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Bennett RJ, Forche A, Berman J. Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb Perspect Med 2014; 4:cshperspect.a019604. [PMID: 25081629 DOI: 10.1101/cshperspect.a019604] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Human fungal pathogens can exist in a variety of ploidy states, including euploid and aneuploid forms. Ploidy change has a major impact on phenotypic properties, including the regulation of interactions with the human host. In addition, the rapid emergence of drug-resistant isolates is often associated with the formation of specific supernumerary chromosomes. Pathogens such as Candida albicans and Cryptococcus neoformans appear particularly well adapted for propagation in multiple ploidy states with novel pathways driving ploidy variation. In both species, heterozygous cells also readily undergo loss of heterozygosity (LOH), leading to additional phenotypic changes such as altered drug resistance. Here, we examine the sexual and parasexual cycles that drive ploidy variation in human fungal pathogens and discuss ploidy and LOH events with respect to their far-reaching roles in fungal adaptation and pathogenesis.
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Affiliation(s)
- Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, Maine 04011
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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Gostinčar C, Ohm RA, Kogej T, Sonjak S, Turk M, Zajc J, Zalar P, Grube M, Sun H, Han J, Sharma A, Chiniquy J, Ngan CY, Lipzen A, Barry K, Grigoriev IV, Gunde-Cimerman N. Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. BMC Genomics 2014; 15:549. [PMID: 24984952 PMCID: PMC4227064 DOI: 10.1186/1471-2164-15-549] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/20/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Aureobasidium pullulans is a black-yeast-like fungus used for production of the polysaccharide pullulan and the antimycotic aureobasidin A, and as a biocontrol agent in agriculture. It can cause opportunistic human infections, and it inhabits various extreme environments. To promote the understanding of these traits, we performed de-novo genome sequencing of the four varieties of A. pullulans. RESULTS The 25.43-29.62 Mb genomes of these four varieties of A. pullulans encode between 10266 and 11866 predicted proteins. Their genomes encode most of the enzyme families involved in degradation of plant material and many sugar transporters, and they have genes possibly associated with degradation of plastic and aromatic compounds. Proteins believed to be involved in the synthesis of pullulan and siderophores, but not of aureobasidin A, are predicted. Putative stress-tolerance genes include several aquaporins and aquaglyceroporins, large numbers of alkali-metal cation transporters, genes for the synthesis of compatible solutes and melanin, all of the components of the high-osmolarity glycerol pathway, and bacteriorhodopsin-like proteins. All of these genomes contain a homothallic mating-type locus. CONCLUSIONS The differences between these four varieties of A. pullulans are large enough to justify their redefinition as separate species: A. pullulans, A. melanogenum, A. subglaciale and A. namibiae. The redundancy observed in several gene families can be linked to the nutritional versatility of these species and their particular stress tolerance. The availability of the genome sequences of the four Aureobasidium species should improve their biotechnological exploitation and promote our understanding of their stress-tolerance mechanisms, diverse lifestyles, and pathogenic potential.
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Affiliation(s)
- Cene Gostinčar
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
- />National Institute of Biology, Večna pot 111, Ljubljana, SI 1000 Slovenia
| | - Robin A Ohm
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Tina Kogej
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
| | - Silva Sonjak
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
| | - Martina Turk
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
| | - Janja Zajc
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
| | - Polona Zalar
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
| | - Martin Grube
- />Institute of Plant Sciences, Karl-Franzens-University Graz, Holteigasse 6, Graz, A-8010 Austria
| | - Hui Sun
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - James Han
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Aditi Sharma
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Jennifer Chiniquy
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Chew Yee Ngan
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Kerrie Barry
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Igor V Grigoriev
- />US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598 USA
| | - Nina Gunde-Cimerman
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI 1000 Slovenia
- />Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova 39, Ljubljana, SI 1000 Slovenia
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Veselská T, Svoboda J, Růžičková Ž, Kolařík M. Application of flow cytometry for genome size determination inGeosmithiafungi: A comparison of methods. Cytometry A 2014; 85:854-61. [DOI: 10.1002/cyto.a.22500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 04/18/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Tereza Veselská
- Department of Botany; Faculty of Science; Charles University; Czech Republic
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
| | - Jan Svoboda
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
| | - Žaneta Růžičková
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
| | - Miroslav Kolařík
- Department of Botany; Faculty of Science; Charles University; Czech Republic
- Institute of Microbiology of the ASCR; 142 20 Praha 4 Czech Republic
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104
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Solieri L, Dakal TC, Giudici P, Cassanelli S. Sex-determination system in the diploid yeast Zygosaccharomyces sapae. G3 (BETHESDA, MD.) 2014; 4:1011-25. [PMID: 24939186 PMCID: PMC4065246 DOI: 10.1534/g3.114.010405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/06/2014] [Indexed: 11/18/2022]
Abstract
Sexual reproduction and breeding systems are driving forces for genetic diversity. The mating-type (MAT) locus represents a mutation and chromosome rearrangement hotspot in yeasts. Zygosaccharomyces rouxii complex yeasts are naturally faced with hostile low water activity (aw) environments and are characterized by gene copy number variation, genome instability, and aneuploidy/allodiploidy. Here, we investigated sex-determination system in Zygosaccharomyces sapae diploid strain ABT301(T), a member of the Z. rouxii complex. We cloned three divergent mating type-like (MTL) α-idiomorph sequences and designated them as ZsMTLα copies 1, 2, and 3. They encode homologs of Z. rouxii CBS 732(T) MATα2 (amino acid sequence identities spanning from 67.0 to 99.5%) and MATα1 (identity range 81.5-99.5%). ABT301(T) possesses two divergent HO genes encoding distinct endonucleases 100% and 92.3% identical to Z. rouxii HO. Cloning of MATA: -idiomorph resulted in a single ZsMTLA: locus encoding two Z. rouxii-like proteins MATA: 1 and MATA: 2. To assign the cloned ZsMTLα and ZsMTLA: idiomorphs as MAT, HML, and HMR cassettes, we analyzed their flanking regions. Three ZsMTLα loci exhibited the DIC1-MAT-SLA2 gene order canonical for MAT expression loci. Furthermore, four putative HML cassettes were identified, two containing the ZsMTLα copy 1 and the remaining harboring ZsMTLα copies 2 and 3. Finally, the ZsMTLA: locus was 3'-flanked by SLA2, suggesting the status of MAT expression locus. In conclusion, Z. sapae ABT301(T) displays an aααα genotype missing of the HMR silent cassette. Our results demonstrated that mating-type switching is a hypermutagenic process in Z. rouxii complex that generates genetic diversity de novo. This error-prone mechanism could be suitable to generate progenies more rapidly adaptable to hostile environments.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Tikam Chand Dakal
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122, Reggio Emilia, Italy
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Covo S, Puccia CM, Argueso JL, Gordenin DA, Resnick MA. The sister chromatid cohesion pathway suppresses multiple chromosome gain and chromosome amplification. Genetics 2014; 196:373-84. [PMID: 24298060 PMCID: PMC3914611 DOI: 10.1534/genetics.113.159202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 11/18/2022] Open
Abstract
Gain or loss of chromosomes resulting in aneuploidy can be important factors in cancer and adaptive evolution. Although chromosome gain is a frequent event in eukaryotes, there is limited information on its genetic control. Here we measured the rates of chromosome gain in wild-type yeast and sister chromatid cohesion (SCC) compromised strains. SCC tethers the newly replicated chromatids until anaphase via the cohesin complex. Chromosome gain was measured by selecting and characterizing copper-resistant colonies that emerged due to increased copies of the metallothionein gene CUP1. Although all defective SCC diploid strains exhibited increased rates of chromosome gain, there were 15-fold differences between them. Of all mutants examined, a hypomorphic mutation at the cohesin complex caused the highest rate of chromosome gain while disruption of WPL1, an important regulator of SCC and chromosome condensation, resulted in the smallest increase in chromosome gain. In addition to defects in SCC, yeast cell type contributed significantly to chromosome gain, with the greatest rates observed for homozygous mating-type diploids, followed by heterozygous mating type, and smallest in haploids. In fact, wpl1-deficient haploids did not show any difference in chromosome gain rates compared to wild-type haploids. Genomic analysis of copper-resistant colonies revealed that the "driver" chromosome for which selection was applied could be amplified to over five copies per diploid cell. In addition, an increase in the expected driver chromosome was often accompanied by a gain of a small number of other chromosomes. We suggest that while chromosome gain due to SCC malfunction can have negative effects through gene imbalance, it could also facilitate opportunities for adaptive changes. In multicellular organisms, both factors could lead to somatic diseases including cancer.
