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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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Peng CA, Gaertner AAE, Henriquez SA, Fang D, Colon-Reyes RJ, Brumaghim JL, Kozubowski L. Fluconazole induces ROS in Cryptococcus neoformans and contributes to DNA damage in vitro. PLoS One 2018; 13:e0208471. [PMID: 30532246 PMCID: PMC6286144 DOI: 10.1371/journal.pone.0208471] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/16/2018] [Indexed: 11/24/2022] Open
Abstract
Pathogenic basidiomycetous yeast, Cryptococcus neoformans, causes fatal meningitis in immunocompromised individuals. Fluconazole (FLC) is a fungistatic drug commonly administered to treat cryptococcosis. Unfortunately, FLC-resistant strains characterized by various degree of chromosomal instability were isolated from clinical patients. Importantly, the underlying mechanisms that lead to chromosomal instability in FLC-treated C. neoformans remain elusive. Previous studies in fungal and mammalian cells link chromosomal instability to the reactive oxygen species (ROS). This study provides the evidence that exposure of C. neoformans to FLC induces accumulation of intracellular ROS, which correlates with plasma membrane damage. FLC caused transcription changes of oxidative stress related genes encoding superoxide dismutase (SOD1), catalase (CAT3), and thioredoxin reductase (TRR1). Strikingly, FLC contributed to an increase of the DNA damage in vitro, when complexed with iron or copper in the presence of hydrogen peroxide. Strains with isogenic deletion of copper response protein metallothionein were more susceptible to FLC. Addition of ascorbic acid (AA), an anti-oxidant at 10 mM, reduced the inhibitory effects of FLC. Consistent with potential effects of FLC on DNA integrity and chromosomal segregation, FLC treatment led to elevated transcription of RAD54 and repression of cohesin-encoding gene SCC1. We propose that FLC forms complexes with metals and contributes to elevated ROS, which may lead to chromosomal instability in C. neoformans.
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Affiliation(s)
- Congyue Annie Peng
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Andrea A. E. Gaertner
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Sarah Ana Henriquez
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Diana Fang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Rodney J. Colon-Reyes
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Julia L. Brumaghim
- Department of Chemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Lukasz Kozubowski
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- * E-mail:
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3
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Sharp NP, Sandell L, James CG, Otto SP. The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast. Proc Natl Acad Sci U S A 2018; 115:E5046-E5055. [PMID: 29760081 PMCID: PMC5984525 DOI: 10.1073/pnas.1801040115] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report a direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploids and diploids following a mutation-accumulation experiment in the budding yeast Saccharomyces cerevisiae Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide mutations (SNMs) and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that mutations would have weaker effects, due to masking, in diploids. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to SNMs in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids, we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.
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Affiliation(s)
- Nathaniel P Sharp
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Linnea Sandell
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Christopher G James
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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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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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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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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7
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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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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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