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Lairón-Peris M, Castiglioni GL, Routledge SJ, Alonso-Del-Real J, Linney JA, Pitt AR, Melcr J, Goddard AD, Barrio E, Querol A. Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid. Microb Genom 2021; 7. [PMID: 34448691 PMCID: PMC8549368 DOI: 10.1099/mgen.0.000628] [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] [Indexed: 12/01/2022] Open
Abstract
During industrial processes, yeasts are exposed to harsh conditions, which eventually lead to adaptation of the strains. In the laboratory, it is possible to use experimental evolution to link the evolutionary biology response to these adaptation pressures for the industrial improvement of a specific yeast strain. In this work, we aimed to study the adaptation of a wine industrial yeast in stress conditions of the high ethanol concentrations present in stopped fermentations and secondary fermentations in the processes of champagne production. We used a commercial Saccharomyces cerevisiae × S. uvarum hybrid and assessed its adaptation in a modified synthetic must (M-SM) containing high ethanol, which also contained metabisulfite, a preservative that is used during wine fermentation as it converts to sulfite. After the adaptation process under these selected stressful environmental conditions, the tolerance of the adapted strain (H14A7-etoh) to sulfite and ethanol was investigated, revealing that the adapted hybrid is more resistant to sulfite compared to the original H14A7 strain, whereas ethanol tolerance improvement was slight. However, a trade-off in the adapted hybrid was found, as it had a lower capacity to ferment glucose and fructose in comparison with H14A7. Hybrid genomes are almost always unstable, and different signals of adaptation on H14A7-etoh genome were detected. Each subgenome present in the adapted strain had adapted differently. Chromosome aneuploidies were present in S. cerevisiae chromosome III and in S. uvarum chromosome VII–XVI, which had been duplicated. Moreover, S. uvarum chromosome I was not present in H14A7-etoh and a loss of heterozygosity (LOH) event arose on S. cerevisiae chromosome I. RNA-sequencing analysis showed differential gene expression between H14A7-etoh and H14A7, which can be easily correlated with the signals of adaptation that were found on the H14A7-etoh genome. Finally, we report alterations in the lipid composition of the membrane, consistent with conserved tolerance mechanisms.
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Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Gabriel L Castiglioni
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Sarah J Routledge
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - John A Linney
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Andrew R Pitt
- College of Health and Life Sciences, Aston University, Birmingham, UK.,Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, UK
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands
| | - Alan D Goddard
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
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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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Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation. G3-GENES GENOMES GENETICS 2016; 6:2421-34. [PMID: 27317778 PMCID: PMC4978896 DOI: 10.1534/g3.116.029397] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker's/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation.
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Potapova TA, Zhu J, Li R. Aneuploidy and chromosomal instability: a vicious cycle driving cellular evolution and cancer genome chaos. Cancer Metastasis Rev 2014; 32:377-89. [PMID: 23709119 DOI: 10.1007/s10555-013-9436-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aneuploidy and chromosomal instability frequently co-exist, and aneuploidy is recognized as a direct outcome of chromosomal instability. However, chromosomal instability is widely viewed as a consequence of mutations in genes involved in DNA replication, chromosome segregation, and cell cycle checkpoints. Telomere attrition and presence of extra centrosomes have also been recognized as causative for errors in genomic transmission. Here, we examine recent studies suggesting that aneuploidy itself can be responsible for the procreation of chromosomal instability. Evidence from both yeast and mammalian experimental models suggests that changes in chromosome copy number can cause changes in dosage of the products of many genes located on aneuploid chromosomes. These effects on gene expression can alter the balanced stoichiometry of various protein complexes, causing perturbations of their functions. Therefore, phenotypic consequences of aneuploidy will include chromosomal instability if the balanced stoichiometry of protein machineries responsible for accurate chromosome segregation is affected enough to perturb the function. The degree of chromosomal instability will depend on specific karyotypic changes, which may be due to dosage imbalances of specific genes or lack of scaling between chromosome segregation load and the capacity of the mitotic system. We propose that the relationship between aneuploidy and chromosomal instability can be envisioned as a "vicious cycle," where aneuploidy potentiates chromosomal instability leading to further karyotype diversity in the affected population.
