1
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Tosato V, Rossi B, Sims J, Bruschi CV. Timing of Chromosome DNA Integration throughout the Yeast Cell Cycle. Biomolecules 2023; 13:biom13040614. [PMID: 37189362 DOI: 10.3390/biom13040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
The dynamic mechanism of cell uptake and genomic integration of exogenous linear DNA still has to be completely clarified, especially within each phase of the cell cycle. We present a study of integration events of double-stranded linear DNA molecules harboring at their ends sequence homologies to the host’s genome, all throughout the cell cycle of the model organism Saccharomyces cerevisiae, comparing the efficiency of chromosomal integration of two types of DNA cassettes tailored for site-specific integration and bridge-induced translocation. Transformability increases in S phase regardless of the sequence homologies, while the efficiency of chromosomal integration during a specific cycle phase depends upon the genomic targets. Moreover, the frequency of a specific translocation between chromosomes XV and VIII strongly increased during DNA synthesis under the control of Pol32 polymerase. Finally, in the null POL32 double mutant, different pathways drove the integration in the various phases of the cell cycle and bridge-induced translocation was possible outside the S phase even without Pol32. The discovery of this cell-cycle dependent regulation of specific pathways of DNA integration, associated with an increase of ROS levels following translocation events, is a further demonstration of a sensing ability of the yeast cell in determining a cell-cycle-related choice of DNA repair pathways under stress.
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2
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Ren H, Yin A, Wu P, Zhou H, Zhou J, Yu Y, Lu H. Establishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus. Microorganisms 2022; 10:microorganisms10061240. [PMID: 35744758 PMCID: PMC9227491 DOI: 10.3390/microorganisms10061240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The Cre-loxP system produces structural variations, such as deletion, duplication, inversion and translocation, at specific loci and induces chromosomal rearrangements in the genome. To achieve chromosomal rearrangements in Kluyveromyces marxianus, the positions and sequences of centromeres were identified in this species for the first time. Next, a Cre-loxP system was established in K. marxianus. In this system, the Cre recombinase was expressed from a leaky LAC4 promoter in a plasmid to alleviate the cytotoxicity of Cre, and the unstable plasmid contained a panARS element to facilitate the clearance of the plasmid from the cells. By using LAC4 as a reporter gene, the recombination frequencies between loxP sites or loxPsym sites were 99% and 73%, respectively. A K. marxianus strain containing 16 loxPsym sites in the genome was constructed. The recombination frequency of large-scale chromosomal rearrangements between 16 loxPsym sites was up to 38.9%. Our study provides valuable information and tools for studying chromosomal structures and functions in K. marxianus.
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Affiliation(s)
- Haiyan Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Anqi Yin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Huanyu Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.Y.); (H.L.)
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (H.R.); (A.Y.); (P.W.); (H.Z.); (J.Z.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China
- Correspondence: (Y.Y.); (H.L.)
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3
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Wang HY, Sokol ES, Goodman AM, Feldman AL, Mulroney CM. Case Report: Multiple Chromosomal Translocations Including Novel CIITA-CREBBP Fusion and Mutations in a Follicular Lymphoma. Front Oncol 2021; 11:620435. [PMID: 33777766 PMCID: PMC7988195 DOI: 10.3389/fonc.2021.620435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
The pathogenesis of follicular lymphoma is a multi-step process, in which chromosomal translocation between immunoglobulin heavy chain (IgH) and anti-apoptotic B-cell lymphoma 2 (BCL2), namely IgH-BCL2, is an earliest step, followed by other genetic/genomic alterations including but not limited to mutation of CREB binding protein (CREBBP). MHC class II transactivator (CIITA) is a transcription regulator responsible for expression of MHC class II molecules including HLA-DR in human. We report herein a novel fusion gene involving CIITA and CREBBP in a patient with a low-grade follicular lymphoma (FL) but with high Ki-67 proliferation index. In addition, our patient also harbors CREBBP mutation. Together, we postulate that total loss of CREBBP function may contribute, in part, to the lymphoma genesis. Furthermore, this patient has addition rare (TBL1XR1-TP63) and common (IgH-BCL2) chromosomal translocations and multiple mutations including BCL2, BRAF, MUTYH, and STAT6.
