101
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Shapiro JA. What can evolutionary biology learn from cancer biology? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:19-28. [PMID: 33930405 DOI: 10.1016/j.pbiomolbio.2021.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022]
Abstract
Detecting and treating cancer effectively involves understanding the disease as one of somatic cell and tumor macroevolution. That understanding is key to avoid triggering an adverse reaction to therapy that generates an untreatable and deadly tumor population. Macroevolution differs from microevolution by karyotype changes rather than isolated localized mutations being the major source of hereditary variation. Cancer cells display major multi-site chromosome rearrangements that appear to have arisen in many different cases abruptly in the history of tumor evolution. These genome restructuring events help explain the punctuated macroevolutionary changes that mark major transitions in cancer progression. At least two different nonrandom patterns of rapid multisite genome restructuring - chromothripsis ("chromosome shattering") and chromoplexy ("chromosome weaving") - are clearly distinct in their distribution within the genome and in the cell biology of the stress-induced processes responsible for their occurrence. These observations tell us that eukaryotic cells have the capacity to reorganize their genomes rapidly in response to calamity. Since chromothripsis and chromoplexy have been identified in the human germline and in other eukaryotes, they provide a model for organismal macroevolution in response to the kinds of stresses that lead to mass extinctions.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, United States.
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102
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Thomson GJ, Kakade P, Hirakawa MP, Ene IV, Bennett RJ. Adaptation to the dietary sugar D-tagatose via genome instability in polyploid Candida albicans cells. G3-GENES GENOMES GENETICS 2021; 11:6219300. [PMID: 33836061 PMCID: PMC8495922 DOI: 10.1093/g3journal/jkab110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
The opportunistic fungal pathogen Candida albicans undergoes an unusual parasexual cycle wherein diploid cells mate to form tetraploid cells that can generate genetically diverse progeny via a non-meiotic program of chromosome loss. The genetic diversity afforded by parasex impacts clinically relevant features including drug resistance and virulence, and yet the factors influencing genome instability in C. albicans are not well defined. To understand how environmental cues impact genome instability, we monitored ploidy change following tetraploid cell growth in a panel of different carbon sources. We found that growth in one carbon source, D-tagatose, led to high levels of genomic instability and chromosome loss in tetraploid cells. This sugar is a stereoisomer of L-sorbose which was previously shown to promote karyotypic changes in C. albicans. However, while expression of the SOU1 gene enabled utilization of L-sorbose, overexpression of this gene did not promote growth in D-tagatose, indicating differences in assimilation of the two sugars. In addition, genome sequencing of multiple progeny recovered from D-tagatose cultures revealed increased relative copy numbers of chromosome 4, suggestive of chromosome-level regulation of D-tagatose metabolism. Together, these studies identify a novel environmental cue that induces genome instability in C. albicans, and further implicate chromosomal changes in supporting metabolic adaptation in this species.
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Affiliation(s)
- Gregory J Thomson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Pallavi Kakade
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Matthew P Hirakawa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.,Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Iuliana V Ene
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.,Mycology Department, Pasteur Institute, Paris 75015, France
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
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103
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Yang F, Todd RT, Selmecki A, Jiang YY, Cao YB, Berman J. The fitness costs and benefits of trisomy of each Candida albicans chromosome. Genetics 2021; 218:6218773. [PMID: 33837402 DOI: 10.1093/genetics/iyab056] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/01/2021] [Indexed: 01/05/2023] Open
Abstract
Candida albicans is a prevalent human fungal pathogen. Rapid genomic change, due to aneuploidy, is a common mechanism that facilitates survival from multiple types of stresses including the few classes of available antifungal drugs. The stress survival of aneuploids occurs despite the fitness costs attributed to most aneuploids growing under idealized lab conditions. Systematic study of the aneuploid state in C. albicans has been hindered by the lack of a comprehensive collection of aneuploid strains. Here, we describe a collection of diploid C. albicans aneuploid strains, each carrying one extra copy of each chromosome, all from the same genetic background. We tested the fitness of this collection under several physiological conditions including shifts in pH, low glucose, oxidative stress, temperature, high osmolarity, membrane stress, and cell wall stress. We found that most aneuploids, under most conditions, were less fit than their euploid parent, yet there were specific conditions under which specific aneuploid isolates provided a fitness benefit relative to the euploid parent strain. Importantly, this fitness benefit was attributable to the change in the copy number of specific chromosomes. Thus, C. albicans can tolerate aneuploidy of each chromosome and some aneuploids confer improved growth under conditions that the yeast encounters in its host niches.
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Affiliation(s)
- Feng Yang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200086, China.,Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Yuan-Ying Jiang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yong-Bing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200086, China
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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104
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Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. THE NEW PHYTOLOGIST 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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105
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Schmickl R, Yant L. Adaptive introgression: how polyploidy reshapes gene flow landscapes. THE NEW PHYTOLOGIST 2021; 230:457-461. [PMID: 33454987 DOI: 10.1111/nph.17204] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Rare yet accumulating evidence in both plants and animals shows that whole genome duplication (WGD, leading to polyploidy) can break down reproductive barriers, facilitating gene flow between otherwise isolated species. Recent population genomic studies in wild, outcrossing Arabidopsis arenosa and Arabidopsis lyrata indicate that this WGD-potentiated gene flow can be adaptive and highly specific in response to particular environmental and intracellular challenges. The mechanistic basis of WGD-mediated easing of species barrier strength seems to primarily lie in the relative dosage of each parental genome in the endosperm. While generalisations about polyploids can be fraught, this evidence indicates that the breakdown of these barriers, combined with diploid to polyploid gene flow and gene flow between polyploids, allows some polyploids to act as adaptable 'allelic sponges', enjoying increased potential to respond to challenging environments.