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Affiliation(s)
- Shay Covo
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Christopher M. Puccia
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Dmitry A. Gordenin
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael A. Resnick
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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106
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Alcasabas AA, de Clare M, Pir P, Oliver SG. Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids. BMC Genomics 2013; 14:744. [PMID: 24176122 PMCID: PMC3826841 DOI: 10.1186/1471-2164-14-744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/18/2013] [Indexed: 11/29/2022] Open
Abstract
Background In the model eukaryote, Saccharomyces cerevisiae, previous experiments have identified those genes that exert the most significant control over cell growth rate. These genes are termed HFC for high flux control. Such genes are overrepresented within pathways controlling the mitotic cell cycle. Results We postulated that the increase/decrease in growth rate is due to a change in the rate of progression through specific cell cycle steps. We extended and further developed an existing logical model of the yeast cell cycle in order elucidate how the HFC genes modulated progress through the cycle. This model can simulate gene dosage-variation and calculate the cycle time, determine the order and relative speed at which events occur, and predict arrests and failures to correctly execute a step. To experimentally test our model’s predictions, we constructed a tetraploid series of deletion mutants for a set of eight genes that control the G2/M transition. This system allowed us to vary gene copy number through more intermediate levels than previous studies and examine the impact of copy-number variation on growth, cell-cycle phenotype, and response to different cellular stresses. Conclusions For the majority of strains, the predictions agreed with experimental observations, validating our model and its use for further predictions. Where simulation and experiment diverged, we uncovered both novel tetraploid-specific phenotypes and a switch in the determinative execution point of a key cell-cycle regulator, the Cdc28 kinase, from the G1/S to the S/G2 boundaries.
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Affiliation(s)
| | | | | | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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Abstract
Candida species exhibit a variety of ploidy states and modes of sexual reproduction. Most species possess the requisite genes for sexual reproduction, recombination, and meiosis, yet only a few have been reported to undergo a complete sexual cycle including mating and sporulation. Candida albicans, the most studied Candida species and a prevalent human fungal pathogen, completes its sexual cycle via a parasexual process of concerted chromosome loss rather than a conventional meiosis. In this study, we examine ploidy changes in Candida tropicalis, a closely related species to C. albicans that was recently revealed to undergo sexual mating. C. tropicalis diploid cells mate to form tetraploid cells, and we show that these can be induced to undergo chromosome loss to regenerate diploid forms by growth on sorbose medium. The diploid products are themselves mating competent, thereby establishing a parasexual cycle in this species for the first time. Extended incubation (>120 generations) of C. tropicalis tetraploid cells under rich culture conditions also resulted in instability of the tetraploid form and a gradual reduction in ploidy back to the diploid state. The fitness levels of C. tropicalis diploid and tetraploid cells were compared, and diploid cells exhibited increased fitness relative to tetraploid cells in vitro, despite diploid and tetraploid cells having similar doubling times. Collectively, these experiments demonstrate distinct pathways by which a parasexual cycle can occur in C. tropicalis and indicate that nonmeiotic mechanisms drive ploidy changes in this prevalent human pathogen.
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108
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Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J 2013; 8:1017-34. [PMID: 24031036 PMCID: PMC3910164 DOI: 10.1002/biot.201300138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/15/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Abstract
There is an increasing use of systems biology approaches in both "red" and "white" biotechnology in order to enable medical, medicinal, and industrial applications. The intricate links between genotype and phenotype may be explained through the use of the tools developed in systems biology, synthetic biology, and evolutionary engineering. Biomedical and biotechnological research are among the fields that could benefit most from the elucidation of this complex relationship. Researchers have studied fitness extensively to explain the phenotypic impacts of genetic variations. This elaborate network of dependencies and relationships so revealed are further complicated by the influence of environmental effects that present major challenges to our achieving an understanding of the cellular mechanisms leading to healthy or diseased phenotypes or optimized production yields. An improved comprehension of complex genotype-phenotype interactions and their accurate prediction should enable us to more effectively engineer yeast as a cell factory and to use it as a living model of human or pathogen cells in intelligent screens for new drugs. This review presents different methods and approaches undertaken toward improving our understanding and prediction of the growth phenotype of the yeast Saccharomyces cerevisiae as both a model and a production organism.
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Affiliation(s)
- Duygu Dikicioglu
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
| | - Pınar Pir
- Babraham Institute, Babraham Research Campus, CB22 3AT, Cambridge, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
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109
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Demeke MM, Dumortier F, Li Y, Broeckx T, Foulquié-Moreno MR, Thevelein JM. Combining inhibitor tolerance and D-xylose fermentation in industrial Saccharomyces cerevisiae for efficient lignocellulose-based bioethanol production. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:120. [PMID: 23971950 PMCID: PMC3765968 DOI: 10.1186/1754-6834-6-120] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/20/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND In addition to efficient pentose utilization, high inhibitor tolerance is a key trait required in any organism used for economically viable industrial bioethanol production with lignocellulose biomass. Although recent work has succeeded in establishing efficient xylose fermentation in robust industrial Saccharomyces cerevisiae strains, the resulting strains still lacked sufficient inhibitor tolerance for efficient sugar fermentation in lignocellulose hydrolysates. The aim of the present work was to combine high xylose fermentation activity and high inhibitor tolerance in a single industrial yeast strain. RESULTS We have screened 580 yeast strains for high inhibitor tolerance using undetoxified acid-pretreated spruce hydrolysate and identified a triploid industrial baker's yeast strain as having the highest inhibitor tolerance. From this strain, a mating competent diploid segregant with even higher inhibitor tolerance was obtained. It was crossed with the recently developed D-xylose fermenting diploid industrial strain GS1.11-26, with the Ethanol Red genetic background. Screening of 819 diploid segregants from the tetraploid hybrid resulted in two strains, GSF335 and GSF767, combining high inhibitor tolerance and efficient xylose fermentation. In a parallel approach, meiotic recombination of GS1.11-26 with a haploid segregant of Ethanol Red and screening of 104 segregants resulted in a similar inhibitor tolerant diploid strain, GSE16. The three superior strains exhibited significantly improved tolerance to inhibitors in spruce hydrolysate, higher glucose consumption rates, higher aerobic growth rates and higher maximal ethanol accumulation capacity in very-high gravity fermentation, compared to GS1.11-26. In complex medium, the D-xylose utilization rate by the three superior strains ranged from 0.36 to 0.67 g/g DW/h, which was lower than that of GS1.11-26 (1.10 g/g DW/h). On the other hand, in batch fermentation of undetoxified acid-pretreated spruce hydrolysate, the three superior strains showed comparable D-xylose utilization rates as GS1.11-26, probably because of their higher inhibitor tolerance. They produced up to 23% more ethanol compared to Ethanol Red. CONCLUSIONS We have successfully constructed three superior industrial S. cerevisiae strains that combine efficient D-xylose utilization with high inhibitor tolerance. Since the background strain Ethanol Red has a proven record of successful industrial application, the three new superior strains have strong potential for direct application in industrial bioethanol production.