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Affiliation(s)
- Huan-You Wang
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health System, La Jolla, CA, United States
| | | | - Aaron M Goodman
- Division of Blood and Bone Marrow Transplant, Department of Medicine, University of California San Diego Health System, La Jolla, CA, United States
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Carolyn M Mulroney
- Division of Blood and Bone Marrow Transplant, Department of Medicine, University of California San Diego Health System, La Jolla, CA, United States
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4
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Tosato V, West N, Zrimec J, Nikitin DV, Del Sal G, Marano R, Breitenbach M, Bruschi CV. Bridge-Induced Translocation between NUP145 and TOP2 Yeast Genes Models the Genetic Fusion between the Human Orthologs Associated With Acute Myeloid Leukemia. Front Oncol 2017; 7:231. [PMID: 29034209 PMCID: PMC5626878 DOI: 10.3389/fonc.2017.00231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/07/2017] [Indexed: 01/03/2023] Open
Abstract
In mammalian organisms liquid tumors such as acute myeloid leukemia (AML) are related to spontaneous chromosomal translocations ensuing in gene fusions. We previously developed a system named bridge-induced translocation (BIT) that allows linking together two different chromosomes exploiting the strong endogenous homologous recombination system of the yeast Saccharomyces cerevisiae. The BIT system generates a heterogeneous population of cells with different aneuploidies and severe aberrant phenotypes reminiscent of a cancerogenic transformation. In this work, thanks to a complex pop-out methodology of the marker used for the selection of translocants, we succeeded by BIT technology to precisely reproduce in yeast the peculiar chromosome translocation that has been associated with AML, characterized by the fusion between the human genes NUP98 and TOP2B. To shed light on the origin of the DNA fragility within NUP98, an extensive analysis of the curvature, bending, thermostability, and B-Z transition aptitude of the breakpoint region of NUP98 and of its yeast ortholog NUP145 has been performed. On this basis, a DNA cassette carrying homologous tails to the two genes was amplified by PCR and allowed the targeted fusion between NUP145 and TOP2, leading to reproduce the chimeric transcript in a diploid strain of S. cerevisiae. The resulting translocated yeast obtained through BIT appears characterized by abnormal spherical bodies of nearly 500 nm of diameter, absence of external membrane and defined cytoplasmic localization. Since Nup98 is a well-known regulator of the post-transcriptional modification of P53 target genes, and P53 mutations are occasionally reported in AML, this translocant yeast strain can be used as a model to test the constitutive expression of human P53. Although the abnormal phenotype of the translocant yeast was never rescued by its expression, an exogenous P53 was recognized to confer increased vitality to the translocants, in spite of its usual and well-documented toxicity to wild-type yeast strains. These results obtained in yeast could provide new grounds for the interpretation of past observations made in leukemic patients indicating a possible involvement of P53 in cell transformation toward AML.