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Affiliation(s)
- Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, 128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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106
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Bohutínská M, Alston M, Monnahan P, Mandáková T, Bray S, Paajanen P, Kolář F, Yant L. Novelty and convergence in adaptation to whole genome duplication. Mol Biol Evol 2021; 38:3910-3924. [PMID: 33783509 PMCID: PMC8382928 DOI: 10.1093/molbev/msab096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimised in an autotetraploid (within-species polyploid) to avoid mis-segregation. Here we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 million years diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodelling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organisation, stress signalling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Mark Alston
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Patrick Monnahan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Sian Bray
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Biosciences University of Nottingham, Nottingham, UK
| | - Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Life Sciences University of Nottingham, Nottingham, UK
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107
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 264] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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108
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Wawro A. Improvement of Acetic Acid Tolerance in Saccharomyces cerevisiae by Novel Genome Shuffling. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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109
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Liu L, Jin M, Huang M, Zhu Y, Yuan W, Kang Y, Kong M, Ali S, Jia Z, Xu Z, Xiao W, Cao L. Engineered Polyploid Yeast Strains Enable Efficient Xylose Utilization and Ethanol Production in Corn Hydrolysates. Front Bioeng Biotechnol 2021; 9:655272. [PMID: 33748094 PMCID: PMC7973232 DOI: 10.3389/fbioe.2021.655272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/08/2021] [Indexed: 02/01/2023] Open
Abstract
The reported haploid Saccharomyces cerevisiae strain F106 can utilize xylose for ethanol production. After a series of XR and/or XDH mutations were introduced into F106, the XR-K270R mutant was found to outperform others. The corresponding haploid, diploid, and triploid strains were then constructed and their fermentation performance was compared. Strains F106-KR and the diploid produced an ethanol yield of 0.45 and 0.48 g/g total sugars, respectively, in simulated corn hydrolysates within 36 h. Using non-detoxicated corncob hydrolysate as the substrate, the ethanol yield with the triploid was approximately sevenfold than that of the diploid at 40°C. After a comprehensive evaluation of growth on corn stover hydrolysates pretreated with diluted acid or alkali and different substrate concentrations, ethanol yields of the triploid strain were consistently higher than those of the diploid using acid-pretreatment. These results demonstrate that the yeast chromosomal copy number is positively correlated with increased ethanol production under our experimental conditions.
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Affiliation(s)
- Lulu Liu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Yixuan Zhu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Wenjie Yuan
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Meilin Kong
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Sajid Ali
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Zefang Jia
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Wei Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Limin Cao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, China
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110
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Bautista C, Marsit S, Landry CR. Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions. Evol Appl 2021; 14:758-769. [PMID: 33767750 PMCID: PMC7980265 DOI: 10.1111/eva.13155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022] Open
Abstract
Hybridization may increase the probability of adaptation to extreme stresses. This advantage could be caused by an increased genome plasticity in hybrids, which could accelerate the search for adaptive mutations. High ultraviolet (UV) radiation is a particular challenge in terms of adaptation because it affects the viability of organisms by directly damaging DNA, while also challenging future generations by increasing mutation rate. Here we test whether hybridization accelerates adaptive evolution in response to DNA damage, using yeast as a model. We exposed 180 populations of hybrids between species (Saccharomyces cerevisiae and Saccharomyces paradoxus) and their parental strains to UV mimetic and control conditions for approximately 100 generations. Although we found that adaptation occurs in both hybrids and parents, hybrids achieved a lower rate of adaptation, contrary to our expectations. Adaptation to DNA damage conditions comes with a large and similar cost for parents and hybrids, suggesting that this cost is not responsible for the lower adaptability of hybrids. We suggest that the lower adaptive potential of hybrids in this condition may result from the interaction between DNA damage and the inherent genetic instability of hybrids.
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Affiliation(s)
- Carla Bautista
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
- Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO)Université LavalQuébecQCCanada
- Centre de Recherche en Données Massives (CRDM)Université LavalQuébecQCCanada
- Département de Biochimie, de Microbiologie et de Bio‐informatiqueFaculté des Sciences et de GénieUniversité LavalQuébecQCCanada
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111
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Thermo-adaptive evolution to generate improved Saccharomyces cerevisiae strains for cocoa pulp fermentations. Int J Food Microbiol 2021; 342:109077. [PMID: 33550155 DOI: 10.1016/j.ijfoodmicro.2021.109077] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022]
Abstract
Cocoa pulp fermentation is a consequence of the succession of indigenous yeasts, lactic acid bacteria and acetic acid bacteria that not only produce a diversity of metabolites, but also cause the production of flavour precursors. However, as such spontaneous fermentations are less reproducible and contribute to produce variability, interest in a microbial starter culture is growing that could be used to inoculate cocoa pulp fermentations. This study aimed to generate robust S. cerevisiae strains by thermo-adaptive evolution that could be used in cocoa fermentation. We evolved a cocoa strain in a sugary defined medium at high temperature to improve both fermentation and growth capacity. Moreover, adaptive evolution at high temperature (40 °C) also enabled us to unveil the molecular basis underlying the improved phenotype by analysing the whole genome sequence of the evolved strain. Adaptation to high-temperature conditions occurred at different genomic levels, and promoted aneuploidies, segmental duplication, and SNVs in the evolved strain. The lipid profile analysis of the evolved strain also evidenced changes in the membrane composition that contribute to maintain an appropriate cell membrane state at high temperature. Our work demonstrates that experimental evolution is an effective approach to generate better-adapted yeast strains at high temperature for industrial processes.
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112
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Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature 2021; 590:492-497. [PMID: 33505027 PMCID: PMC7889737 DOI: 10.1038/s41586-020-03133-3] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 12/17/2020] [Indexed: 01/09/2023]
Abstract
Whole genome doubling (WGD) occurs early in tumorigenesis and generates genetically unstable tetraploid cells that fuel tumor development1,2. Cells that undergo WGD (WGD+) must adapt to accommodate their abnormal tetraploid state; however, the nature of these adaptations, and whether they confer vulnerabilities that can subsequently be exploited therapeutically, is unclear. Using sequencing data from ~10,000 primary human cancer samples and essentiality data from ~600 cancer cell lines, we show that WGD gives rise to common genetic traits that are accompanied by unique vulnerabilities. We reveal that WGD+ cells are more dependent on spindle assembly checkpoint signaling, DNA replication factors, and proteasome function than WGD– cells. We also identify KIF18A, which encodes for a mitotic kinesin, as being specifically required for the viability of WGD+ cells. While loss of KIF18A is largely dispensable for accurate chromosome segregation during mitosis in WGD– cells, its loss induces dramatic mitotic errors in WGD+ cells, ultimately impairing cell viability. Collectively, our results reveal new strategies to specifically target WGD+ cancer cells while sparing the normal, non-transformed WGD– cells that comprise human tissue.
