved in the positioning of chromatin and have allowed testing of the functional role of higher-order chromatin organization. The unequal distribution of silent information regulatory factors and histone modifying enzymes, which arises in part from the juxtaposition of telomeric repeats, has been shown to influence chromatin-mediated transcriptional repression. Other localization events suppress unwanted recombination. These findings highlight the contribution budding yeast genetics and cytology have made to dissecting the functional role of nuclear structure.
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Affiliation(s)
- Angela Taddei
- UMR 218, Centre National de la Recherche Scientifique, 26 rue d'Ulm, 75231 Paris Cedex 05, France
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Traven A, Lo TL, Pike BL, Friesen H, Guzzo J, Andrews B, Heierhorst J. Dual functions of Mdt1 in genome maintenance and cell integrity pathways in Saccharomyces cerevisiae. Yeast 2010; 27:41-52. [PMID: 19894211 DOI: 10.1002/yea.1730] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Recent evidence indicates considerable cross-talk between genome maintenance and cell integrity control pathways. The RNA recognition motif (RRM)- and SQ/TQ cluster domain (SCD)-containing protein Mdt1 is required for repair of 3'-blocked DNA double-strand breaks (DSBs) and efficient recombinational maintenance of telomeres in budding yeast. Here we show that deletion of MDT1 (PIN4/YBL051C) leads to severe synthetic sickness in the absence of the genes for the central cell integrity MAP kinases Bck1 and Slt2/Mpk1. Consistent with a cell integrity function, mdt1Delta cells are hypersensitive to the cell wall toxin calcofluor white and the Bck1-Slt2 pathway activator caffeine. An RRM-deficient mdt1-RRM0 allele shares the severe bleomycin hypersensitivity, inefficient recombinational telomere maintenance and slt2 synthetic sickness phenotypes, but not the cell wall toxin hypersensitivity with mdt1Delta. However, the mdt1-RRM(3A) allele, where only the RNA-binding site is mutated, behaves similarly to the wild-type, suggesting that the Mdt1 RRM functions as a protein-protein interaction rather than a nucleic acid-binding module. Surprisingly, in a strain background where double mutants are sick but still viable, bck1Deltamdt1Delta and slt2Deltamdt1Delta mutants differ in some of their phenotypes, consistent with the emerging concept of flexible signal entry and exit points in the Bck1-Mkk1/2-Slt2 pathway. Overall, the results indicate that Mdt1 has partially separable functions in both cell wall and genome integrity pathways.
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Affiliation(s)
- Ana Traven
- St. Vincent's Institute of Medical Research and Department of Medicine SVH, University of Melbourne, Fitzroy, Victoria 3065, Australia
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45
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Radman-Livaja M, Liu CL, Friedman N, Schreiber SL, Rando OJ. Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast. PLoS Genet 2010; 6:e1000837. [PMID: 20140185 PMCID: PMC2816684 DOI: 10.1371/journal.pgen.1000837] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 01/04/2010] [Indexed: 12/04/2022] Open
Abstract
Histone modifications affect DNA–templated processes ranging from transcription to genomic replication. In this study, we examine the cell cycle dynamics of the trimethylated form of histone H3 lysine 4 (H3K4me3), a mark of active chromatin that is viewed as “long-lived” and that is involved in memory during cell state inheritance in metazoans. We synchronized yeast using two different protocols, then followed H3K4me3 patterns as yeast passed through subsequent cell cycles. While most H3K4me3 patterns were conserved from one generation to the next, we found that methylation patterns induced by alpha factor or high temperature were erased within one cell cycle, during S phase. Early-replicating regions were erased before late-replicating regions, implicating replication in H3K4me3 loss. However, nearly complete H3K4me3 erasure occurred at the majority of loci even when replication was prevented, suggesting that most erasure results from an active process. Indeed, deletion of the demethylase Jhd2 slowed erasure at most loci. Together, these results indicate overlapping roles for passive dilution and active enzymatic demethylation in erasing ancestral histone methylation states in yeast. Organisms can inherit information beyond DNA sequence, a phenomenon known as epigenetic inheritance. It is widely believed that chromatin marks provide a carrier for epigenetic information, a hypothesis that is less-supported than generally believed. In this study, we measure the erasure of a “memory” mark of active transcription, H3K4me3. We find that this signal-responsive chromatin mark largely returns to baseline levels within one generation. Furthermore, we find that this erasure occurs during S phase in a manner consistent with its loss during replication, yet we find that replication only contributes modestly to the erasure process. Instead, active enzymatic demethylation is required for erasure. Together, these results show that even chromatin states widely associated with epigenetic memory are only maintained in the ongoing presence of activating signals, and are not generally heritable.