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Affiliation(s)
- Valentina Tosato
- Ulisse Biomed S.r.l., AREA Science Park, Trieste, Italy.,Faculty of Health Sciences, University of Primorska, Izola, Slovenia.,Yeast Molecular Genetics, ICGEB, AREA Science Park, Trieste, Italy
| | - Nicole West
- Clinical Pathology, Hospital Maggiore, Trieste, Italy
| | - Jan Zrimec
- Faculty of Health Sciences, University of Primorska, Izola, Slovenia
| | - Dmitri V Nikitin
- Biology Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Giannino Del Sal
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberto Marano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Michael Breitenbach
- Genetics Division, Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Carlo V Bruschi
- Yeast Molecular Genetics, ICGEB, AREA Science Park, Trieste, Italy.,Genetics Division, Department of Cell Biology, University of Salzburg, Salzburg, Austria
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5
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Piazza A, Wright WD, Heyer WD. Multi-invasions Are Recombination Byproducts that Induce Chromosomal Rearrangements. Cell 2017; 170:760-773.e15. [PMID: 28781165 PMCID: PMC5554464 DOI: 10.1016/j.cell.2017.06.052] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/02/2017] [Accepted: 06/30/2017] [Indexed: 11/18/2022]
Abstract
Inaccurate repair of broken chromosomes generates structural variants that can fuel evolution and inflict pathology. We describe a novel rearrangement mechanism in which translocation between intact chromosomes is induced by a lesion on a third chromosome. This multi-invasion-induced rearrangement (MIR) stems from a homologous recombination byproduct, where a broken DNA end simultaneously invades two intact donors. No homology is required between the donors, and the intervening sequence from the invading molecule is inserted at the translocation site. MIR is stimulated by increasing homology length and spatial proximity of the donors and depends on the overlapping activities of the structure-selective endonucleases Mus81-Mms4, Slx1-Slx4, and Yen1. Conversely, the 3'-flap nuclease Rad1-Rad10 and enzymes known to disrupt recombination intermediates (Sgs1-Top3-Rmi1, Srs2, and Mph1) inhibit MIR. Resolution of MIR intermediates propagates secondary chromosome breaks that frequently cause additional rearrangements. MIR features have implications for the formation of simple and complex rearrangements underlying human pathologies.
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Affiliation(s)
- Aurèle Piazza
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - William Douglass Wright
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Avenue, University of California, Davis, Davis, CA 95616, USA; Department of Molecular and Cellular Biology, One Shields Avenue, University of California, Davis, Davis, CA 95616, USA.
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6
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Tosato V, Sims J, West N, Colombin M, Bruschi CV. Post-translocational adaptation drives evolution through genetic selection and transcriptional shift in Saccharomyces cerevisiae. Curr Genet 2016; 63:281-292. [PMID: 27491680 DOI: 10.1007/s00294-016-0635-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Adaptation by natural selection might improve the fitness of an organism and its probability to survive in unfavorable environmental conditions. Decoding the genetic basis of adaptive evolution is one of the great challenges to deal with. To this purpose, Saccharomyces cerevisiae has been largely investigated because of its short division time, excellent aneuploidy tolerance and the availability of the complete sequence of its genome with a thorough genome database. In the past, we developed a system, named bridge-induced translocation, to trigger specific, non-reciprocal translocations, exploiting the endogenous recombination system of budding yeast. This technique allows users to generate a heterogeneous population of cells with different aneuploidies and increased phenotypic variation. In this work, we demonstrate that ad hoc chromosomal translocations might induce adaptation, fostering selection of thermo-tolerant yeast strains with improved phenotypic fitness. This "yeast eugenomics" correlates with a shift to enhanced expression of genes involved in stress response, heat shock as well as carbohydrate metabolism. We propose that the bridge-induced translocation is a suitable approach to generate adapted, physiologically boosted strains for biotechnological applications.