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Affiliation(s)
- Tamara A Potapova
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA,
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5
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Waghmare SK, Tumbar T. Adult hair follicle stem cells do not retain the older DNA strands in vivo during normal tissue homeostasis. Chromosome Res 2014; 21:203-12. [PMID: 23681654 DOI: 10.1007/s10577-013-9355-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tissue stem cells have been proposed to segregate the chromosomes asymmetrically (in a non-random manner), thereby retaining preferentially the older "immortal" DNA strands bearing the stemness characteristics into one daughter cell, whereas the newly synthesized strands are segregated to the other daughter cell that will commit to differentiation. Moreover, this non-random segregation would protect the stem cell genome from accumulating multiple mutations during repeated DNA replication. This long-standing hypothesis remains an active subject of study due to conflicting results for some systems and lack of consistency among different tissue stem cell populations. In this review, we will focus on work done in the hair follicle, which is one of the best-understood vertebrate tissue stem cell system to date. In cell culture analysis of paired cultured keratinocytes derived from hair follicle, stem cells suggested a non-random segregation of chromosome with respect to the older DNA strand. In vivo, the hair follicle stem cells appear to self-renew and differentiate at different phases of their homeostatic cycle. The fate decisions occur in quiescence when some stem cells migrate out of their niche and commit to differentiation without self-renewal. The stem cells left behind in the niche self-renew symmetrically and randomly segregate the chromosomes at each division, making more stem cells. This model seems to apply to at least a few other vertebrate tissue stem cells in vivo.
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Affiliation(s)
- Sanjeev K Waghmare
- Advanced Centre for Treatment, Research and Education in Cancer ACTREC, Tata Memorial Centre, Navi Mumbai, 410210, India.
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Donnelly N, Storchová Z. Dynamic karyotype, dynamic proteome: buffering the effects of aneuploidy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:473-81. [DOI: 10.1016/j.bbamcr.2013.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 12/18/2022]
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Mulla W, Zhu J, Li R. Yeast: a simple model system to study complex phenomena of aneuploidy. FEMS Microbiol Rev 2013; 38:201-12. [PMID: 24118136 DOI: 10.1111/1574-6976.12048] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/29/2013] [Accepted: 09/30/2013] [Indexed: 12/29/2022] Open
Abstract
Aneuploidy, the state of having a chromosome number different from a multiple of the haploid number, has been associated with diseases and developmental disorders. The role of aneuploidy in human disease pathology, especially in cancer, has been a subject of much attention and debate over the last century due to the intrinsic complexity of the phenomena and experimental challenges. Over the last decade, yeast has been an invaluable model for driving discoveries about the genetic and molecular aspects of aneuploidy. The understanding of aneuploidy has been significantly improved owing to the methods for selectively generating aneuploid yeast strains without causing other genetic changes, techniques for detecting aneuploidy, and cutting-edge genetics and 'omics' approaches. In this review, we discuss the contribution of studies in yeast to current knowledge about aneuploidy. Special emphasis is placed on experimental features that make yeast a simpler and efficient model to investigate the complex questions in the field of aneuploidy.
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Affiliation(s)
- Wahid Mulla
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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Construction of ploidy series of Saccharomyces cerevisiae by the plasmid YCplac33-GHK. ACTA ACUST UNITED AC 2013; 40:393-7. [DOI: 10.1007/s10295-013-1241-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/02/2013] [Indexed: 10/27/2022]
Abstract
Abstract
An effective approach, using the plasmid YCplac33-GHK, is developed to construct a ploidy series of Saccharomyces cerevisiae. YCplac33-GHK harbors the HO gene under the control of galactose-inducible promoter and KanMX4 as the selective marker. The simple method can solve the problem of industrial applications of strains with resistance genes.
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9
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Dunn B, Paulish T, Stanbery A, Piotrowski J, Koniges G, Kroll E, Louis EJ, Liti G, Sherlock G, Rosenzweig F. Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. PLoS Genet 2013; 9:e1003366. [PMID: 23555283 PMCID: PMC3605161 DOI: 10.1371/journal.pgen.1003366] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 01/20/2013] [Indexed: 12/17/2022] Open
Abstract
Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ~1-kb region of chromosome 14, and all producing an "interspecific fusion junction" within the MEP2 gene coding sequence, such that the 5' portion derives from S. cerevisiae and the 3' portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not require repeated backcrossing to one of the parental species.