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Affiliation(s)
- Mekonnen M Demeke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Françoise Dumortier
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Yingying Li
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Tom Broeckx
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
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Lenassi M, Gostinčar C, Jackman S, Turk M, Sadowski I, Nislow C, Jones S, Birol I, Cimerman NG, Plemenitaš A. Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii. PLoS One 2013; 8:e71328. [PMID: 23977017 PMCID: PMC3744574 DOI: 10.1371/journal.pone.0071328] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/27/2013] [Indexed: 01/14/2023] Open
Abstract
Hortaea werneckii, ascomycetous yeast from the order Capnodiales, shows an exceptional adaptability to osmotically stressful conditions. To investigate this unusual phenotype we obtained a draft genomic sequence of a H. werneckii strain isolated from hypersaline water of solar saltern. Two of its most striking characteristics that may be associated with a halotolerant lifestyle are the large genetic redundancy and the expansion of genes encoding metal cation transporters. Although no sexual state of H. werneckii has yet been described, a mating locus with characteristics of heterothallic fungi was found. The total assembly size of the genome is 51.6 Mb, larger than most phylogenetically related fungi, coding for almost twice the usual number of predicted genes (23333). The genome appears to have experienced a relatively recent whole genome duplication, and contains two highly identical gene copies of almost every protein. This is consistent with some previous studies that reported increases in genomic DNA content triggered by exposure to salt stress. In hypersaline conditions transmembrane ion transport is of utmost importance. The analysis of predicted metal cation transporters showed that most types of transporters experienced several gene duplications at various points during their evolution. Consequently they are present in much higher numbers than expected. The resulting diversity of transporters presents interesting biotechnological opportunities for improvement of halotolerance of salt-sensitive species. The involvement of plasma P-type H⁺ ATPases in adaptation to different concentrations of salt was indicated by their salt dependent transcription. This was not the case with vacuolar H⁺ ATPases, which were transcribed constitutively. The availability of this genomic sequence is expected to promote the research of H. werneckii. Studying its extreme halotolerance will not only contribute to our understanding of life in hypersaline environments, but should also identify targets for improving the salt- and osmotolerance of economically important plants and microorganisms.
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Affiliation(s)
- Metka Lenassi
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
- * E-mail:
| | - Cene Gostinčar
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Shaun Jackman
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martina Turk
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivan Sadowski
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Inanc Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Nina Gunde Cimerman
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Tofalo R, Perpetuini G, Schirone M, Fasoli G, Aguzzi I, Corsetti A, Suzzi G. Biogeographical characterization of Saccharomyces cerevisiae wine yeast by molecular methods. Front Microbiol 2013; 4:166. [PMID: 23805132 PMCID: PMC3690337 DOI: 10.3389/fmicb.2013.00166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/03/2013] [Indexed: 11/16/2022] Open
Abstract
Biogeography is the descriptive and explanatory study of spatial patterns and processes involved in the distribution of biodiversity. Without biogeography, it would be difficult to study the diversity of microorganisms because there would be no way to visualize patterns in variation. Saccharomyces cerevisiae, "the wine yeast," is the most important species involved in alcoholic fermentation, and in vineyard ecosystems, it follows the principle of "everything is everywhere." Agricultural practices such as farming (organic versus conventional) and floor management systems have selected different populations within this species that are phylogenetically distinct. In fact, recent ecological and geographic studies highlighted that unique strains are associated with particular grape varieties in specific geographical locations. These studies also highlighted that significant diversity and regional character, or 'terroir,' have been introduced into the winemaking process via this association. This diversity of wild strains preserves typicity, the high quality, and the unique flavor of wines. Recently, different molecular methods were developed to study population dynamics of S. cerevisiae strains in both vineyards and wineries. In this review, we will provide an update on the current molecular methods used to reveal the geographical distribution of S. cerevisiae wine yeast.
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Affiliation(s)
- Rosanna Tofalo
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of TeramoMosciano Sant’Angelo, TE, Italy
| | | | | | | | | | | | - Giovanna Suzzi
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of TeramoMosciano Sant’Angelo, TE, Italy
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Bellon JR, Schmid F, Capone DL, Dunn BL, Chambers PJ. Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae. PLoS One 2013; 8:e62053. [PMID: 23614011 PMCID: PMC3629166 DOI: 10.1371/journal.pone.0062053] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/18/2013] [Indexed: 11/19/2022] Open
Abstract
Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.
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113
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Zörgö E, Chwialkowska K, Gjuvsland AB, Garré E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J. Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genet 2013; 9:e1003388. [PMID: 23555297 PMCID: PMC3605057 DOI: 10.1371/journal.pgen.1003388] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/31/2013] [Indexed: 11/18/2022] Open
Abstract
The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy–environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%–17% of ploidy–environment interactions. The mechanism of the cell size–based superior reproductive efficiency of haploids during Li+ exposure was traced to the Li+ exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li+ tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots. Organisms vary in the number of chromosome sets contained within the nucleus of each cell, but neither the reasons nor the consequences of this variation are well understood. We designed yeasts that differed in the number of chromosome sets but were otherwise identical and mapped the consequences of such ploidy variations during exposure to a large palette of environments. Contrary to commonly held assumptions, we found ploidy effects on the mitotic reproductive capacity of yeast to be the rule rather than the exception and to be highly evolutionarily conserved. Furthermore, our data rejected previously contemplated hypotheses of generalizable advantages of haploidy or diploidy when cells face nutrient starvation or are exposed to toxins or increased mutation rates. We also mapped the molecular processes mediating ploidy–environment interactions, showing that cell size and mating type locus composition had equal explanatory power. Finally we show that ploidy effects can be mechanistically very subtle, as a designed shift from one plasma membrane Li+ transporter to another completely altered the relative merits of having one or two chromosome sets when exposed to high Li+ concentrations. This complex and dynamic interplay between the number of chromosomes sets and the fluctuating environment must be taken into account when considering organismal form and behavior.
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Affiliation(s)
- Enikö Zörgö
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karolina Chwialkowska
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Arne B. Gjuvsland
- Centre for Integrative Genetics (CIGENE), Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences (UMB), Ås, Norway
| | - Elena Garré
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, Nice, France
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stig W. Omholt
- NTNU Norwegian University of Science and Technology, Faculty of Natural Sciences and Technology, Department of Biotechnology, Trondheim, Norway
| | - Jonas Warringer
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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114
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Randez-Gil F, Córcoles-Sáez I, Prieto JA. Genetic and Phenotypic Characteristics of Baker's Yeast: Relevance to Baking. Annu Rev Food Sci Technol 2013; 4:191-214. [DOI: 10.1146/annurev-food-030212-182609] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Francisca Randez-Gil
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
| | - Isaac Córcoles-Sáez
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
| | - José A. Prieto
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, 46980 Paterna, Valencia, Spain;
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115
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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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116
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Neiman M, Kay AD, Krist AC. Can resource costs of polyploidy provide an advantage to sex? Heredity (Edinb) 2013; 110:152-9. [PMID: 23188174 PMCID: PMC3554456 DOI: 10.1038/hdy.2012.78] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/26/2012] [Accepted: 08/01/2012] [Indexed: 12/26/2022] Open
Abstract
The predominance of sexual reproduction despite its costs indicates that sex provides substantial benefits, which are usually thought to derive from the direct genetic consequences of recombination and syngamy. While genetic benefits of sex are certainly important, sexual and asexual individuals, lineages, or populations may also differ in physiological and life history traits that could influence outcomes of competition between sexuals and asexuals across environmental gradients. Here, we address possible phenotypic costs of a very common correlate of asexuality, polyploidy. We suggest that polyploidy could confer resource costs related to the dietary phosphorus demands of nucleic acid production; such costs could facilitate the persistence of sex in situations where asexual taxa are of higher ploidy level and phosphorus availability limits important traits like growth and reproduction. We outline predictions regarding the distribution of diploid sexual and polyploid asexual taxa across biogeochemical gradients and provide suggestions for study systems and empirical approaches for testing elements of our hypothesis.