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Chih Long Liu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
- The Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Stuart L. Schreiber
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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Luo Z, van Vuuren HJJ. Functional analyses of PAU genes in Saccharomyces cerevisiae. Microbiology (Reading) 2009; 155:4036-4049. [DOI: 10.1099/mic.0.030726-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PAU genes constitute the largest gene family in Saccharomyces cerevisiae, with 24 members mostly located in the subtelomeric regions of chromosomes. Little information is available about PAU genes, other than expression data for some members. In this study, we systematically compared the sequences of all 24 members, examined the expression of PAU3, PAU5, DAN2, PAU17 and PAU20 in response to stresses, and investigated the stability of all Pau proteins. The chromosomal localization, synteny and sequence analyses revealed that PAU genes could have been amplified by segmental and retroposition duplication through mechanisms of chromosomal end translocation and Ty-associated recombination. The coding sequences diverged through nucleotide substitution and insertion/deletion of one to four codons, thus causing changes in amino acids, truncation or extension of Pau proteins. Pairwise comparison of non-coding regions revealed little homology in flanking sequences of some members. All 24 PAU promoters contain a TATA box, and 22 PAU promoters contain at least one copy of the anaerobic response element and the aerobic repression motif. Differential expression was observed among PAU3, PAU5, PAU17, PAU20 and DAN2 in response to stress, with PAU5 having the highest capacity to be induced by anaerobic conditions, low temperature and wine fermentations. Furthermore, Pau proteins with 124 aa were less stable than those with 120 or 122 aa. Our results indicate that duplicated PAU genes have been evolving, and the individual Pau proteins might possess specific roles for the adaptation of S. cerevisiae to certain environmental stresses.
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Affiliation(s)
- Zongli Luo
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Hennie J. J. van Vuuren
- Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Telomere shortening relaxes X chromosome inactivation and forces global transcriptome alterations. Proc Natl Acad Sci U S A 2009; 106:19393-8. [PMID: 19887628 DOI: 10.1073/pnas.0909265106] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Telomeres are heterochromatic structures at chromosome ends essential for chromosomal stability. Telomere shortening and the accumulation of dysfunctional telomeres are associated with organismal aging. Using telomerase-deficient TRF2-overexpressing mice (K5TRF2/Terc(-/-)) as a model for accelerated aging, we show that telomere shortening is paralleled by a gradual deregulation of the mammalian transcriptome leading to cumulative changes in a defined set of genes, including up-regulation of the mTOR and Akt survival pathways and down-regulation of cell cycle and DNA repair pathways. Increased DNA damage from dysfunctional telomeres leads to reduced deposition of H3K27me3 onto the inactive X chromosome (Xi), impaired association of the Xi with telomeric transcript accumulations (Tacs), and reactivation of an X chromosome-linked K5TRF2 transgene that is subjected to X-chromosome inactivation in female mice with sufficiently long telomeres. Exogenously induced DNA damage also disrupts Xi-Tacs, suggesting DNA damage at the origin of these alterations. Collectively, these findings suggest that critically short telomeres activate a persistent DNA damage response that alters gene expression programs in a nonstochastic manner toward cell cycle arrest and activation of survival pathways, as well as impacts the maintenance of epigenetic memory and nuclear organization, thereby contributing to organismal aging.