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Affiliation(s)
- Valentina Tosato
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310, Izola, Slovenia. .,Yeast Molecular Genetics, ICGEB, AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Jason Sims
- Department of Chromosome Biology, Max Perutz Laboratories, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Nicole West
- Yeast Molecular Genetics, ICGEB, AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.,Clinical Pathology, Maggiore Hospital, Piazza dell' Ospitale 2, 34125, Trieste, Italy
| | - Martina Colombin
- Yeast Molecular Genetics, ICGEB, AREA Science Park, Padriciano, 99, 34149, Trieste, Italy
| | - Carlo V Bruschi
- Yeast Molecular Genetics, ICGEB, AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.,Genetics Division, Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
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7
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Sims J, Bruschi CV, Bertin C, West N, Breitenbach M, Schroeder S, Eisenberg T, Rinnerthaler M, Raspor P, Tosato V. High reactive oxygen species levels are detected at the end of the chronological life span of translocant yeast cells. Mol Genet Genomics 2015; 291:423-35. [PMID: 26423068 DOI: 10.1007/s00438-015-1120-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/18/2015] [Indexed: 12/23/2022]
Abstract
Chromosome translocation is a major genomic event for a cell, affecting almost every of its life aspects ranging from metabolism, organelle maintenance and homeostasis to gene maintenance and expression. By using the bridge-induced translocation system, we defined the effects of induced chromosome translocation on the chronological life span (CLS) of yeast with particular interest to the oxidative stress condition. The results demonstrate that every translocant strain has a different CLS, but all have a high increase in reactive oxygen species and in lipid peroxides levels at the end of the life span. This could be due to the very unique and strong deregulation of the oxidative stress network. Furthermore, the loss of the translocated chromosome occurs at the end of the life span and is locus dependent. Additionally, the RDH54 gene may play a role in the correct segregation of the translocant chromosome, since in its absence there is an increase in loss of the bridge-induced translocated chromosome.
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Affiliation(s)
- Jason Sims
- Yeast Molecular Genetics Group, ICGEB, Area Science Park, Padriciano 99, 34149, Trieste, Italy.,Department of Chromosome Biology, Max Perutz Laboratories, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Carlo V Bruschi
- Yeast Molecular Genetics Group, ICGEB, Area Science Park, Padriciano 99, 34149, Trieste, Italy.,Central European Initiative, Via Genova 9, 34121, Trieste, Italy
| | - Chloé Bertin
- Cellular and Molecular Life Sciences, University of Rennes, 9 Rue Jean Macé, 35700, Rennes, France
| | - Nicole West
- Yeast Molecular Genetics Group, ICGEB, Area Science Park, Padriciano 99, 34149, Trieste, Italy
| | - Michael Breitenbach
- Genetics Division, Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Sabrina Schroeder
- Genetics Division, Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Mark Rinnerthaler
- Genetics Division, Department of Cell Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Peter Raspor
- Institute of Food, Nutrition and Health, University of Primorska, Polje 42, 6310, Izola, Slovenia
| | - Valentina Tosato
- Yeast Molecular Genetics Group, ICGEB, Area Science Park, Padriciano 99, 34149, Trieste, Italy.
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8
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Tosato V, Bruschi CV. Per aspera ad astra: When harmful chromosomal translocations become a plus value in genetic evolution. Lessons from Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2015; 2:363-375. [PMID: 28357264 PMCID: PMC5354581 DOI: 10.15698/mic2015.10.230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this review we will focus on chromosomal translocations (either spontaneous or induced) in budding yeast. Indeed, very few organisms tolerate so well aneuploidy like Saccharomyces, allowing in depth studies on chromosomal numerical aberrations. Many wild type strains naturally develop chromosomal rearrangements while adapting to different environmental conditions. Translocations, in particular, are valuable not only because they naturally drive species evolution, but because they might allow the artificial generation of new strains that can be optimized for industrial purposes. In this area, several methodologies to artificially trigger chromosomal translocations have been conceived in the past years, such as the chromosomal fragmentation vector (CFV) technique, the Cre-loxP procedure, the FLP/FRT recombination method and, recently, the bridge - induced translocation (BIT) system. An overview of the methodologies to generate chromosomal translocations in yeast will be presented and discussed considering advantages and drawbacks of each technology, focusing in particular on the recent BIT system. Translocants are important for clinical studies because translocated yeast cells resemble cancer cells from morphological and physiological points of view and because the translocation event ensues in a transcriptional de-regulation with a subsequent multi-factorial genetic adaptation to new, selective environmental conditions. The phenomenon of post-translocational adaptation (PTA) is discussed, providing some new unpublished data and proposing the hypothesis that translocations may drive evolution through adaptive genetic selection.