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Affiliation(s)
- M Neiman
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
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117
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Kondrashov FA. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc Biol Sci 2012; 279:5048-57. [PMID: 22977152 PMCID: PMC3497230 DOI: 10.1098/rspb.2012.1108] [Citation(s) in RCA: 386] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/21/2012] [Indexed: 01/13/2023] Open
Abstract
A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.
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Affiliation(s)
- Fyodor A Kondrashov
- Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, 88 Dr Aiguader, Barcelona 08003, Spain.
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118
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Jasmin JN, Dillon MM, Zeyl C. The yield of experimental yeast populations declines during selection. Proc Biol Sci 2012; 279:4382-8. [PMID: 22951743 DOI: 10.1098/rspb.2012.1659] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The trade-off between growth rate and yield can limit population productivity. Here we tested for this life-history trade-off in replicate haploid and diploid populations of Saccharomyces cerevisiae propagated in glucose-limited medium in batch cultures for 5000 generations. The yield of single clones isolated from the haploid lineages, measured as both optical and population density at the end of a growth cycle, declined during selection and was negatively correlated with growth rate. Initially, diploid populations did not pay this cost of adaptation but haploidized after about 1000-3000 generations of selection, and this ploidy transition was associated with a decline in yield caused by reduced cell size. These results demonstrate the experimental evolution of a trade-off between growth rate and yield, caused by antagonistic pleiotropy, during adaptation in haploids and after an adaptive transition from diploidy to haploidy.
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Affiliation(s)
- Jean-Nicolas Jasmin
- Department of Biology, Wake Forest University, Winston-Salem, NC 27106, USA.
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119
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Reis VCB, Nicola AM, de Souza Oliveira Neto O, Batista VDF, de Moraes LMP, Torres FAG. Genetic characterization and construction of an auxotrophic strain of Saccharomyces cerevisiae JP1, a Brazilian industrial yeast strain for bioethanol production. J Ind Microbiol Biotechnol 2012; 39:1673-83. [PMID: 22892884 DOI: 10.1007/s10295-012-1170-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/10/2012] [Indexed: 02/08/2023]
Abstract
Used for millennia to produce beverages and food, Saccharomyces cerevisiae also became a workhorse in the production of biofuels, most notably bioethanol. Yeast strains have acquired distinct characteristics that are the result of evolutionary adaptation to the stresses of industrial ethanol production. JP1 is a dominant industrial S. cerevisiae strain isolated from a sugarcane mill and is becoming increasingly popular for bioethanol production in Brazil. In this work, we carried out the genetic characterization of this strain and developed a set of tools to permit its genetic manipulation. Using flow cytometry, mating type, and sporulation analysis, we verified that JP1 is diploid and homothallic. Vectors with dominant selective markers for G418, hygromycin B, zeocin, and ρ-fluoro-DL-phenylalanine were used to successfully transform JP1 cells. Also, an auxotrophic ura3 mutant strain of JP1 was created by gene disruption using integration cassettes with dominant markers flanked by loxP sites. Marker excision was accomplished by the Cre/loxP system. The resulting auxotrophic strain was successfully transformed with an episomal vector that allowed green fluorescent protein expression.
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Affiliation(s)
- Viviane Castelo Branco Reis
- Centro de Biotecnologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil
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120
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Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, Whitlock MC. Experimental evolution. Trends Ecol Evol 2012; 27:547-60. [PMID: 22819306 DOI: 10.1016/j.tree.2012.06.001] [Citation(s) in RCA: 466] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/03/2012] [Accepted: 06/13/2012] [Indexed: 12/26/2022]
Abstract
Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions imposed by the experimenter. This research approach is increasingly used to study adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses. Long applied in vaccine development, experimental evolution also finds new applications in biotechnology. Recent technological developments provide a path towards detailed understanding of the genomic and molecular basis of experimental evolutionary change, while new findings raise new questions that can be addressed with this approach. However, experimental evolution has important limitations, and the interpretation of results is subject to caveats resulting from small population sizes, limited timescales, the simplified nature of laboratory environments, and, in some cases, the potential to misinterpret the selective forces and other processes at work.
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Affiliation(s)
- Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
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121
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Albertin W, Marullo P. Polyploidy in fungi: evolution after whole-genome duplication. Proc Biol Sci 2012; 279:2497-509. [PMID: 22492065 PMCID: PMC3350714 DOI: 10.1098/rspb.2012.0434] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 03/13/2012] [Indexed: 01/21/2023] Open
Abstract
Polyploidy is a major evolutionary process in eukaryotes-particularly in plants and, to a less extent, in animals, wherein several past and recent whole-genome duplication events have been described. Surprisingly, the incidence of polyploidy in other eukaryote kingdoms, particularly within fungi, remained largely disregarded by the scientific community working on the evolutionary consequences of polyploidy. Recent studies have significantly increased our knowledge of the occurrence and evolutionary significance of fungal polyploidy. The ecological, structural and functional consequences of polyploidy in fungi are reviewed here and compared with the knowledge acquired with conventional plant and animal models. In particular, the genus Saccharomyces emerges as a relevant model for polyploid studies, in addition to plant and animal models.
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Affiliation(s)
- Warren Albertin
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, 91190 Gif-sur-Yvette, France.
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122
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The Evolution of Low Mutation Rates in Experimental Mutator Populations of Saccharomyces cerevisiae. Curr Biol 2012; 22:1235-40. [DOI: 10.1016/j.cub.2012.04.056] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 02/01/2012] [Accepted: 04/26/2012] [Indexed: 01/05/2023]
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123
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Abstract
In the diploid cells of most organisms, including humans, each chromosome is usually distinguishable from its partner homolog by multiple single-nucleotide polymorphisms. One common type of genetic alteration observed in tumor cells is uniparental disomy (UPD), in which a pair of homologous chromosomes are derived from a single parent, resulting in loss of heterozygosity for all single-nucleotide polymorphisms while maintaining diploidy. Somatic UPD events are usually explained as reflecting two consecutive nondisjunction events. Here we report a previously undescribed mode of chromosome segregation in Saccharomyces cerevisiae in which one cell division produces daughter cells with reciprocal UPD for the same pair of chromosomes without an aneuploid intermediate. One pair of sister chromatids is segregated into one daughter cell and the other pair is segregated into the other daughter cell, mimicking a meiotic chromosome segregation pattern. We term this process "reciprocal uniparental disomy."
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124
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Evaluation of different genetic procedures for the generation of artificial hybrids in Saccharomyces genus for winemaking. Int J Food Microbiol 2012; 156:102-11. [DOI: 10.1016/j.ijfoodmicro.2012.03.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 03/04/2012] [Accepted: 03/07/2012] [Indexed: 11/20/2022]
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125
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Abstract
Diploid Saccharomyes cerevisae strains lacking the RAD52 gene required for homologous recombination have a very high rate of chromosome loss. Two of four isolates subcultured ∼20 times (∼500 cell divisions) became haploid. These strains were capable of mating with wild-type haploids to produce diploid progeny capable of undergoing meiosis to produce four viable spores.