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Affiliation(s)
- Barbara Dunn
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Terry Paulish
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Alison Stanbery
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Jeff Piotrowski
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Chemical Genomics Research Group, RIKEN Advance Science Institute, Wako, Japan
| | - Gregory Koniges
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Evgueny Kroll
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Edward J. Louis
- Center of Genetics and Genomics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Gianni Liti
- Center of Genetics and Genomics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (GS); (FR)
| | - Frank Rosenzweig
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- * E-mail: (GS); (FR)
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11
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Alabrudzinska M, Skoneczny M, Skoneczna A. Diploid-specific [corrected] genome stability genes of S. cerevisiae: genomic screen reveals haploidization as an escape from persisting DNA rearrangement stress. PLoS One 2011; 6:e21124. [PMID: 21695049 PMCID: PMC3117874 DOI: 10.1371/journal.pone.0021124] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 05/19/2011] [Indexed: 12/11/2022] Open
Abstract
Maintaining a stable genome is one of the most important tasks of every living cell and the mechanisms ensuring it are similar in all of them. The events leading to changes in DNA sequence (mutations) in diploid cells occur one to two orders of magnitude more frequently than in haploid cells. The majority of those events lead to loss of heterozygosity at the mutagenesis marker, thus diploid-specific genome stability mechanisms can be anticipated. In a new global screen for spontaneous loss of function at heterozygous forward mutagenesis marker locus, employing three different mutagenesis markers, we selected genes whose deletion causes genetic instability in diploid Saccharomyces cerevisiae cells. We have found numerous genes connected with DNA replication and repair, remodeling of chromatin, cell cycle control, stress response, and in particular the structural maintenance of chromosome complexes. We have also identified 59 uncharacterized or dubious ORFs, which show the genome instability phenotype when deleted. For one of the strongest mutators revealed in our screen, ctf18Δ/ctf18Δ the genome instability manifests as a tendency to lose the whole set of chromosomes. We postulate that this phenomenon might diminish the devastating effects of DNA rearrangements, thereby increasing the cell's chances of surviving stressful conditions. We believe that numerous new genes implicated in genome maintenance, together with newly discovered phenomenon of ploidy reduction, will help revealing novel molecular processes involved in the genome stability of diploid cells. They also provide the clues in the quest for new therapeutic targets to cure human genome instability-related diseases.
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Affiliation(s)
- Malgorzata Alabrudzinska
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, Warsaw, Poland
- * E-mail:
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Different aneuploidies arise from the same bridge-induced chromosomal translocation event in Saccharomyces cerevisiae. Genetics 2010; 186:775-90. [PMID: 20805555 DOI: 10.1534/genetics.110.120683] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Chromosome translocations are gross chromosomal rearrangements that have often been associated with cancer development in mammalian cells. The feasibility of drastically reshaping the genome with a single translocation event also gives this molecular event a powerful capacity to drive evolution. Despite these implications and their role in genome instability, very little is known about the molecular mechanisms that promote and accompany these events. Here, at the molecular level, we describe 10 morphologically and physiologically different translocants ensuing from the induction of the same bridge-induced translocation (BIT) event in the budding yeast Saccharomyces cerevisiae. We have demonstrated that, despite their common origin from the integration of the same linear DNA construct, all 10 translocation mutant strains have different phenotypes and the ability to sporulate and regulate gene expression and morphology. We also provide insights into how heterogeneous phenotypic variations originate from the same initial genomic event. Here we show eight different ways in which yeast cells have dealt with a single initial event inducing translocation. Our results are in agreement with the formation of complex rearrangements and abnormal karyotypes described in many leukemia patients, thus confirming the modellistic value of the yeast BIT system for mammalian cells.
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Hou L, Cao X, Wang C. A novel approach for the improvement of ethanol fermentation by Saccharomyces cerevisiae. Can J Microbiol 2010; 56:495-500. [DOI: 10.1139/w10-032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fermentation properties under the control of multiple genes are difficult to alter with traditional methods in Saccharomyces cerevisiae . Here, a novel genome engineering approach is developed to improve ethanol production in very high gravity fermentation with 300 g/L glucose as the carbon source. This strategy involved constructing aneuploid strains on the base of tetraploid cells. The tetraploid strain was constructed by using the plasmid YCplac33-GHK, which harbored the HO gene encoding the site-specific Ho endonucleases. The aneuploid strain, WT4-M, was selected and screened after the tetraploid cells were treated with methyl benzimidazole-2-yl-carbamate to induce loss of mitotic chromosomes. It was found that aneuploid strain WT4-M not only exhibited an increase in ethanol production and osmotic and thermal tolerance, but also an improvement in the sugar–ethanol conversion rate. Notably, WT4-M provided up to 9.8% improvement in ethanol production compared with the control strain. The results demonstrated that the strategy of aneuploidy was valuable for creating yeast strains with better fermentation characteristics.