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113
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Gerstein AC, Sharp NP. The population genetics of ploidy change in unicellular fungi. FEMS Microbiol Rev 2021; 45:6121427. [PMID: 33503232 DOI: 10.1093/femsre/fuab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.
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Affiliation(s)
- Aleeza C Gerstein
- Dept. of Microbiology, Dept. of Statistics, University of Manitoba Canada
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114
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Chen J, Xiong Z, Miller DE, Yu Z, McCroskey S, Bradford WD, Cavanaugh AM, Jaspersen SL. The role of gene dosage in budding yeast centrosome scaling and spontaneous diploidization. PLoS Genet 2020; 16:e1008911. [PMID: 33332348 PMCID: PMC7775121 DOI: 10.1371/journal.pgen.1008911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/31/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Ploidy is the number of whole sets of chromosomes in a species. Ploidy is typically a stable cellular feature that is critical for survival. Polyploidization is a route recognized to increase gene dosage, improve fitness under stressful conditions and promote evolutionary diversity. However, the mechanism of regulation and maintenance of ploidy is not well characterized. Here, we examine the spontaneous diploidization associated with mutations in components of the Saccharomyces cerevisiae centrosome, known as the spindle pole body (SPB). Although SPB mutants are associated with defects in spindle formation, we show that two copies of the mutant in a haploid yeast favors diploidization in some cases, leading us to speculate that the increased gene dosage in diploids ‘rescues’ SPB duplication defects, allowing cells to successfully propagate with a stable diploid karyotype. This copy number-based rescue is linked to SPB scaling: certain SPB subcomplexes do not scale or only minimally scale with ploidy. We hypothesize that lesions in structures with incompatible allometries such as the centrosome may drive changes such as whole genome duplication, which have shaped the evolutionary landscape of many eukaryotes. Ploidy is the number of whole sets of chromosomes in a species. Most eukaryotes alternate between a diploid (two copy) and haploid (one copy) state during their life and sexual cycle. However, as part of normal human development, specific tissues increase their DNA content. This gain of entire sets of chromosomes is known as polyploidization, and it is observed in invertebrates, plants and fungi, as well. Polyploidy is thought to improve fitness under stressful conditions and promote evolutionary diversity, but how ploidy is determined is poorly understood. Here, we use budding yeast to investigate mechanisms underlying the ploidy of wild-type cells and specific mutants that affect the centrosome, a conserved structure involved in chromosome segregation during cell division. Our work suggests that different scaling relationships (allometry) between the genome and cellular structures underlies alterations in ploidy. Furthermore, mutations in cellular structures with incompatible allometric relationships with the genome may drive genomic changes such duplications, which are underly the evolution of many species including both yeasts and humans.
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Affiliation(s)
- Jingjing Chen
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Zhiyong Xiong
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Danny E. Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Scott McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William D. Bradford
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Ann M. Cavanaugh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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115
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Fischer G, Liti G, Llorente B. The budding yeast life cycle: More complex than anticipated? Yeast 2020; 38:5-11. [PMID: 33197073 DOI: 10.1002/yea.3533] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 11/07/2022] Open
Abstract
The budding yeast, Saccharomyces cerevisiae, has served as a model for nearly a century to understand the principles of the eukaryotic life cycle. The canonical life cycle of S. cerevisiae comprises a regular alternation between haploid and diploid phases. Haploid gametes generated by sporulation are expected to quickly restore the diploid phase mainly through inbreeding via intratetrad mating or haploselfing, thereby promoting genome homozygotization. However, recent large population genomics data unveiled that heterozygosity and polyploidy are unexpectedly common. This raises the interesting paradox of a haplo-diplobiontic species being well-adapted to inbreeding and able to maintain high levels of heterozygosity and polyploidy, thereby suggesting an unanticipated complexity of the yeast life cycle. Here, we propose that unprogrammed mating type switching, heterothallism, reduced spore formation and viability, cell-cell fusion and dioecy could play key and uncharted contributions to generate and maintain heterozygosity through polyploidization.
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Affiliation(s)
- Gilles Fischer
- CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Sorbonne Université, Paris, France
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
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116
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Cancer cells employ an evolutionarily conserved polyploidization program to resist therapy. Semin Cancer Biol 2020; 81:145-159. [PMID: 33276091 DOI: 10.1016/j.semcancer.2020.11.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022]
Abstract
Unusually large cancer cells with abnormal nuclei have been documented in the cancer literature since 1858. For more than 100 years, they have been generally disregarded as irreversibly senescent or dying cells, too morphologically misshapen and chromatin too disorganized to be functional. Cell enlargement, accompanied by whole genome doubling or more, is observed across organisms, often associated with mitigation strategies against environmental change, severe stress, or the lack of nutrients. Our comparison of the mechanisms for polyploidization in other organisms and non-transformed tissues suggest that cancer cells draw from a conserved program for their survival, utilizing whole genome doubling and pausing proliferation to survive stress. These polyaneuploid cancer cells (PACCs) are the source of therapeutic resistance, responsible for cancer recurrence and, ultimately, cancer lethality.
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117
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Bell EA, Cable J, Oliveira C, Richardson DS, Yant L, Taylor MI. Help or hindrance? The evolutionary impact of whole-genome duplication on immunogenetic diversity and parasite load. Ecol Evol 2020; 10:13949-13956. [PMID: 33391693 PMCID: PMC7771170 DOI: 10.1002/ece3.6987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplication (WGD) events occur in all kingdoms and have been hypothesized to promote adaptability. WGDs identified in the early history of vertebrates, teleosts, and angiosperms have been linked to the large-scale diversification of these lineages. However, the mechanics and full outcomes of WGD regarding potential evolutionary impacts remain a topic of debate. The Corydoradinae are a diverse subfamily of Neotropical catfishes with over 170 species described and a history of WGDs. They are divided into nine mtDNA lineages, with species coexisting in sympatric-and often mimetic-communities containing representatives of two or more of the nine lineages. Given their similar life histories, coexisting species of Corydoras might be exposed to similar parasite loads and because of their different histories of WGD and genome size they provide a powerful system for investigating the impacts of WGD on immune diversity and function in an animal system. Here, we compared parasite counts and the diversity of the immune-related toll-like receptors (TLR) in two coexisting species of Corydoras catfish (C. maculifer and C. araguaiaensis), one diploid and one putative tetraploid. In the putative tetraploid C. araguaiaensis, we found significantly lower numbers of parasites and significantly higher diversity (measured by both synonymous and nonsynonymous SNP counts) in two TLR genes than in the diploid C. maculifer. These results provide insight into how WGD may impact evolution, in this case by providing greater immunogenetic diversity.