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126
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Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, Neuvéglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 (BETHESDA, MD.) 2012; 2:299-311. [PMID: 22384408 PMCID: PMC3284337 DOI: 10.1534/g3.111.000745] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/16/2011] [Indexed: 12/19/2022]
Abstract
Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
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Affiliation(s)
| | - Laurence Despons
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Tiphaine Martin
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Pascal Durrens
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Serge Casarégola
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Cécile Neuvéglise
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR CNRS 8621, F-91405 Orsay CEDEX, France
| | - Christian Marck
- Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, F-91191 Gif-sur-Yvette CEDEX, France
| | - José A. Cruz
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | | | - Valérie Kugler
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Christine Sacerdot
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Zlatyo Uzunov
- Sofia University St. Kliment Ohridski, Faculty of Biology, Department of General and Applied Microbiology, 1164, Sofia, Bulgaria
| | - Agnes Thierry
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Stéphanie Weiss
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | | | | | - Noemie Jacques
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Paul Jung
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Marc Lemaire
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne; CNRS, UMR5240 Microbiologie, Adaptation et Pathogénie; INSA de Lyon, F-69621, Villeurbanne, France
| | - Sandrine Mallet
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Guillaume Morel
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Guy-Franck Richard
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Anasua Sarkar
- Université de Bordeaux 1, CNRS UMR5800, F-33405 Talence, France
| | - Guilhem Savel
- Université de Bordeaux 1, CNRS UMR5800, F-33405 Talence, France
| | | | - Marie-Line Seret
- Earth and Life Institute, Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Emmanuel Talla
- Université de la Méditerranée, Laboratoire de Chimie Bactérienne, CNRS-UPR9043, 31 chemin Joseph Aiguier, F-13402 Marseille CEDEX 20, France
| | - Gaelle Samson
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Claire Jubin
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Julie Poulain
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Benoît Vacherie
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Valérie Barbe
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Eric Pelletier
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - David J. Sherman
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Eric Westhof
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Jean Weissenbach
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Philippe V. Baret
- Earth and Life Institute, Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Patrick Wincker
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Claude Gaillardin
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Bernard Dujon
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
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127
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Genome reversion process of endopolyploidy confers chromosome instability on the descendent diploid cells. Cell Biol Int 2011; 36:137-45. [DOI: 10.1042/cbi20110052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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128
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Gerstein AC, Otto SP. Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays. PLoS One 2011; 6:e26599. [PMID: 22174734 PMCID: PMC3235103 DOI: 10.1371/journal.pone.0026599] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/29/2011] [Indexed: 11/21/2022] Open
Abstract
Ploidy varies tremendously within and between species, yet the factors that influence when or why ploidy variants are adaptive remains poorly understood. Our previous work found that diploid individuals repeatedly arose within ten replicate haploid populations of Saccharomyces cerevisiae, and in each case we witnessed diploid takeover within 1800 asexual generations of batch culture evolution in the lab. The character that allowed diploids to rise in frequency within haploid populations remains unknown. Here we present a number of experiments conducted with the goal to determine what this trait (or traits) might have been. Experiments were conducted both by sampling a small number of colonies from the stocks frozen every two weeks (93 generations) during the original experiment, as well through sampling a larger number of colonies at the two time points where polymorphism for ploidy was most prevalent. Surprisingly, none of our fitness component measures (lag phase, growth rate, biomass production) indicated an advantage to diploidy. Similarly, competition assays against a common competitor and direct competition between haploid and diploid colonies isolated from the same time point failed to indicate a diploid advantage. Furthermore, we uncovered a tremendous amount of trait variation among colonies of the same ploidy level. Only late-appearing diploids showed a competitive advantage over haploids, indicating that the fitness advantage that allowed eventual takeover was not diploidy per se but an attribute of a subset of diploid lineages. Nevertheless, the initial rise in diploids to intermediate frequency cannot be explained by any of the fitness measures used; we suggest that the resolution to this mystery is negative frequency-dependent selection, which is ignored in the standard fitness measures used.
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Affiliation(s)
- Aleeza C Gerstein
- Zoology Department, Biodiversity Research Center, The University of British Columbia, Vancouver, British Columbia, Canada.
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129
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Lewis MD, Llewellyn MS, Yeo M, Acosta N, Gaunt MW, Miles MA. Recent, independent and anthropogenic origins of Trypanosoma cruzi hybrids. PLoS Negl Trop Dis 2011; 5:e1363. [PMID: 22022633 PMCID: PMC3191134 DOI: 10.1371/journal.pntd.0001363] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 08/31/2011] [Indexed: 12/29/2022] Open
Abstract
The single celled eukaryote Trypanosoma cruzi, a parasite transmitted by numerous species of triatomine bug in the Americas, causes Chagas disease in humans. T. cruzi generally reproduces asexually and appears to have a clonal population structure. However, two of the six major circulating genetic lineages, TcV and TcVI, are TcII-TcIII inter-lineage hybrids that are frequently isolated from humans in regions where chronic Chagas disease is particularly severe. Nevertheless, a prevalent view is that hybridisation events in T. cruzi were evolutionarily ancient and that active recombination is of little epidemiological importance. We analysed genotypes of hybrid and non-hybrid T. cruzi strains for markers representing three distinct evolutionary rates: nuclear GPI sequences (n = 88), mitochondrial COII-ND1 sequences (n = 107) and 28 polymorphic microsatellite loci (n = 35). Using Maximum Likelihood and Bayesian phylogenetic approaches we dated key evolutionary events in the T. cruzi clade including the emergence of hybrid lineages TcV and TcVI, which we estimated to have occurred within the last 60,000 years. We also found evidence for recent genetic exchange between TcIII and TcIV and between TcI and TcIV. These findings show that evolution of novel recombinants remains a potential epidemiological risk. The clearly distinguishable microsatellite genotypes of TcV and TcVI were highly heterozygous and displayed minimal intra-lineage diversity indicative of even earlier origins than sequence-based estimates. Natural hybrid genotypes resembled typical meiotic F1 progeny, however, evidence for mitochondrial introgression, absence of haploid forms and previous experimental crosses indicate that sexual reproduction in T. cruzi may involve alternatives to canonical meiosis. Overall, the data support two independent hybridisation events between TcII and TcIII and a recent, rapid spread of the hybrid progeny in domestic transmission cycles concomitant with, or as a result of, disruption of natural transmission cycles by human activities.
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Affiliation(s)
- Michael D Lewis
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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130
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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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131
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Martinez A, Aliouat EM, Standaert-Vitse A, Werkmeister E, Pottier M, Pinçon C, Dei-Cas E, Aliouat-Denis CM. Ploidy of cell-sorted trophic and cystic forms of Pneumocystis carinii. PLoS One 2011; 6:e20935. [PMID: 21695077 PMCID: PMC3114859 DOI: 10.1371/journal.pone.0020935] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/13/2011] [Indexed: 01/15/2023] Open
Abstract
Once regarded as an AIDS-defining illness, Pneumocystis pneumonia (PcP) is nowadays prevailing in immunocompromised HIV-negative individuals such as patients receiving immunosuppressive therapies or affected by primary immunodeficiency. Moreover, Pneumocystis clinical spectrum is broadening to non-severely-immunocompromised subjects who could be colonized by the fungus while remaining asymptomatic for PcP, thus being able to transmit the infection by airborne route to susceptible hosts. Although the taxonomical position of the Pneumocystis genus has been clarified, several aspects of its life cycle remain elusive such as its mode of proliferation within the alveolus or its ploidy level. As no long-term culture model exists to grow Pneumocystis organisms in vitro, an option was to use a model of immunosuppressed rat infected with Pneumocystis carinii and sort life cycle stage fractions using a high-through-put cytometer. Subsequently, ploidy levels of the P. carinii trophic and cystic form fractions were measured by flow cytometry. In the cystic form, eight contents of DNA were measured thus strengthening the fact that each mature cyst contains eight haploid spores. Following release, each spore evolves into a trophic form. The majority of the trophic form fraction was haploid in our study. Some less abundant trophic forms displayed two contents of DNA indicating that they could undergo (i) mating/fusion leading to a diploid status or (ii) asexual mitotic division or (iii) both. Even less abundant trophic forms with four contents of DNA were suggestive of mitotic divisions occurring following mating in diploid trophic forms. Of interest, was the presence of trophic forms with three contents of DNA, an unusual finding that could be related to asymmetrical mitotic divisions occurring in other fungal species to create genetic diversity at lower energetic expenses than mating. Overall, ploidy data of P. carinii life cycle stages shed new light on the complexity of its modes of proliferation.