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Affiliation(s)
- Lihua Hou
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin 300457, P.R. China
| | - Xiaohong Cao
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin 300457, P.R. China
| | - Chunling Wang
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin 300457, P.R. China
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Wu X, Strome ED, Meng Q, Hastings PJ, Plon SE, Kimmel M. A robust estimator of mutation rates. Mutat Res 2009; 661:101-109. [PMID: 19100753 DOI: 10.1016/j.mrfmmm.2008.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 11/13/2008] [Accepted: 11/21/2008] [Indexed: 05/27/2023]
Abstract
Fluctuation analysis is an established and widely used technique of estimating mutation rates in cultured cells. This paper presents a modified median estimator of mutation rates, which is novel because it allows for unequal population sizes N(t) of the parallel cultures, and helps to detect and reduce the estimation variability. Simulation results show a good accuracy and robustness of the modified median estimator compared with the median estimator and the maximum likelihood estimator. The proposed estimator, based on the Luria-Delbrück model, is applied to 20 yeast datasets collected during 3 different days for a study of chromosome loss and recombination in wild-type Saccharomyces cerevisiae strains. The estimates obtained display among-experiment variability, which is inflated with respect to the model predictions on simulated data. Further investigation in S. cerevisiae and Escherichia coli uncovers an empirical inverse relationship between the population sizes N(t) and the mutation rate estimates under certain experimental conditions. The impact of these effects on the practice of fluctuation analysis is discussed.
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Affiliation(s)
- Xiaowei Wu
- Department of Statistics, Rice University, Houston, TX 77005, USA.
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DNA bridging of yeast chromosomes VIII leads to near-reciprocal translocation and loss of heterozygosity with minor cellular defects. Chromosoma 2008; 118:179-91. [PMID: 19015868 DOI: 10.1007/s00412-008-0187-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 08/12/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
Abstract
Loss of heterozygosity (LOH) of tumor suppressor genes in somatic cells is a major process leading to several types of cancer; however, its underlying molecular mechanism is still poorly understood. In the present work, we demonstrate that a linear DNA molecule bridging two homologous chromosomes in diploid yeast cells via homologous recombination produce LOH-generating regions of hemizygosity by deletion. The result is a near-reciprocal translocation mutant that is characterized by slight cell cycle defects and increased expression of the multidrug-resistant gene VMR1. When the distance between target regions is approximately 40 kb, the specificity of gene targeting becomes less stringent and an ensemble of gross chromosomal rearrangements arises. These heterogeneous genomic events, together with the low frequency of specific translocation, confirm that several pathways contribute to the healing of a broken chromosome and suggest that uncontrolled recombination between parental homologs is actively avoided by the cell. Moreover, this work demonstrates that the common laboratory practice of making targeted gene deletions may result in a low, but not negligible, frequency of LOH due to the recombination events triggered between homologous chromosomes in mitosis.
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Abstract
Loss of heterozygosity (LOH) can be a driving force in the evolution of mitotic/somatic diploid cells, and cellular changes that increase the rate of LOH have been proposed to facilitate this process. In the yeast Saccharomyces cerevisiae, spontaneous LOH occurs by a number of mechanisms including chromosome loss and reciprocal and nonreciprocal recombination. We performed a screen in diploid yeast to identify mutants with increased rates of LOH using the collection of homozygous deletion alleles of nonessential genes. Increased LOH was quantified at three loci (MET15, SAM2, and MAT) on three different chromosomes, and the LOH events were analyzed as to whether they were reciprocal or nonreciprocal in nature. Nonreciprocal LOH was further characterized as chromosome loss or truncation, a local mutational event (gene conversion or point mutation), or break-induced replication (BIR). The 61 mutants identified could be divided into several groups, including ones that had locus-specific effects. Mutations in genes involved in DNA replication and chromatin assembly led to LOH predominantly via reciprocal recombination. In contrast, nonreciprocal LOH events with increased chromosome loss largely resulted from mutations in genes implicated in kinetochore function, sister chromatid cohesion, or relatively late steps of DNA recombination. Mutants of genes normally involved in early steps of DNA damage repair and signaling produced nonreciprocal LOH without an increased proportion of chromosome loss. Altogether, this study defines a genetic landscape for the basis of increased LOH and the processes by which it occurs.