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Affiliation(s)
- Ellen A. Bell
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Jo Cable
- School of BiosciencesCardiff UniversityCardiffUK
| | - Claudio Oliveira
- Departmento de MorfologiaInstituto de Biosiências/UNESPSão PauloBrazil
| | | | - Levi Yant
- Department of Cell and Developmental BiologyJohn Innes CentreNorwichUK
- Present address:
Future Food Beacon of Excellence and the School of Life SciencesUniversity of NottinghamNottinghamUK
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Lahue C, Madden AA, Dunn RR, Smukowski Heil C. History and Domestication of Saccharomyces cerevisiae in Bread Baking. Front Genet 2020; 11:584718. [PMID: 33262788 PMCID: PMC7686800 DOI: 10.3389/fgene.2020.584718] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.
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Affiliation(s)
- Caitlin Lahue
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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119
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Sui Y, Qi L, Wu JK, Wen XP, Tang XX, Ma ZJ, Wu XC, Zhang K, Kokoska RJ, Zheng DQ, Petes TD. Genome-wide mapping of spontaneous genetic alterations in diploid yeast cells. Proc Natl Acad Sci U S A 2020; 117:28191-28200. [PMID: 33106417 PMCID: PMC7668089 DOI: 10.1073/pnas.2018633117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomic alterations including single-base mutations, deletions and duplications, translocations, mitotic recombination events, and chromosome aneuploidy generate genetic diversity. We examined the rates of all of these genetic changes in a diploid strain of Saccharomyces cerevisiae by whole-genome sequencing of many independent isolates (n = 93) subcloned about 100 times in unstressed growth conditions. The most common alterations were point mutations and small (<100 bp) insertion/deletions (n = 1,337) and mitotic recombination events (n = 1,215). The diploid cells of most eukaryotes are heterozygous for many single-nucleotide polymorphisms (SNPs). During mitotic cell divisions, recombination can produce derivatives of these cells that have become homozygous for the polymorphisms, termed loss-of-heterozygosity (LOH) events. LOH events can change the phenotype of the cells and contribute to tumor formation in humans. We observed two types of LOH events: interstitial events (conversions) resulting in a short LOH tract (usually less than 15 kb) and terminal events (mostly cross-overs) in which the LOH tract extends to the end of the chromosome. These two types of LOH events had different distributions, suggesting that they may have initiated by different mechanisms. Based on our results, we present a method of calculating the probability of an LOH event for individual SNPs located throughout the genome. We also identified several hotspots for chromosomal rearrangements (large deletions and duplications). Our results provide insights into the relative importance of different types of genetic alterations produced during vegetative growth.
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Affiliation(s)
- Yang Sui
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27705
| | - Lei Qi
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27705
| | - Jian-Kun Wu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Xue-Ping Wen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Xing-Xing Tang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Zhong-Jun Ma
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Xue-Chang Wu
- Institute of Microbiology, College of Life Science, Zhejiang University, 310058 Hangzhou, China
| | - Ke Zhang
- Institute of Microbiology, College of Life Science, Zhejiang University, 310058 Hangzhou, China;
| | - Robert J Kokoska
- Physical Sciences Directorate, United States Army Research Office, Research Triangle Park, NC 27709
| | - Dao-Qiong Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, 316021 Zhoushan, China;
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27705;
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Xu S, Wang J, Guo Z, He Z, Shi S. Genomic Convergence in the Adaptation to Extreme Environments. PLANT COMMUNICATIONS 2020; 1:100117. [PMID: 33367270 PMCID: PMC7747959 DOI: 10.1016/j.xplc.2020.100117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 05/08/2023]
Abstract
Convergent evolution is especially common in plants that have independently adapted to the same extreme environments (i.e., extremophile plants). The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants. In this review, we summarize cases of genomic convergence in these taxa to examine the extent and type of genomic convergence during the process of adaptation to extreme environments. Despite being well studied by candidate gene approaches, convergent evolution at individual sites is rare and often has a high false-positive rate when assessed in whole genomes. By contrast, genomic convergence at higher genetic levels has been detected during adaptation to the same extreme environments. Examples include the convergence of biological pathways and changes in gene expression, gene copy number, amino acid usage, and GC content. Higher convergence levels play important roles in the adaptive evolution of extremophiles and may be more frequent and involve more genes. In several cases, multiple types of convergence events have been found to co-occur. However, empirical and theoretical studies of this higher level convergent evolution are still limited. In conclusion, both the development of powerful approaches and the detection of convergence at various genetic levels are needed to further reveal the genetic mechanisms of plant adaptation to extreme environments.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiayan Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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Schindler D. Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology. Bioengineering (Basel) 2020; 7:E137. [PMID: 33138080 PMCID: PMC7711850 DOI: 10.3390/bioengineering7040137] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
The field of genetic engineering was born in 1973 with the "construction of biologically functional bacterial plasmids in vitro". Since then, a vast number of technologies have been developed allowing large-scale reading and writing of DNA, as well as tools for complex modifications and alterations of the genetic code. Natural genomes can be seen as software version 1.0; synthetic genomics aims to rewrite this software with "build to understand" and "build to apply" philosophies. One of the predominant model organisms is the baker's yeast Saccharomyces cerevisiae. Its importance ranges from ancient biotechnologies such as baking and brewing, to high-end valuable compound synthesis on industrial scales. This tiny sugar fungus contributed greatly to enabling humankind to reach its current development status. This review discusses recent developments in the field of genetic engineering for budding yeast S. cerevisiae, and its application in biotechnology. The article highlights advances from Sc1.0 to the developments in synthetic genomics paving the way towards Sc2.0. With the synthetic genome of Sc2.0 nearing completion, the article also aims to propose perspectives for potential Sc3.0 and subsequent versions as well as its implications for basic and applied research.