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Affiliation(s)
- Anna Martinez
- Université Lille Nord de France, Lille, France
- INSERM U1019, CNRS UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
- Institut Pasteur de Lille, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
| | - El Moukhtar Aliouat
- Université Lille Nord de France, Lille, France
- INSERM U1019, CNRS UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
- Institut Pasteur de Lille, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
| | - Annie Standaert-Vitse
- Université Lille Nord de France, Lille, France
- INSERM U1019, CNRS UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
- Institut Pasteur de Lille, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
| | - Elisabeth Werkmeister
- Institut Pasteur de Lille, Lille, France
- MICPaL Facility, IFR142, CNRS UMR 8161, Lille, France
| | - Muriel Pottier
- Université Lille Nord de France, Lille, France
- INSERM U1019, CNRS UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
- Institut Pasteur de Lille, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
| | - Claire Pinçon
- Université Lille Nord de France, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
- EA2694, Department of Biostatistics, Lille, France
| | - Eduardo Dei-Cas
- Université Lille Nord de France, Lille, France
- INSERM U1019, CNRS UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
- Institut Pasteur de Lille, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
- Regional and University Hospital Center (CHULille), Biology & Pathology Center (CBP), Parasitology-Mycology, Lille, France
| | - Cécile-Marie Aliouat-Denis
- Université Lille Nord de France, Lille, France
- INSERM U1019, CNRS UMR 8204, Center for Infection and Immunity of Lille (CIIL), Lille, France
- Institut Pasteur de Lille, Lille, France
- UDSL (Université Droit et Santé de Lille), Lille, France
- * E-mail:
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132
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Dhar R, Sägesser R, Weikert C, Yuan J, Wagner A. Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J Evol Biol 2011; 24:1135-53. [PMID: 21375649 DOI: 10.1111/j.1420-9101.2011.02249.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.
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Affiliation(s)
- R Dhar
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
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133
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Levasseur A, Pontarotti P. The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics. Biol Direct 2011; 6:11. [PMID: 21333002 PMCID: PMC3052240 DOI: 10.1186/1745-6150-6-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 02/18/2011] [Indexed: 12/02/2022] Open
Abstract
Understanding the evolutionary plasticity of the genome requires a global, comparative approach in which genetic events are considered both in a phylogenetic framework and with regard to population genetics and environmental variables. In the mechanisms that generate adaptive and non-adaptive changes in genomes, segmental duplications (duplication of individual genes or genomic regions) and polyploidization (whole genome duplications) are well-known driving forces. The probability of fixation and maintenance of duplicates depends on many variables, including population sizes and selection regimes experienced by the corresponding genes: a combination of stochastic and adaptive mechanisms has shaped all genomes. A survey of experimental work shows that the distinction made between fixation and maintenance of duplicates still needs to be conceptualized and mathematically modeled. Here we review the mechanisms that increase or decrease the probability of fixation or maintenance of duplicated genes, and examine the outcome of these events on the adaptation of the organisms. Reviewers This article was reviewed by Dr. Etienne Joly, Dr. Lutz Walter and Dr. W. Ford Doolittle.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.
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134
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Gerstein AC, Cleathero LA, Mandegar MA, Otto SP. Haploids adapt faster than diploids across a range of environments. J Evol Biol 2010; 24:531-40. [PMID: 21159002 DOI: 10.1111/j.1420-9101.2010.02188.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Despite a great deal of theoretical attention, we have limited empirical data about how ploidy influences the rate of adaptation. We evolved isogenic haploid and diploid populations of Saccharomyces cerevisiae for 200 generations in seven different environments. We measured the competitive fitness of all ancestral and evolved lines against a common competitor and find that in all seven environments, haploid lines adapted faster than diploids, significantly so in three environments. We apply theory that relates the rates of adaptation and measured effective population sizes to the properties of beneficial mutations. We obtained rough estimates of the average selection coefficients in haploids between 2% and 10% for these first selected mutations. Results were consistent with semi-dominant to dominant mutations in four environments and recessive to additive mutations in two other environments. These results are consistent with theory that predicts haploids should evolve faster than diploids at large population sizes.
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Affiliation(s)
- A C Gerstein
- Biodiversity Research Centre and Department of Zoology, The University of British Columbia, Vancouver, BC, Canada.
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135
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Maclean CJ, Greig D. Reciprocal gene loss following experimental whole-genome duplication causes reproductive isolation in yeast. Evolution 2010; 65:932-45. [PMID: 21114494 DOI: 10.1111/j.1558-5646.2010.01171.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Whole-genome duplication has shaped the genomes of extant lineages ranging from unicellular fungi to vertebrates, and its association with several species-rich taxa has fueled interest in its potential as a catalyst for speciation. One well-established model for the evolution of reproductive isolation involves the reciprocal loss of redundant genes at different loci in allopatric populations. Whole-genome duplication simultaneously doubles the entire gene content of an organism, resulting in massive levels of genetic redundancy and potential for reciprocal gene loss that may produce postzygotic reproductive isolation. Following whole-genome duplication, different populations can potentially change or lose gene function at different duplicate loci. If such populations come back into contact any F1 hybrids that are formed may suffer reduced fertility as some of the gametes they produce may not carry a full complement of functional genes. This reduction in hybrid fertility will be directly proportional to the number of divergently resolved loci between the populations. In this work, we demonstrate that initially identical populations of allotetraploid yeast subjected to mutagenesis rapidly evolve postzygotic reproductive isolation, consistent with the divergent loss of function of redundant gene copies.
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Affiliation(s)
- Calum J Maclean
- Research Department of Genetics, Evolution, and Environment, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom.
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136
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Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. PLoS Genet 2010; 6:e1001109. [PMID: 20838597 PMCID: PMC2936533 DOI: 10.1371/journal.pgen.1001109] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/03/2010] [Indexed: 11/18/2022] Open
Abstract
Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of Saccharomyces cerevisiae. The vegetative lines underwent only mitotic divisions while the meiotic lines underwent a meiotic cycle every ∼20 vegetative divisions. Similar base substitution rates were estimated for both lines. Given our experimental design, these measures indicated that the meiotic mutation rate is within the range of being equal to zero to being 55-fold higher than the vegetative rate. Mutations detected in vegetative lines were all heterozygous while those in meiotic lines were homozygous. A quantitative analysis of intra-tetrad mating events in the meiotic lines showed that inter-spore mating is primarily responsible for rapidly fixing mutations to homozygosity as well as for removing mutations. We did not observe 1-2 nt insertion/deletion (in-del) mutations in any of the sequenced lines and only one structural variant in a non-telomeric location was found. However, a large number of structural variations in subtelomeric sequences were seen in both vegetative and meiotic lines that did not affect viability. Our results indicate that the diploid yeast nuclear genome is remarkably stable during the vegetative and meiotic cell cycles and support the hypothesis that peripheral regions of chromosomes are more dynamic than gene-rich central sections where structural rearrangements could be deleterious. This work also provides an improved estimate for the mutational load carried by diploid organisms.
