1
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Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
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Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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2
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Molecular signatures of aneuploidy-driven adaptive evolution. Nat Commun 2020; 11:588. [PMID: 32001709 PMCID: PMC6992709 DOI: 10.1038/s41467-019-13669-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
Alteration of normal ploidy (aneuploidy) can have a number of opposing effects, such as unbalancing protein abundances and inhibiting cell growth but also accelerating genetic diversification and rapid adaptation. The interplay of these detrimental and beneficial effects remains puzzling. Here, to understand how cells develop tolerance to aneuploidy, we subject disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution under strong selection, by forcing disomy maintenance and daily population dilution. We characterize mutations, karyotype alterations and gene expression changes, and dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates and displayed diverse adaptive events. They tended to evolve towards normal ploidy through chromosomal DNA loss and gene expression changes. We identify genes with recurrent mutations and altered expression in multiple lines, revealing a variant that improves growth under genotoxic stresses. These findings support rapid evolvability of disomic strains that can be used to characterize fitness effects of mutations under different stress conditions. Aneuploidy (abnormal chromosome number) can enable rapid adaptation to stress conditions, but it also entails fitness costs from gene imbalance. Here, the authors experimentally evolve yeast while forcing maintenance of aneuploidy to identify the mechanisms that promote tolerance of aneuploidy.
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3
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Benstead-Hume G, Wooller SK, Downs JA, Pearl FMG. Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers. Int J Mol Sci 2019; 20:E5762. [PMID: 31744086 PMCID: PMC6887958 DOI: 10.3390/ijms20225762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/15/2023] Open
Abstract
Using pan-cancer data from The Cancer Genome Atlas (TCGA), we investigated how patterns in copy number alterations in cancer cells vary both by tissue type and as a function of genetic alteration. We find that patterns in both chromosomal ploidy and individual arm copy number are dependent on tumour type. We highlight for example, the significant losses in chromosome arm 3p and the gain of ploidy in 5q in kidney clear cell renal cell carcinoma tissue samples. We find that specific gene mutations are associated with genome-wide copy number changes. Using signatures derived from non-negative factorisation, we also find gene mutations that are associated with particular patterns of ploidy change. Finally, utilising a set of machine learning classifiers, we successfully predicted the presence of mutated genes in a sample using arm-wise copy number patterns as features. This demonstrates that mutations in specific genes are correlated and may lead to specific patterns of ploidy loss and gain across chromosome arms. Using these same classifiers, we highlight which arms are most predictive of commonly mutated genes in kidney renal clear cell carcinoma (KIRC).
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Affiliation(s)
- Graeme Benstead-Hume
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| | - Sarah K. Wooller
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| | - Jessica A Downs
- Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK;
| | - Frances M. G. Pearl
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
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4
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Tsai HJ, Nelliat A. A Double-Edged Sword: Aneuploidy is a Prevalent Strategy in Fungal Adaptation. Genes (Basel) 2019; 10:E787. [PMID: 31658789 PMCID: PMC6826469 DOI: 10.3390/genes10100787] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/28/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Aneuploidy, a deviation from a balanced genome by either gain or loss of chromosomes, is generally associated with impaired fitness and developmental defects in eukaryotic organisms. While the general physiological impact of aneuploidy remains largely elusive, many phenotypes associated with aneuploidy link to a common theme of stress adaptation. Here, we review previously identified mechanisms and observations related to aneuploidy, focusing on the highly diverse eukaryotes, fungi. Fungi, which have conquered virtually all environments, including several hostile ecological niches, exhibit widespread aneuploidy and employ it as an adaptive strategy under severe stress. Gambling with the balance between genome plasticity and stability has its cost and in fact, most aneuploidies have fitness defects. How can this fitness defect be reconciled with the prevalence of aneuploidy in fungi? It is likely that the fitness cost of the extra chromosomes is outweighed by the advantage they confer under life-threatening stresses. In fact, once the selective pressures are withdrawn, aneuploidy is often lost and replaced by less drastic mutations that possibly incur a lower fitness cost. We discuss representative examples across hostile environments, including medically and industrially relevant cases, to highlight potential adaptive mechanisms in aneuploid yeast.