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Affiliation(s)
- Daniel Schindler
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany; ; Tel.: +49-6421-178533
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122
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Fasanello VJ, Liu P, Botero CA, Fay JC. High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae. PeerJ 2020; 8:e10118. [PMID: 33088623 PMCID: PMC7571412 DOI: 10.7717/peerj.10118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge. RESULTS We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics. CONCLUSIONS Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
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Affiliation(s)
- Vincent J. Fasanello
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Ping Liu
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Carlos A. Botero
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Justin C. Fay
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States of America
- Department of Biology, University of Rochester, Rochester, NY, United States of America
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123
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Fan S, Li C, Bing J, Huang G, Du H. Discovery of the Diploid Form of the Emerging Fungal Pathogen Candida auris. ACS Infect Dis 2020; 6:2641-2646. [PMID: 32902947 DOI: 10.1021/acsinfecdis.0c00282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The new multidrug-resistant pathogen Candida auris was first described in 2009 in Japan and has emerged in many countries worldwide. This human fungal pathogen has long been considered a haploid fungus. Here, we report the discovery of the diploid form and spontaneous ploidy shifts in clinical isolates of C. auris. Haploid and diploid cells of C. auris differ in several aspects including growth rates, virulence, and global gene expression profiles. For example, diploid cells exhibit a slower growth rate than haploid cells in in vitro culture media; however, they are more virulent than haploid cells in a mouse systemic infection model. Global transcriptional expression analysis demonstrates that both haploid and diploid cells express a set of ploidy-enriched genes, which are involved in the regulation of metabolism, cell wall maintenance, translation and DNA replication, and other important biological processes. Antifungal susceptibility testing shows that haploid and diploid cells exhibit similar responses when treated with a number of antifungals. Taken together, haploid and diploid cells may have different fitness responses to diverse niches, and ploidy changes could be an adaptive strategy of C. auris to environmental changes. Our findings shed new light on the biology and pathogenesis of this emerging fungal pathogen.
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Affiliation(s)
- Shuru Fan
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chao Li
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Bing
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Han Du
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Ma P, Zhang X, Chen L, Zhao Q, Zhang Q, Hua X, Wang Z, Tang H, Yu Q, Zhang M, Ming R, Zhang J. Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum. BMC PLANT BIOLOGY 2020; 20:422. [PMID: 32928111 PMCID: PMC7488781 DOI: 10.1186/s12870-020-02599-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/13/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. RESULTS In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. CONCLUSIONS SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.
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Affiliation(s)
- Panpan Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lanping Chen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qian Zhao
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qingyi Yu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Muqing Zhang
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
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Heasley LR, Watson RA, Argueso JL. Punctuated Aneuploidization of the Budding Yeast Genome. Genetics 2020; 216:43-50. [PMID: 32753390 PMCID: PMC7463280 DOI: 10.1534/genetics.120.303536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/30/2020] [Indexed: 11/18/2022] Open
Abstract
Remarkably complex patterns of aneuploidy have been observed in the genomes of many eukaryotic cell types, ranging from brewing yeasts to tumor cells. Such aberrant karyotypes are generally thought to take shape progressively over many generations, but evidence also suggests that genomes may undergo faster modes of evolution. Here, we used diploid Saccharomyces cerevisiae cells to investigate the dynamics with which aneuploidies arise. We found that cells selected for the loss of a single chromosome often acquired additional unselected aneuploidies concomitantly. The degrees to which these genomes were altered fell along a spectrum, ranging from simple events affecting just a single chromosome, to systemic events involving many. The striking complexity of karyotypes arising from systemic events, combined with the high frequency at which we detected them, demonstrates that cells can rapidly achieve highly altered genomic configurations during temporally restricted episodes of genomic instability.
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Affiliation(s)
- Lydia R Heasley
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523
| | - Ruth A Watson
- 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
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127
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Cancer regeneration: Polyploid cells are the key drivers of tumor progression. Biochim Biophys Acta Rev Cancer 2020; 1874:188408. [PMID: 32827584 DOI: 10.1016/j.bbcan.2020.188408] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022]
Abstract
In spite of significant advancements of therapies for initial eradication of cancers, tumor relapse remains a major challenge. It is for a long time known that polyploid malignant cells are a main source of resistance against chemotherapy and irradiation. However, therapeutic approaches targeting these cells have not been appropriately pursued which could partly be due to the shortage of knowledge on the molecular biology of cell polyploidy. On the other hand, there is a rising trend to appreciate polyploid/ multinucleated cells as key players in tissue regeneration. In this review, we suggest an analogy between the functions of polyploid cells in normal and malignant tissues and discuss the idea that cell polyploidy is an evolutionary conserved source of tissue regeneration also exploited by cancers as a survival factor. In addition, polyploid cells are highlighted as a promising therapeutic target to overcome drug resistance and relapse.
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128
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Yeast chromosomal engineering to improve industrially-relevant phenotypes. Curr Opin Biotechnol 2020; 66:165-170. [PMID: 32818746 DOI: 10.1016/j.copbio.2020.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/30/2020] [Accepted: 07/05/2020] [Indexed: 11/27/2022]
Abstract
Genome structural variations enable microbes to evolve quickly under environmental stress. Recent efforts in synthetic biology have shown the ability of yeast chromosomal engineering to generate a larger scale of genome structural variations, which require a high efficiency of DNA rearrangement technology. In this review, we summarize the recent development of the SCRaMbLE system, an evolutionary approach, and the CRISPR/Cas9 technology to generate yeast genome rearrangement. Both technologies exhibit the powerful applications of chromosomal engineering to accelerate phenotypic evolution. We highlight several studies where yeast genome rearrangement has successfully improved industrially-relevant phenotypes, including the production of novel medicine, nutrition supplements, anti-tumor molecules, and the tolerance of environmental stress and drug resistance.