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Affiliation(s)
- K. T. Nishant
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Wu Wei
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Juan Lucas Argueso
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | | | - Xin Ma
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jan O. Korbel
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Lars M. Steinmetz
- European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail: (LMS); (EA)
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (LMS); (EA)
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137
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Anderson JB, Funt J, Thompson DA, Prabhu S, Socha A, Sirjusingh C, Dettman JR, Parreiras L, Guttman DS, Regev A, Kohn LM. Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Curr Biol 2010; 20:1383-8. [PMID: 20637622 DOI: 10.1016/j.cub.2010.06.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 10/19/2022]
Abstract
Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here, whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations, six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt, two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose, one mutation occurred in MDS3, which modulates growth at high pH, and one in MKT1, a global regulator of mRNAs encoding mitochondrial proteins, the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong.
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Affiliation(s)
- James B Anderson
- Centre for the Analysis of Genome Function, Department of Cell and Systems Biology, and Department of Ecology and Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
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138
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Al Safadi R, Weiss-Gayet M, Briolay J, Aigle M. A polyploid population of Saccharomyces cerevisiae with separate sexes (dioecy). FEMS Yeast Res 2010; 10:757-68. [PMID: 20662936 DOI: 10.1111/j.1567-1364.2010.00660.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Saccharomyces cerevisiae has proved to be an interesting model for studies of evolution, with whole-genome duplication shown to have played an important role in the evolution of this species. This phenomenon depends on the formation of a transient stable polyploid state. Previous studies have reported polyploidy to be an unstable state in yeast, but here, we describe a polyploid population of S. cerevisiae. The evolution of higher eukaryotes has also involved the development of different systems of sexual reproduction, the choice between self-fertilization and out-crossing becoming a key issue. Saccharomyces cerevisiae is a hermaphrodite eukaryote, despite the theoretical genetic disadvantages of this strategy, in which self-fertilization occurs. We describe, for the first time, a near-dioecious (with separate sexes) population in this species. Mating type and the MAT locus display complex segregations. Essentially, each strain produces, by meiosis, spores of only one mating type: mata or matalpha. Moreover, strains are heterothallic, and diploid nonmating clones generated from a single spore do not sporulate. These three properties limit self-fertilization and strongly favour out-crossing. We suggest that the shift in sexual strategy, from hermaphroditism to dioecy, is specific to the brewing process, which overcomes the sexual isolation probably found in natural biotopes.
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Affiliation(s)
- Rim Al Safadi
- Génétique Moléculaire des levures, UMR5240, Université de Lyon, Université Lyon 1, Villeurbanne, France
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139
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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140
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Veitia RA, Bottani S. Whole genome duplications and a 'function' for junk DNA? Facts and hypotheses. PLoS One 2009; 4:e8201. [PMID: 20011530 PMCID: PMC2788606 DOI: 10.1371/journal.pone.0008201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Accepted: 11/09/2009] [Indexed: 12/18/2022] Open
Abstract
Background The lack of correlation between genome size and organismal complexity is understood in terms of the massive presence of repetitive and non-coding DNA. This non-coding subgenome has long been called “junk” DNA. However, it might have important functions. Generation of junk DNA depends on proliferation of selfish DNA elements and on local or global DNA duplication followed by genic non-fonctionalization. Methodology/Principal Findings Evidence from genomic analyses and experimental data indicates that Whole Genome Duplications (WGD) are often followed by a return to the diploid state, through DNA deletions and intra/interchromosomal rearrangements. We use simple theoretical models and simulations to explore how a WGD accompanied by sequence deletions might affect the dosage balance often required among several gene products involved in regulatory processes. We find that potential genomic deletions leading to changes in nuclear and cell volume might potentially perturb gene dosage balance. Conclusions/Significance The potentially negative impact of DNA deletions can be buffered if deleted genic DNA is, at least temporarily, replaced by repetitive DNA so that the nuclear/cell volume remains compatible with normal living. Thus, we speculate that retention of non-functionalized non-coding DNA, and replacement of deleted DNA through proliferation of selfish elements, might help avoid dosage imbalances in cycles of polyploidization and diploidization, which are particularly frequent in plants.
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141
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Mayrose I, Barker MS, Otto SP. Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy. Syst Biol 2009; 59:132-44. [PMID: 20525626 DOI: 10.1093/sysbio/syp083] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Itay Mayrose
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Michael S. Barker
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Sarah P. Otto
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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142
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Hufton AL, Panopoulou G. Polyploidy and genome restructuring: a variety of outcomes. Curr Opin Genet Dev 2009; 19:600-6. [PMID: 19900800 DOI: 10.1016/j.gde.2009.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 09/02/2009] [Accepted: 10/07/2009] [Indexed: 02/08/2023]
Abstract
Dramatic genome rearrangement has been observed after whole genome duplication (WGD) in some plant species, leading many to suggest that genome restructuring may be a common consequence of WGD. However, recent analyses of ancient WGDs in yeast and vertebrates have not shown any evidence for increased rearrangement after WGD. When WGD events across all three kingdoms of eukaryotic life are considered-including plants, yeast, vertebrates, and human cancers-we find that a variety of outcomes are possible, from genome restructuring to genome stasis. In fact, striking differences in genome change after WGD can be observed within single plant genera, indicating that there are no simple rules that can predict a genome's reaction to WGD.
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Affiliation(s)
- Andrew L Hufton
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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143
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Abstract
The many different mechanisms that fungi use to transmit and share genetic material are mediated by a broad range of chromosome and nuclear dynamics. The mechanics underlying nuclear migration are well integrated into detailed models, in which the forces supplied by plus- and minus-end-directed microtubule motors position and move the nucleus in a cell. Although we know much about how cells move nuclei, we know much less about why the cell invests in so many different nuclear 'dances'. Here, we briefly survey the available models for the mechanics of nuclear migration in fungi and then focus on examples of how fungal cells use these nuclear dances - the movement of intact nuclei in and between cells - to control the integrity, ploidy and assortment of specific genomes or individual chromosomes.
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Affiliation(s)
- Amy Gladfelter
- Department of Biological Sciences, Gillman Hall, Dartmouth College, Hanover, New Hampshire 03755, USA
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144
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Lewis MD, Llewellyn MS, Gaunt MW, Yeo M, Carrasco HJ, Miles MA. Flow cytometric analysis and microsatellite genotyping reveal extensive DNA content variation in Trypanosoma cruzi populations and expose contrasts between natural and experimental hybrids. Int J Parasitol 2009; 39:1305-17. [PMID: 19393242 PMCID: PMC2731025 DOI: 10.1016/j.ijpara.2009.04.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 04/03/2009] [Accepted: 04/06/2009] [Indexed: 12/05/2022]
Abstract
Trypanosoma cruzi exhibits remarkable genetic heterogeneity. This is evident at the nucleotide level but also structurally, in the form of karyotypic variation and DNA content differences between strains. Although natural populations of T. cruzi are predominantly clonal, hybrid lineages (TcIId and TcIIe) have been identified and hybridisation has been demonstrated in vitro, raising the possibility that genetic exchange may continue to shape the evolution of this pathogen. The mechanism of genetic exchange identified in the laboratory is unusual, apparently involving fusion of diploid parents followed by genome erosion. We investigated DNA content diversity in natural populations of T. cruzi in the context of its genetic subdivisions by using flow cytometric analysis and multilocus microsatellite genotyping to determine the relative DNA content and estimate the ploidy of 54 cloned isolates. The maximum difference observed was 47.5% between strain Tu18 cl2 (TcIIb) and strain C8 cl1 (TcI), which we estimated to be equivalent to ∼73 Mb of DNA. Large DNA content differences were identified within and between discrete typing units (DTUs). In particular, the mean DNA content of TcI strains was significantly less than that for TcII strains (P < 0.001). Comparisons of hybrid DTUs TcIId/IIe with corresponding parental DTUs TcIIb/IIc indicated that natural hybrids are predominantly diploid. We also measured the relative DNA content of six in vitro-generated TcI hybrid clones and their parents. In contrast to TcIId/IIe hybrid strains these experimental hybrids comprised populations of sub-tetraploid organisms with mean DNA contents 1.65–1.72 times higher than the parental organisms. The DNA contents of both parents and hybrids were shown to be relatively stable after passage through a mammalian host, heat shock or nutritional stress. The results are discussed in the context of hybridisation mechanisms in both natural and in vitro settings.