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Affiliation(s)
- Valentina Tosato
- Yeast Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Carlo V Bruschi
- Yeast Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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9
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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10
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Chromosome translocation may lead to PRK1-dependent anticancer drug resistance in yeast via endocytic actin network deregulation. Eur J Cell Biol 2014; 93:145-56. [DOI: 10.1016/j.ejcb.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/24/2014] [Accepted: 03/31/2014] [Indexed: 11/21/2022] Open
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QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite. PLoS One 2014; 9:e86298. [PMID: 24489712 PMCID: PMC3904918 DOI: 10.1371/journal.pone.0086298] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/10/2013] [Indexed: 12/03/2022] Open
Abstract
Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI) involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.
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12
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Tosato V, Sidari S, Bruschi CV. Bridge-induced chromosome translocation in yeast relies upon a Rad54/Rdh54-dependent, Pol32-independent pathway. PLoS One 2013; 8:e60926. [PMID: 23613757 PMCID: PMC3629078 DOI: 10.1371/journal.pone.0060926] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 03/04/2013] [Indexed: 11/18/2022] Open
Abstract
While in mammalian cells the genetic determinism of chromosomal translocation remains unclear, the yeast Saccharomyces cerevisiae has become an ideal model system to generate ad hoc translocations and analyze their cellular and molecular outcome. A linear DNA cassette carrying a selectable marker flanked by perfect homologies to two chromosomes triggers a bridge-induced translocation (BIT) in budding yeast, with variable efficiency. A postulated two-step process to produce BIT translocants is based on the cooperation between the Homologous Recombination System (HRS) and Break-Induced Replication (BIR); however, a clear indication of the molecular factors underlying the genetic mechanism is still missing. In this work we provide evidence that BIT translocation is elicited by the Rad54 helicase and completed by a Pol32-independent replication pathway. Our results demonstrate also that Rdh54 is involved in the stability of the translocants, suggesting a mitotic role in chromosome pairing and segregation. Moreover, when RAD54 is over-expressed, an ensemble of secondary rearrangements between repeated DNA tracts arise after the initial translocation event, leading to severe aneuploidy with loss of genetic material, which prompts the identification of fragile sites within the yeast genome.
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Affiliation(s)
- Valentina Tosato
- Yeast Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
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13
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Rancati G, Pavelka N. Karyotypic changes as drivers and catalyzers of cellular evolvability: a perspective from non-pathogenic yeasts. Semin Cell Dev Biol 2013; 24:332-8. [PMID: 23403271 DOI: 10.1016/j.semcdb.2013.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/17/2013] [Accepted: 01/25/2013] [Indexed: 02/08/2023]
Abstract
In spite of the existence of multiple cellular mechanisms that ensure genome stability, thanks to the advent of quantitative genomic assays in the last decade, an unforeseen level of plasticity in cellular genomes has begun to emerge in many different fields of cell biology. Eukaryotic cells not only have a remarkable ability to change their karyotypes in response to various perturbations, but also these karyotypic changes impact cellular fitness and in some circumstances enable evolutionary adaptation. In this review, we focus on recent findings in non-pathogenic yeasts indicating that karyotypic changes generate selectable phenotypic variation and alter genomic instability. Based on these findings, we propose that in highly stressful and thus strongly selective environments karyotypic changes could act both as a driver and as a catalyzer of cellular adaptation, i.e. karyotypic changes drive large phenotypic leaps and at the same time catalyze the accumulation of even more genotypic and karyotypic changes.
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Affiliation(s)
- Giulia Rancati
- Institute of Medical Biology, Agency of Science, Technology and Research, 8A Biomedical Grove, Singapore 138648, Singapore.