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Affiliation(s)
- Hung-Ji Tsai
- Institute of Microbiology and Infection, and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Anjali Nelliat
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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5
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Co-Operation between Aneuploidy and Metabolic Changes in Driving Tumorigenesis. Int J Mol Sci 2019; 20:ijms20184611. [PMID: 31540349 PMCID: PMC6770258 DOI: 10.3390/ijms20184611] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Alterations from the normal set of chromosomes are extremely common as cells progress toward tumourigenesis. Similarly, we expect to see disruption of normal cellular metabolism, particularly in the use of glucose. In this review, we discuss the connections between these two processes: how chromosomal aberrations lead to metabolic disruption, and vice versa. Both processes typically result in the production of elevated levels of reactive oxygen species, so we particularly focus on their role in mediating oncogenic changes.
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6
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Eberhard S, Valuchova S, Ravat J, Fulneček J, Jolivet P, Bujaldon S, Lemaire SD, Wollman FA, Teixeira MT, Riha K, Xu Z. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants. Life Sci Alliance 2019; 2:2/3/e201900315. [PMID: 31160377 PMCID: PMC6549138 DOI: 10.26508/lsa.201900315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance. Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.
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Affiliation(s)
- Stephan Eberhard
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Sona Valuchova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Julie Ravat
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Jaroslav Fulneček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pascale Jolivet
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Sandrine Bujaldon
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Stéphane D Lemaire
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Francis-André Wollman
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Maria Teresa Teixeira
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zhou Xu
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France .,Sorbonne Université, CNRS, UMR 7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
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7
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Coutelier H, Xu Z. Adaptation in replicative senescence: a risky business. Curr Genet 2019; 65:711-716. [PMID: 30637477 DOI: 10.1007/s00294-019-00933-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/04/2019] [Accepted: 01/05/2019] [Indexed: 12/16/2022]
Abstract
Cell proliferation is tightly regulated to avoid propagating DNA damage and mutations, which can lead to pathologies such as cancer. To ensure genome integrity, cells activate the DNA damage checkpoint in response to genotoxic lesions to block cell cycle progression. This surveillance mechanism provides time to repair the damage before resuming cell cycle with an intact genome. When the damage is not repaired, cells can, in some conditions, override the cell cycle arrest and proceed with proliferation, a phenomenon known as adaptation to DNA damage. A subpopulation of adapted cells might eventually survive, but only at the cost of extensive genome instability. How and in which context adaptation operates the trade-off between survival and genome stability is a fascinating question. After a brief review of the current knowledge on adaptation to DNA damage in budding yeast, we will discuss a new role of adaptation in the context of telomerase-negative cells and replicative senescence. We highlight the idea that, in all settings studied so far, survival through adaptation is a double-edged sword as it comes with increased genomic instability.
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Affiliation(s)
- Héloïse Coutelier
- Sorbonne Université, PSL Research University, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, 75005, Paris, France
| | - Zhou Xu
- Sorbonne Université, PSL Research University, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, 75005, Paris, France. .,Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005, Paris, France.