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145
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Albertin W, Marullo P, Aigle M, Bourgais A, Bely M, Dillmann C, DE Vienne D, Sicard D. Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J Evol Biol 2009; 22:2157-70. [PMID: 19765175 DOI: 10.1111/j.1420-9101.2009.01828.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Partial or whole-genome duplications have played a major role in the evolution of new species. We have investigated the variation of ploidy level in a panel of domesticated strains of Saccharomyces cerevisiae coming from different geographical origins. Segregation studies and crosses with tester strains of different ploidy levels showed that part of the strains were well-balanced autotetraploids displaying tetrasomic inheritance. The presence of up to four different alleles for various loci is consistent with a polyploidization mechanism relying on the fusion of two nonreduced meiospores coming from two S. cerevisiae strains. Autotetraploidy was also in accordance with karyotype and flow cytometry analyses. Interestingly, most bakery strains were tetraploids, suggesting a link between ploidy level and human use. The null or drastically reduced fertility of the hybrids between tetraploid and diploid strains indicated that domesticated S. cerevisiae strains are composed of two groups isolated by post-zygotic reproductive barriers.
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Affiliation(s)
- W Albertin
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Gif-sur-Yvette, France
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146
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147
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Aguilera J, Andreu P, Randez-Gil F, Prieto JA. Adaptive evolution of baker's yeast in a dough-like environment enhances freeze and salinity tolerance. Microb Biotechnol 2009; 3:210-21. [PMID: 21255321 PMCID: PMC3836578 DOI: 10.1111/j.1751-7915.2009.00136.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We used adaptive evolution to improve freeze tolerance of industrial baker's yeast. Our hypothesis was that adaptation to low temperature is accompanied by enhanced resistance of yeast to freezing. Based on this hypothesis, yeast was propagated in a flour‐free liquid dough model system, which contained sorbitol and NaCl, by successive batch refreshments maintained constantly at 12°C over at least 200 generations. Relative to the parental population, the maximal growth rate (µmax) under the restrictive conditions, increased gradually over the time course of the experiment. This increase was accompanied by enhanced freeze tolerance. However, these changes were not the consequence of genetic adaptation to low temperature, a fact that was confirmed by prolonged selection of yeast cells in YPD at 12°C. Instead, the experimental populations showed a progressive increase in NaCl tolerance. This phenotype was likely achieved at the expense of others traits, since evolved cells showed a ploidy reduction, a defect in the glucose derepression mechanism and a loss in their ability to utilize gluconeogenic carbon sources. We discuss the genetic flexibility of S. cerevisiae in terms of adaptation to the multiple constraints of the experimental design applied to drive adaptive evolution and the technologically advantageous phenotype of the evolved population.
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Affiliation(s)
- Jaime Aguilera
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Poligono de la Coma, s/n, PO Box 73. 46100-Burjassot, Valencia, Spain
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148
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Gilbert A, Sangurdekar DP, Srienc F. Rapid strain improvement through optimized evolution in the cytostat. Biotechnol Bioeng 2009; 103:500-12. [DOI: 10.1002/bit.22272] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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149
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Comet assay on tetraploid yeast cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2009; 673:53-8. [DOI: 10.1016/j.mrgentox.2008.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 11/20/2008] [Accepted: 11/30/2008] [Indexed: 11/19/2022]
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150
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Lin X, Patel S, Litvintseva AP, Floyd A, Mitchell TG, Heitman J. Diploids in the Cryptococcus neoformans serotype A population homozygous for the alpha mating type originate via unisexual mating. PLoS Pathog 2009; 5:e1000283. [PMID: 19180236 PMCID: PMC2629120 DOI: 10.1371/journal.ppat.1000283] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 12/30/2008] [Indexed: 01/03/2023] Open
Abstract
The ubiquitous environmental human pathogen Cryptococcus neoformans is traditionally considered a haploid fungus with a bipolar mating system. In nature, the α mating type is overwhelmingly predominant over a. How genetic diversity is generated and maintained by this heterothallic fungus in a largely unisexual α population is unclear. Recently it was discovered that C. neoformans can undergo same-sex mating under laboratory conditions generating both diploid intermediates and haploid recombinant progeny. Same-sex mating (α-α) also occurs in nature as evidenced by the existence of natural diploid αADα hybrids that arose by fusion between two α cells of different serotypes (A and D). How significantly this novel sexual style contributes to genetic diversity of the Cryptococcus population was unknown. In this study, ∼500 natural C. neoformans isolates were tested for ploidy and close to 8% were found to be diploid by fluorescence flow cytometry analysis. The majority of these diploids were serotype A isolates with two copies of the α MAT locus allele. Among those, several are intra-varietal allodiploid hybrids produced by fusion of two genetically distinct α cells through same-sex mating. The majority, however, are autodiploids that harbor two seemingly identical copies of the genome and arose via either endoreplication or clonal mating. The diploids identified were isolated from different geographic locations and varied genotypically and phenotypically, indicating independent non-clonal origins. The present study demonstrates that unisexual mating produces diploid isolates of C. neoformans in nature, giving rise to populations of hybrids and mixed ploidy. Our findings underscore the importance of same-sex mating in shaping the current population structure of this important human pathogenic fungus, with implications for mechanisms of selfing and inbreeding in other microbial pathogens. Although sex typically involves partners of opposite mating type (sexuality), it can also occur with just one mating type and even single individuals (parthenogenesis, homothallism). However, from a population perspective, sexual reproduction occurs by either outcrossing or inbreeding regardless of the partners' sexuality. Here the impact of sex was studied for Cryptococcus neoformans, a pathogen that causes fungal meningitis. While sex in the laboratory is known to occur via opposite-sex-mating, the population is largely unisexual (α) in nature. Recently, an unusual α-α unisexual mating process involving only mating type α was discovered in the lab, but the impact of unisexual mating in nature was unknown. The global survey of this typically haploid organism reveals ∼8% diploids in the population produced by unisexual α-α mating. Some diploids result from fusion of two genetically distinct parents while other diploids arise via sibling mating or genome duplication. Although hybrid fitness is well-documented, how sex between identical isolates benefits the population is a conundrum. The diploid state may confer growth advantages or serve as a capacitor for evolution, allowing mutations to arise that would be deleterious on their own in the haploid, and then releasing these in novel combinations by meiosis and sporulation.
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Affiliation(s)
- Xiaorong Lin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sweta Patel
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anastasia P. Litvintseva
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anna Floyd
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Thomas G. Mitchell
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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