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48
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Kozak ML, Chavez A, Dang W, Berger SL, Ashok A, Guo X, Johnson FB. Inactivation of the Sas2 histone acetyltransferase delays senescence driven by telomere dysfunction. EMBO J 2009; 29:158-70. [PMID: 19875981 DOI: 10.1038/emboj.2009.314] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 09/24/2009] [Indexed: 01/28/2023] Open
Abstract
Changes in telomere chromatin have been linked to cellular senescence, but the underlying mechanisms and impact on lifespan are unclear. We found that inactivation of the Sas2 histone acetyltransferase delays senescence in Saccharomyces cerevisiae telomerase (tlc1) mutants through a homologous recombination-dependent mechanism. Sas2 acetylates histone H4 lysine 16 (H4K16), and telomere shortening in tlc1 mutants was accompanied by a selective and Sas2-dependent increase in subtelomeric H4K16 acetylation. Further, mutation of H4 lysine 16 to arginine, which mimics constitutively deacetylated H4K16, delayed senescence and was epistatic to sas2 deletion, indicating that deacetylated H4K16 mediates the delay caused by sas2 deletion. Sas2 normally prevents the Sir2/3/4 heterochromatin complex from leaving the telomere and spreading to internal euchromatic loci. Senescence was delayed by sir3 deletion, but not sir2 deletion, indicating that senescence delay is mediated by release of Sir3 specifically from the telomere repeats. In contrast, sir4 deletion sped senescence and blocked the delay conferred by sas2 or sir3 deletion. We thus show that manipulation of telomere chromatin modulates senescence caused by telomere shortening.
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Affiliation(s)
- Marina L Kozak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6100, USA
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49
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Deleting the 14-3-3 protein Bmh1 extends life span in Saccharomyces cerevisiae by increasing stress response. Genetics 2009; 183:1373-84. [PMID: 19805817 DOI: 10.1534/genetics.109.107797] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Enhanced stress response has been suggested to promote longevity in many species. Calorie restriction (CR) and conserved nutrient-sensing target of rapamycin (TOR) and protein kinase A (PKA) pathways have also been suggested to extend life span by increasing stress response, which protects cells from age-dependent accumulation of oxidative damages. Here we show that deleting the yeast 14-3-3 protein, Bmh1, extends chronological life span (CLS) by activating the stress response. 14-3-3 proteins are highly conserved chaperone-like proteins that play important roles in many cellular processes. bmh1Delta-induced heat resistance and CLS extension require the general stress-response transcription factors Msn2, Msn4, and Rim15. The bmh1Delta mutant also displays a decreased reactive oxygen species level and increased heat-shock-element-driven transcription activity. We also show that BMH1 genetically interacts with CR and conserved nutrient-sensing TOR- and PKA-signaling pathways to regulate life span. Interestingly, the level of phosphorylated Ser238 on Bmh1 increases during chronological aging, which is delayed by CR or by reduced TOR activities. In addition, we demonstrate that PKA can directly phosphorylate Ser238 on Bmh1. The status of Bmh1 phosphorylation is therefore likely to play important roles in life-span regulation. Together, our studies suggest that phosphorylated Bmh1 may cause inhibitory effects on downstream longevity factors, including stress-response proteins. Deleting Bmh1 may eliminate the inhibitory effects of Bmh1 on these longevity factors and therefore extends life span.
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50
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Abstract
Since the earliest stages of evolution, organisms have faced the challenge of sensing and adapting to environmental changes for their survival under compromising conditions such as food depletion or stress. Implicit in these responses are mechanisms developed during evolution that include the targeting of chromatin to allow or prevent expression of fundamental genes and to protect genome integrity. Among the different approaches to study these mechanisms, the analysis of the response to a moderate reduction of energy intake, also known as calorie restriction (CR), has become one of the best sources of information regarding the factors and pathways involved in metabolic adaptation from lower to higher eukaryotes. Furthermore, responses to CR are involved in life span regulation-conserved from yeast to mammals-and therefore have garnered major research interest. Herein we review current knowledge of responses to CR at the molecular level and their functional link to chromatin.
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Affiliation(s)
- Alejandro Vaquero
- Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), ICREA, and IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.
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