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8
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Beaupere C, Dinatto L, Wasko BM, Chen RB, VanValkenburg L, Kiflezghi MG, Lee MB, Promislow DEL, Dang W, Kaeberlein M, Labunskyy VM. Genetic screen identifies adaptive aneuploidy as a key mediator of ER stress resistance in yeast. Proc Natl Acad Sci U S A 2018; 115:9586-9591. [PMID: 30185560 PMCID: PMC6156608 DOI: 10.1073/pnas.1804264115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The yeast genome becomes unstable during stress, which often results in adaptive aneuploidy, allowing rapid activation of protective mechanisms that restore cellular homeostasis. In this study, we performed a genetic screen in Saccharomyces cerevisiae to identify genome adaptations that confer resistance to tunicamycin-induced endoplasmic reticulum (ER) stress. Whole-genome sequencing of tunicamycin-resistant mutants revealed that ER stress resistance correlated significantly with gains of chromosomes II and XIII. We found that chromosome duplications allow adaptation of yeast cells to ER stress independently of the unfolded protein response, and that the gain of an extra copy of chromosome II alone is sufficient to induce protection from tunicamycin. Moreover, the protective effect of disomic chromosomes can be recapitulated by overexpression of several genes located on chromosome II. Among these genes, overexpression of UDP-N-acetylglucosamine-1-P transferase (ALG7), a subunit of the 20S proteasome (PRE7), and YBR085C-A induced tunicamycin resistance in wild-type cells, whereas deletion of all three genes completely reversed the tunicamycin-resistance phenotype. Together, our data demonstrate that aneuploidy plays a critical role in adaptation to ER stress by increasing the copy number of ER stress protective genes. While aneuploidy itself leads to proteotoxic stress, the gene-specific effects of chromosome II aneuploidy counteract the negative effect resulting in improved protein folding.
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Affiliation(s)
- Carine Beaupere
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118
| | - Leticia Dinatto
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Rosalyn B Chen
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118
| | - Lauren VanValkenburg
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118
| | | | - Mitchell B Lee
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Seattle, WA 98195
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195
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9
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How long does telomerase extend telomeres? Regulation of telomerase release and telomere length homeostasis. Curr Genet 2018; 64:1177-1181. [PMID: 29663033 PMCID: PMC6223848 DOI: 10.1007/s00294-018-0836-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 01/28/2023]
Abstract
Telomerase, the enzyme that replenishes telomeres, is essential for most eukaryotes to maintain their generations. Telomere length homeostasis is achieved via a balance between telomere lengthening by telomerase, and erosion over successive cell divisions. Impaired telomerase regulation leads to shortened telomeres and can cause defects in tissue maintenance. Telomeric DNA is composed of a repetitive sequence, which recruits the protective protein complex, shelterin. Shelterin, together with chromatin remodelling proteins, shapes the heterochromatic structure at the telomere and protects chromosome ends. Shelterin also provides a foothold for telomerase to be recruited and facilitates telomere extension. Such mechanisms of telomere recruitment and activation are conserved from unicellular eukaryotes to humans, with the rate of telomere extension playing an important role in determining the length maintained. Telomerase can be processive, adding multiple telomeric repeats before dissociating. However, a question remains: how does telomerase determine the number of repeats to add? In this review, I will discuss about how telomerase can monitor telomere extension using fission yeast as a model. I propose a model whereby the accumulation of the Pot1 complex on the synthesised telomere single-strand counteracts retention of telomerase via chromatin proteins and the similar system may be conserved in mammals.
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10
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Mason JMO, McEachern MJ. Chromosome ends as adaptive beginnings: the potential role of dysfunctional telomeres in subtelomeric evolvability. Curr Genet 2018; 64:997-1000. [PMID: 29589105 DOI: 10.1007/s00294-018-0822-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Telomeres serve as protective caps that help the cell differentiate between the naturally occurring ends of chromosomes and double-stranded breaks. When telomere capping function becomes compromised, chromosome ends are subjected to elevated rates of chromosome alterations. These effects can be particularly dramatic in the telomere-adjacent subtelomeric region. While the catastrophic impact of severe telomere dysfunction on genome stability has been well documented, the adaptive telomere failure hypothesis considers an alternative role telomere dysfunction may play in adaptive evolution. This hypothesis suggests that low levels of telomere failure, induced by certain environmental stresses, can lead to elevated subtelomeric recombination. Mutational loss, duplication, or modification of subtelomeric contingency genes could ultimately facilitate adaptation by generating novel mutants better able to survive environmental stress. In this perspective, we discuss recent work that examined mild telomere dysfunction and its role in altering the adaptive potential of subtelomeric genes.
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Affiliation(s)
- Jennifer M O Mason
- Department of Genetics, University of Georgia, Athens, GA, 30605, USA. .,Q2 Solutions, Morrisville, NC, 27560, USA.