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Koonthongkaew J, Toyokawa Y, Ohashi M, Large CRL, Dunham MJ, Takagi H. Effect of the Ala234Asp replacement in mitochondrial branched-chain amino acid aminotransferase on the production of BCAAs and fusel alcohols in yeast. Appl Microbiol Biotechnol 2020. [PMID: 32776205 DOI: 10.1101/2020.06.26.166157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the mitochondrial branched-chain amino acid (BCAA) aminotransferase Bat1 plays an important role in the synthesis of BCAAs (valine, leucine, and isoleucine). Our upcoming study (Large et al. bioRχiv. 10.1101/2020.06.26.166157, Large et al. 2020) will show that the heterozygous tetraploid beer yeast strain, Wyeast 1056, which natively has a variant causing one amino acid substitution of Ala234Asp in Bat1 on one of the four chromosomes, produced higher levels of BCAA-derived fusel alcohols in the brewer's wort medium than a derived strain lacking this mutation. Here, we investigated the physiological role of the A234D variant Bat1 in S. cerevisiae. Both bat1∆ and bat1A234D cells exhibited the same phenotypes relative to the wild-type Bat1 strain-namely, a repressive growth rate in the logarithmic phase; decreases in intracellular valine and leucine content in the logarithmic and stationary growth phases, respectively; an increase in fusel alcohol content in culture medium; and a decrease in the carbon dioxide productivity. These results indicate that amino acid change from Ala to Asp at position 234 led to a functional impairment of Bat1, although homology modeling suggests that Asp234 in the variant Bat1 did not inhibit enzymatic activity directly. KEY POINTS: • Yeast cells expressing Bat1A234D exhibited a slower growth phenotype. • The Val and Leu levels were decreased in yeast cells expressing Bat1A234D. • The A234D substitution causes a loss-of-function in Bat1. • The A234D substitution in Bat1 increased fusel alcohol production in yeast cells.
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Affiliation(s)
- Jirasin Koonthongkaew
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Yoichi Toyokawa
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Masataka Ohashi
- Nara Prefecture Institute of Industrial Development, 129-1 Kashiwagi-cho, Nara, Nara, 630-8031, Japan
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Hiroshi Takagi
- Division of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan.
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Comparative Genomic Analyses and a Novel Linkage Map for Cisco ( Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids. G3-GENES GENOMES GENETICS 2020; 10:2863-2878. [PMID: 32611547 PMCID: PMC7407451 DOI: 10.1534/g3.120.401497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.
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131
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Carretero‐Paulet L, Van de Peer Y. The evolutionary conundrum of whole-genome duplication. AMERICAN JOURNAL OF BOTANY 2020; 107:1101-1105. [PMID: 32815563 PMCID: PMC7540024 DOI: 10.1002/ajb2.1520] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/06/2020] [Indexed: 05/07/2023]
Affiliation(s)
| | - Yves Van de Peer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaSouth Africa
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132
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Pienta KJ, Hammarlund EU, Axelrod R, Brown JS, Amend SR. Poly-aneuploid cancer cells promote evolvability, generating lethal cancer. Evol Appl 2020; 13:1626-1634. [PMID: 32952609 PMCID: PMC7484876 DOI: 10.1111/eva.12929] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer cells utilize the forces of natural selection to evolve evolvability allowing a constant supply of heritable variation that permits a cancer species to evolutionary track changing hazards and opportunities. Over time, the dynamic tumor ecosystem is exposed to extreme, catastrophic changes in the conditions of the tumor-natural (e.g., loss of blood supply) or imposed (therapeutic). While the nature of these catastrophes may be varied or unique, their common property may be to doom the current cancer phenotype unless it evolves rapidly. Poly-aneuploid cancer cells (PACCs) may serve as efficient sources of heritable variation that allows cancer cells to evolve rapidly, speciate, evolutionarily track their environment, and most critically for patient outcome and survival, permit evolutionary rescue, therapy resistance, and metastasis. As a conditional evolutionary strategy, they permit the cancer cells to accelerate evolution under stress and slow down the generation of heritable variation when conditions are more favorable or when the cancer cells are closer to an evolutionary optimum. We hypothesize that they play a critical and outsized role in lethality by their increased capacity for invasion and motility, for enduring novel and stressful environments, and for generating heritable variation that can be dispensed to their 2N+ aneuploid progeny that make up the bulk of cancer cells within a tumor, providing population rescue in response to therapeutic stress. Targeting PACCs is essential to cancer therapy and patient cure-without the eradication of the resilient PACCs, cancer will recur in treated patients.
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Affiliation(s)
- Kenneth J. Pienta
- The Brady Urological InstituteJohns Hopkins School of MedicineBaltimoreMDUSA
| | - Emma U. Hammarlund
- Nordic Center for Earth EvolutionUniversity of Southern DenmarkOdenseDenmark
- Translational Cancer ResearchDepartment of Laboratory MedicineLund UniversityLundSweden
| | - Robert Axelrod
- Gerald R. Ford School of Public PolicyUniversity of MichiganAnn ArborMIUSA
| | - Joel S. Brown
- Cancer Biology and Evolution Program and Department of Integrated Mathematical OncologyMoffitt Cancer CenterTampaFLUSA
| | - Sarah R. Amend
- The Brady Urological InstituteJohns Hopkins School of MedicineBaltimoreMDUSA
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Abstract
Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.
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Affiliation(s)
- Shelby J. Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
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134
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Song Q, Ando A, Jiang N, Ikeda Y, Chen ZJ. Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biol 2020; 21:178. [PMID: 32698836 PMCID: PMC7375004 DOI: 10.1186/s13059-020-02094-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect. RESULTS To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER (DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization. CONCLUSIONS Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
| | - Ning Jiang
- Department of Biomedical Engineering, The University of Texas at Austin, 1 University Station C0800, Austin, TX, 78712, USA
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA.
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135
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Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. eLife 2020; 9:e58349. [PMID: 32687060 PMCID: PMC7371428 DOI: 10.7554/elife.58349] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation (CNV), in many diverse isolates of the human fungal pathogen Candida albicans (Todd et al., 2019). Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings.
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Affiliation(s)
- Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
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136
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Seear PJ, France MG, Gregory CL, Heavens D, Schmickl R, Yant L, Higgins JD. A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata. PLoS Genet 2020; 16:e1008900. [PMID: 32667955 PMCID: PMC7392332 DOI: 10.1371/journal.pgen.1008900] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 07/30/2020] [Accepted: 06/01/2020] [Indexed: 01/09/2023] Open
Abstract
In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20-100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.