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Laun P, Bruschi CV, Dickinson JR, Rinnerthaler M, Heeren G, Schwimbersky R, Rid R, Breitenbach M. Yeast mother cell-specific ageing, genetic (in)stability, and the somatic mutation theory of ageing. Nucleic Acids Res 2007; 35:7514-26. [PMID: 17986449 PMCID: PMC2190697 DOI: 10.1093/nar/gkm919] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Yeast mother cell-specific ageing is characterized by a limited capacity to produce daughter cells. The replicative lifespan is determined by the number of cell cycles a mother cell has undergone, not by calendar time, and in a population of cells its distribution follows the Gompertz law. Daughter cells reset their clock to zero and enjoy the full lifespan characteristic for the strain. This kind of replicative ageing of a cell population based on asymmetric cell divisions is investigated as a model for the ageing of a stem cell population in higher organisms. The simple fact that the daughter cells can reset their clock to zero precludes the accumulation of chromosomal mutations as the cause of ageing, because semiconservative replication would lead to the same mutations in the daughters. However, nature is more complicated than that because, (i) the very last daughters of old mothers do not reset the clock; and (ii) mutations in mitochondrial DNA could play a role in ageing due to the large copy number in the cell and a possible asymmetric distribution of damaged mitochondrial DNA between mother and daughter cell. Investigation of the loss of heterozygosity in diploid cells at the end of their mother cell-specific lifespan has shown that genomic rearrangements do occur in old mother cells. However, it is not clear if this kind of genomic instability is causative for the ageing process. Damaged material other than DNA, for instance misfolded, oxidized or otherwise damaged proteins, seem to play a major role in ageing, depending on the balance between production and removal through various repair processes, for instance several kinds of proteolysis and autophagy. We are reviewing here the evidence for genetic change and its causality in the mother cell-specific ageing process of yeast.
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Affiliation(s)
- Peter Laun
- Department of Cell Biology, Division of Genetics, University of Salzburg, Austria.
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18
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Affiliation(s)
- Prasad V Jallepalli
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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19
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Edwards-Ingram L, Gitsham P, Burton N, Warhurst G, Clarke I, Hoyle D, Oliver SG, Stateva L. Genotypic and physiological characterization of Saccharomyces boulardii, the probiotic strain of Saccharomyces cerevisiae. Appl Environ Microbiol 2007; 73:2458-67. [PMID: 17293506 PMCID: PMC1855594 DOI: 10.1128/aem.02201-06] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Saccharomyces boulardii, a yeast that was isolated from fruit in Indochina, has been used as a remedy for diarrhea since 1950 and is now a commercially available treatment throughout Europe, Africa, and South America. Though initially classified as a separate species of Saccharomyces, recent publications have shown that the genome of S. boulardii is so similar to Saccharomyces cerevisiae that the two should be classified as conspecific. This raises the question of the distinguishing molecular and phenotypic characteristics present in S. boulardii that make it perform more effectively as a probiotic organism compared to other strains of S. cerevisiae. This investigation reports some of these distinguishing characteristics including enhanced ability for pseudohyphal switching upon nitrogen limitation and increased resistance to acidic pH. However, these differences did not correlate with increased adherence to epithelial cells or transit through mouse gut. Pertinent characteristics of the S. boulardii genome such as trisomy of chromosome IX, altered copy number of a number of individual genes, and sporulation deficiency have been revealed by comparative genome hybridization using oligonucleotide-based microarrays coupled with a rigorous statistical analysis. The contributions of the different genomic and phenotypic features of S. boulardii to its probiotic nature are discussed.
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Affiliation(s)
- Laura Edwards-Ingram
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
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Current awareness on yeast. Yeast 2005; 22:1249-56. [PMID: 16320446 DOI: 10.1002/yea.1170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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