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11
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Induction and relocalization of telomeric repeat-containing RNAs during diauxic shift in budding yeast. Curr Genet 2018; 64:1117-1127. [PMID: 29569051 DOI: 10.1007/s00294-018-0829-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 02/03/2023]
Abstract
Telomeres are maintained in a heterochromatic state that represses transcription of subtelomeric genes, a phenomenon known as telomere position effect. Nevertheless, telomeric DNA is actively transcribed, leading to the synthesis of telomeric repeat-containing noncoding RNA or TERRA. This nuclear noncoding RNA has been proposed to play important roles at telomeres, regulating their silencing, capping, repair and elongation by telomerase. In the budding yeast Saccharomyces cerevisiae, TERRA accumulation is repressed by telomeric silencing and the Rat1 exonuclease. On the other hand, telomere shortening promotes expression of TERRA. So far, little is known about the biological processes that induce TERRA expression in yeast. Understanding the dynamics of TERRA expression and localization is essential to define its function in telomere biology. Here, we aim to study the dynamics of TERRA expression during yeast cell growth. Using live-cell imaging, RNA-FISH and quantitative RT-PCR, we show that TERRA expression is induced as yeast cells undergo diauxic shift, a lag phase during which yeast cells switch their metabolism from anaerobic fermentation to oxidative respiration. This induction is transient as TERRA levels decrease during post-diauxic shift. The increased expression of TERRA is not due to the shortening of telomeres or increased stability of this transcript. Surprisingly, this induction is coincident with a cytoplasmic accumulation of TERRA molecules. Our results suggest that TERRA transcripts may play extranuclear functions with important implications in telomere biology and add a novel layer of complexity in the interplay between telomere biology, metabolism and stress response.
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12
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Maicher A, Kupiec M. Rnr1's role in telomere elongation cannot be replaced by Rnr3: a role beyond dNTPs? Curr Genet 2017; 64:547-550. [PMID: 29119271 DOI: 10.1007/s00294-017-0779-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 11/29/2022]
Abstract
Telomeres, the nucleoprotein complexes at the end of eukaryotic chromosomes, protect them from degradation and ensure the replicative capacity of cells. In most human tumors and in budding yeast, telomere length is maintained by the activity of telomerase, an enzyme that adds dNTPs according to an internal RNA template. The dNTPs are generated with the help of the ribonucleotide reductase (RNR) complex. We have recently generated strains lacking the large subunit of RNR, Rnr1, which were kept viable by the expression of RNR complexes containing the Rnr1 homolog, Rnr3. Interestingly, we found that these Rnr1-deficient strains have short telomeres that are stably maintained, but cannot become efficiently elongated by telomerase. Thus, a basic maintenance of short telomeres is possible under conditions, where Rnr1 activity is absent, but a sustained elongation of short telomeres fully depends on Rnr1 activity. We show that Rnr3 cannot compensate for this telomeric function of Rnr1 even when overall cellular dNTP values are restored. This suggests that Rnr1 plays a role in telomere elongation beyond increasing cellular dNTP levels. Furthermore, our data indicate that telomerase may act in two different modes, one that is capable of coping with the "end-replication problem" and is functional even in the absence of Rnr1 and another required for the sustained elongation of short telomeres, which fully depends on the presence of Rnr1. Supply of dNTPs for telomere elongation is provided by the Mec1ATR checkpoint, both during regular DNA replication and upon replication fork stalling. We discuss the implications of these results on telomere maintenance in yeast and cancer cells.
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Affiliation(s)
- André Maicher
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 6997801, Israel.