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Affiliation(s)
- Paul J. Seear
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martin G. France
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Catherine L. Gregory
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Darren Heavens
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, United Kingdom
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Levi Yant
- Future Food Beacon of Excellence and the School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- * E-mail: (LY); (JDH)
| | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- * E-mail: (LY); (JDH)
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137
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Fox DT, Soltis DE, Soltis PS, Ashman TL, Van de Peer Y. Polyploidy: A Biological Force From Cells to Ecosystems. Trends Cell Biol 2020; 30:688-694. [PMID: 32646579 DOI: 10.1016/j.tcb.2020.06.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022]
Abstract
Polyploidy, resulting from the duplication of the entire genome of an organism or cell, greatly affects genes and genomes, cells and tissues, organisms, and even entire ecosystems. Despite the wide-reaching importance of polyploidy, communication across disciplinary boundaries to identify common themes at different scales has been almost nonexistent. However, a critical need remains to understand commonalities that derive from shared polyploid cellular processes across organismal diversity, levels of biological organization, and fields of inquiry - from biodiversity and biocomplexity to medicine and agriculture. Here, we review the current understanding of polyploidy at the organismal and suborganismal levels, identify shared research themes and elements, and propose new directions to integrate research on polyploidy toward confronting interdisciplinary grand challenges of the 21st century.
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Affiliation(s)
- Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa; College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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138
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Randez-Gil F, Prieto JA, Rodríguez-Puchades A, Casas J, Sentandreu V, Estruch F. Myriocin-induced adaptive laboratory evolution of an industrial strain of Saccharomyces cerevisiae reveals its potential to remodel lipid composition and heat tolerance. Microb Biotechnol 2020; 13:1066-1081. [PMID: 32212314 PMCID: PMC7264895 DOI: 10.1111/1751-7915.13555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/01/2020] [Indexed: 12/13/2022] Open
Abstract
The modification of lipid composition allows cells to adjust membrane biophysical properties in response to changes in environmental temperature. Here, we use adaptive laboratory evolution (ALE) in the presence of myriocin, a sphingolipid (SLs) biosynthesis inhibitor, to remodel the lipid profile of an industrial yeast strain (LH) of Saccharomyces cerevisiae. The approach enabled to obtain a heterogeneous population (LHev) of myriocin-tolerant evolved clones characterized by its growth capacity at high temperature. Myriocin exposure also caused tolerance to soraphen A, an inhibitor of the acetyl-CoA carboxylase Acc1, the rate-limiting enzyme in fatty acid de novo production, supporting a change in lipid metabolism during ALE. In line with this, characterization of two randomly selected clones, LH03 and LH09, showed the presence of lipids with increased saturation degree and reduced acyl length. In addition, the clone LH03, which displays the greater improvement in fitness at 40°C, exhibited higher SL content as compared with the parental strain. Analysis of the LH03 and LH09 genomes revealed a loss of chromosomes affecting genes that have a role in fatty acid synthesis and elongation. The link between ploidy level and growth at high temperature was further supported by the analysis of a fully isogenic set of yeast strains with ploidy between 1N and 4N which showed that the loss of genome content provides heat tolerance. Consistent with this, a thermotolerant evolved population (LH40°) generated from the parental LH strain by heat-driven ALE exhibited a reduction in the chromosome copy number. Thus, our results identify myriocin-driven evolution as a powerful approach to investigate the mechanisms of acquired thermotolerance and to generate improved strains.
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Affiliation(s)
- Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, Paterna, Valencia, 46980, Spain
| | - Jose A Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, Paterna, Valencia, 46980, Spain
| | - Alejandro Rodríguez-Puchades
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino 7, Paterna, Valencia, 46980, Spain
| | - Josefina Casas
- Research Unit on BioActive Molecules (RUBAM), Instituto de Química Avanzada de Cataluña, Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26., Barcelona, 08034, Spain
- CIBER-EHD, Instituto de Salud Carlos III, Monforte de Lemos 3-5., Madrid, 28029, Spain
| | - Vicente Sentandreu
- Genomics Section, Central Service for Experimental Research (SCSIE), Universitat de València, Dr. Moliner 50, Burjassot, 46100, Spain
| | - Francisco Estruch
- Departament of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, Burjassot, 46100, Spain
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139
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Ryu HY, Ahn SH, Hochstrasser M. SUMO and cellular adaptive mechanisms. Exp Mol Med 2020; 52:931-939. [PMID: 32591648 PMCID: PMC7338444 DOI: 10.1038/s12276-020-0457-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin family member SUMO is a covalent regulator of proteins that functions in response to various stresses, and defects in SUMO-protein conjugation or deconjugation have been implicated in multiple diseases. The loss of the Ulp2 SUMO protease, which reverses SUMO-protein modifications, in the model eukaryote Saccharomyces cerevisiae is severely detrimental to cell fitness and has emerged as a useful model for studying how cells adapt to SUMO system dysfunction. Both short-term and long-term adaptive mechanisms are triggered depending on the length of time cells spend without this SUMO chain-cleaving enzyme. Such short-term adaptations include a highly specific multichromosome aneuploidy and large changes in ribosomal gene transcription. While aneuploid ulp2Δ cells survive, they suffer severe defects in growth and stress resistance. Over many generations, euploidy is restored, transcriptional programs are adjusted, and specific genetic changes that compensate for the loss of the SUMO protease are observed. These long-term adapted cells grow at normal rates with no detectable defects in stress resistance. In this review, we examine the connections between SUMO and cellular adaptive mechanisms more broadly. Cellular stress caused by disrupting attachment of the ubiquitous small ubiquitin-like modifier (SUMO) proteins, which are present in most organisms and regulate numerous DNA processes and stress responses by attaching to key proteins, results in some remarkable adaptations. Mark Hochstrasser at Yale University, New Haven, USA, and co-workers review how this “sumoylation” is reversed by protease enzymes, and how imbalances between sumoylation and desumoylation may be linked to diseases including cancer. When certain SUMO proteases are deliberately disrupted, the cells quickly become aneuploid, i.e., carry an abnormal number of chromosomes. These cells show severe growth defects, but over many generations they regain the normal number of chromosomes. They also undergo genetic changes that promote alternative mechanisms that compensate for losing the SUMO protease and facilitate the same efficient stress responses as the original cells.