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14
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Tosato V, Grüning NM, Breitenbach M, Arnak R, Ralser M, Bruschi CV. Warburg effect and translocation-induced genomic instability: two yeast models for cancer cells. Front Oncol 2013; 2:212. [PMID: 23346549 PMCID: PMC3548335 DOI: 10.3389/fonc.2012.00212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 12/20/2012] [Indexed: 11/13/2022] Open
Abstract
Yeast has been established as an efficient model system to study biological principles underpinning human health. In this review we focus on yeast models covering two aspects of cancer formation and progression (i) the activity of pyruvate kinase (PK), which recapitulates metabolic features of cancer cells, including the Warburg effect, and (ii) chromosome bridge-induced translocation (BIT) mimiking genome instability in cancer. Saccharomyces cerevisiae is an excellent model to study cancer cell metabolism, as exponentially growing yeast cells exhibit many metabolic similarities with rapidly proliferating cancer cells. The metabolic reconfiguration includes an increase in glucose uptake and fermentation, at the expense of respiration and oxidative phosphorylation (the Warburg effect), and involves a broad reconfiguration of nucleotide and amino acid metabolism. Both in yeast and humans, the regulation of this process seems to have a central player, PK, which is up-regulated in cancer, and to occur mostly on a post-transcriptional and post-translational basis. Furthermore, BIT allows to generate selectable translocation-derived recombinants ("translocants"), between any two desired chromosomal locations, in wild-type yeast strains transformed with a linear DNA cassette carrying a selectable marker flanked by two DNA sequences homologous to different chromosomes. Using the BIT system, targeted non-reciprocal translocations in mitosis are easily inducible. An extensive collection of different yeast translocants exhibiting genome instability and aberrant phenotypes similar to cancer cells has been produced and subjected to analysis. In this review, we hence provide an overview upon two yeast cancer models, and extrapolate general principles for mimicking human disease mechanisms in yeast.
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Affiliation(s)
- Valentina Tosato
- International Centre for Genetic Engineering and Biotechnology Trieste, Italy
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Jung PP, Fritsch ES, Blugeon C, Souciet JL, Potier S, Lemoine S, Schacherer J, de Montigny J. Ploidy influences cellular responses to gross chromosomal rearrangements in Saccharomyces cerevisiae. BMC Genomics 2011; 12:331. [PMID: 21711526 PMCID: PMC3157476 DOI: 10.1186/1471-2164-12-331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 06/28/2011] [Indexed: 01/04/2023] Open
Abstract
Background Gross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been completely elucidated and the effects of additional chromosomes in cancer cells are still unknown. Most previous studies in which Saccharomyces cerevisiae has been used as a model for cancer cells have been carried out in the haploid context. To obtain new insights on the role of ploidy, the cellular effects of GCRs were compared between the haploid and diploid contexts. Results A total number of 21 haploid and diploid S. cerevisiae strains carrying various types of GCRs (aneuploidies, nonreciprocal translocations, segmental duplications and deletions) were studied with a view to determining the effects of ploidy on the cellular responses. Differences in colony and cell morphology as well as in the growth rates were observed between mutant and parental strains. These results suggest that cells are impaired physiologically in both contexts. We also investigated the variation in genomic expression in all the mutants. We observed that gene expression was significantly altered. The data obtained here clearly show that genes involved in energy metabolism, especially in the tricarboxylic acid cycle, are up-regulated in all these mutants. However, the genes involved in the composition of the ribosome or in RNA processing are down-regulated in diploids but up-regulated in haploids. Over-expression of genes involved in the regulation of the proteasome was found to occur only in haploid mutants. Conclusion The present comparisons between the cellular responses of strains carrying GCRs in different ploidy contexts bring to light two main findings. First, GCRs induce a general stress response in all studied mutants, regardless of their ploidy. Secondly, the ploidy context plays a crucial role in maintaining the stoichiometric balance of the proteins: the translation rates decrease in diploid strains, whereas the excess protein synthesized is degraded in haploids by proteasome activity.
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Affiliation(s)
- Paul P Jung
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR, Strasbourg, France
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