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13
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The evolutionarily conserved factor Sus1/ENY2 plays a role in telomere length maintenance. Curr Genet 2017; 64:635-644. [DOI: 10.1007/s00294-017-0778-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 11/26/2022]
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14
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Harari Y, Kupiec M. Mec1 ATR is needed for extensive telomere elongation in response to ethanol in yeast. Curr Genet 2017; 64:223-234. [PMID: 28780613 DOI: 10.1007/s00294-017-0728-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 11/26/2022]
Abstract
Telomere length homeostasis is essential for cell survival. In humans, telomeres shorten as a function of age. Short telomeres are known determinants of cell senescence and longevity. The yeast Saccharomyces cerevisiae expresses telomerase and maintains a strict telomere length homeostasis during vegetative growth. We have previously reported that different environmental signals promote changes in telomere length in S. cerevisiae. In particular, exposure to ethanol induces an extensive telomere elongation response due to a reduction in RAP1 mRNA and protein levels. Here we show that the reduction in Rap1 protein levels disrupts the physical interaction between Rap1 and Rif1, which in turn reduces the recruitment of these two proteins to telomeres during G2-phase. Although elongation of the shortest telomeres has been shown to depend on the Rif2 telomeric protein and on the Tel1(ATM) protein kinase, we show here that the extensive telomere elongation in response to ethanol exposure is Rif1 and Mec1 (ATR)-dependent. Our results fit a model in which Rif1 and Rap1 form a complex that is loaded onto telomeres at the end of S-phase. Reduced levels of the Rap1-Rif1 complex in ethanol lead to continuous telomere elongation in a Mec1-dependent process.
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Affiliation(s)
- Yaniv Harari
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
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15
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Abstract
Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact, and evolutionary significance of CCNV. Fundamental studies of this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but also is a key contributor to the diversity of industrially relevant traits. This notion is further supported by the frequent involvement of CCNV in industrially relevant traits acquired during evolutionary engineering. This review describes recent developments in genome sequencing and genome editing techniques and discusses how these offer opportunities to unravel contributions of CCNV in industrial Saccharomyces strains as well as to rationally engineer yeast chromosomal copy numbers and karyotypes.
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16
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Exploring the power of yeast to model aging and age-related neurodegenerative disorders. Biogerontology 2016; 18:3-34. [PMID: 27804052 DOI: 10.1007/s10522-016-9666-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
Abstract
Aging is a multifactorial process determined by molecular, cellular and systemic factors and it is well established that advancing age is a leading risk factor for several neurodegenerative diseases. In fact, the close association of aging and neurodegenerative disorders has placed aging as the greatest social and economic challenge of the 21st century, and age-related diseases have also become a key priority for countries worldwide. The growing need to better understand both aging and neurodegenerative processes has led to the development of simple eukaryotic models amenable for mechanistic studies. Saccharomyces cerevisiae has proven to be an unprecedented experimental model to study the fundamental aspects of aging and to decipher the intricacies of neurodegenerative disorders greatly because the molecular mechanisms underlying these processes are evolutionarily conserved from yeast to human. Moreover, yeast offers several methodological advantages allowing a rapid and relatively easy way of establishing gene-protein-function associations. Here we review different aging theories, common cellular pathways driving aging and neurodegenerative diseases and discuss the major contributions of yeast to the state-of-art knowledge in both research fields.
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Gadaleta MC, González-Medina A, Noguchi E. Timeless protection of telomeres. Curr Genet 2016; 62:725-730. [PMID: 27068713 DOI: 10.1007/s00294-016-0599-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
The DNA replication machinery encounters problems at numerous genomic regions that are inherently difficult to replicate. These genomic regions include telomeres, which contain repetitive DNA and telomere-binding proteins. If not properly regulated, replication of such genomic regions can result in DNA damage, leading to genomic instability. Studies implicated a role of Timeless-related proteins at difficult-to-replicate genomic regions, including telomeres. However, how these proteins maintain telomeres was elusive. In a recent report, we described the role of Swi1, a Timeless-related protein, in telomere maintenance in fission yeast. We demonstrated that Swi1 is required for proper replication of repeat DNA sequences at telomeres. We also showed that Swi1-deficient cells utilize recombination-based ALT (alternative lengthening of telomeres)-like mechanisms to maintain telomeres in the absence of telomerase. Here, we highlight these findings and present additional data to discuss the role of Swi1Timeless in telomere protection and ALT prevention.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Alberto González-Medina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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