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Affiliation(s)
- Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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140
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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141
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Host-Induced Genome Instability Rapidly Generates Phenotypic Variation across Candida albicans Strains and Ploidy States. mSphere 2020; 5:5/3/e00433-20. [PMID: 32493724 PMCID: PMC7273350 DOI: 10.1128/msphere.00433-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Candida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment. Candida albicans is an opportunistic fungal pathogen of humans that is typically diploid yet has a highly labile genome tolerant of large-scale perturbations including chromosomal aneuploidy and loss-of-heterozygosity events. The ability to rapidly generate genetic variation is crucial for C. albicans to adapt to changing or stressful environments, like those encountered in the host. Genetic variation occurs via stress-induced mutagenesis or can be generated through its parasexual cycle, in which tetraploids arise via diploid mating or stress-induced mitotic defects and undergo nonmeiotic ploidy reduction. However, it remains largely unknown how genetic background contributes to C. albicans genome instability in vitro or in the host environment. Here, we tested how genetic background, ploidy, and the host environment impacts C. albicans genome stability. We found that host association induced both loss-of-heterozygosity events and genome size changes, regardless of genetic background or ploidy. However, the magnitude and types of genome changes varied across C. albicans strain background and ploidy state. We then assessed if host-induced genomic changes resulted in fitness consequences on growth rate and nonlethal virulence phenotypes and found that many host-derived isolates significantly changed relative to their parental strain. Interestingly, diploid host-associated C. albicans predominantly decreased host reproductive fitness, whereas tetraploid host-associated C. albicans increased host reproductive fitness. Together, these results are important for understanding how host-induced genomic changes in C. albicans alter its relationship with the host. IMPORTANCECandida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment.
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142
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Lin YH, Zhang S, Zhu M, Lu T, Chen K, Wen Z, Wang S, Xiao G, Luo D, Jia Y, Li L, MacConmara M, Hoshida Y, Singal A, Yopp A, Wang T, Zhu H. Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury. Gastroenterology 2020; 158:1698-1712.e14. [PMID: 31972235 PMCID: PMC8902703 DOI: 10.1053/j.gastro.2020.01.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Thirty to 90% of hepatocytes contain whole-genome duplications, but little is known about the fates or functions of these polyploid cells or how they affect development of liver disease. We investigated the effects of continuous proliferative pressure, observed in chronically damaged liver tissues, on polyploid cells. METHODS We studied Rosa-rtTa mice (controls) and Rosa-rtTa;TRE-short hairpin RNA mice, which have reversible knockdown of anillin, actin binding protein (ANLN). Transient administration of doxycycline increases the frequency and degree of hepatocyte polyploidy without permanently altering levels of ANLN. Mice were then given diethylnitrosamine and carbon tetrachloride (CCl4) to induce mutations, chronic liver damage, and carcinogenesis. We performed partial hepatectomies to test liver regeneration and then RNA-sequencing to identify changes in gene expression. Lineage tracing was used to rule out repopulation from non-hepatocyte sources. We imaged dividing hepatocytes to estimate the frequency of mitotic errors during regeneration. We also performed whole-exome sequencing of 54 liver nodules from patients with cirrhosis to quantify aneuploidy, a possible outcome of polyploid cell divisions. RESULTS Liver tissues from control mice given CCl4 had significant increases in ploidy compared with livers from uninjured mice. Mice with knockdown of ANLN had hepatocyte ploidy above physiologic levels and developed significantly fewer liver tumors after administration of diethylnitrosamine and CCl4 compared with control mice. Increased hepatocyte polyploidy was not associated with altered regenerative capacity or tissue fitness, changes in gene expression, or more mitotic errors. Based on lineage-tracing experiments, non-hepatocytes did not contribute to liver regeneration in mice with increased polyploidy. Despite an equivalent rate of mitosis in hepatocytes of differing ploidies, we found no lagging chromosomes or micronuclei in mitotic polyploid cells. In nodules of human cirrhotic liver tissue, there was no evidence of chromosome-level copy number variations. CONCLUSIONS Mice with increased polyploid hepatocytes develop fewer liver tumors following chronic liver damage. Remarkably, polyploid hepatocytes maintain the ability to regenerate liver tissues during chronic damage without generating mitotic errors, and aneuploidy is not commonly observed in cirrhotic livers. Strategies to increase numbers of polypoid hepatocytes might be effective in preventing liver cancer.
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Affiliation(s)
- Yu-Hsuan Lin
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Shuyuan Zhang
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Min Zhu
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Tianshi Lu
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine,Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Zhuoyu Wen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Danni Luo
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Yuemeng Jia
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Lin Li
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | | | | | | | | | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences,Kidney Cancer Program, Simmons Comprehensive Cancer Center,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.
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143
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Wong GKS, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M. Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:741-765. [PMID: 31851546 DOI: 10.1146/annurev-arplant-042916-041040] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C4 photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.
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Affiliation(s)
- Gane Ka-Shu Wong
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada;
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Douglas E Soltis
- Florida Museum of Natural History, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois 60022, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Michael Melkonian
- Faculty of Biology, University of Duisburg-Essen, D-45141 Essen, Germany
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144
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Abstract
Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy. Many industrial organisms are the result of recent or ancient allopolypoidy events. Here the authors iteratively combine the genomes of six yeast species to generate a viable hybrid.
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145
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Cotton JA, Durrant C, Franssen SU, Gelanew T, Hailu A, Mateus D, Sanders MJ, Berriman M, Volf P, Miles MA, Yeo M. Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani. PLoS Negl Trop Dis 2020; 14:e0007143. [PMID: 32310945 PMCID: PMC7237039 DOI: 10.1371/journal.pntd.0007143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/19/2020] [Accepted: 12/24/2019] [Indexed: 12/30/2022] Open
Abstract
Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also been responsible for major epidemics. The presence of hybrid genotypes has been widely reported in surveys of natural populations, genetic variation reported in a number of Leishmania species, and the extant capacity for genetic exchange demonstrated in laboratory experiments. However, patterns of recombination and the evolutionary history of admixture that produced these hybrid populations remain unclear. Here, we use whole-genome sequence data to investigate Ethiopian L. donovani isolates previously characterized as hybrids by microsatellite and multi-locus sequencing. To date there is only one previous study on a natural population of Leishmania hybrids based on whole-genome sequences. We propose that these hybrids originate from recombination between two different lineages of Ethiopian L. donovani occurring in the same region. Patterns of inheritance are more complex than previously reported with multiple, apparently independent, origins from similar parents that include backcrossing with parental types. Analysis indicates that hybrids are representative of at least three different histories. Furthermore, isolates were highly polysomic at the level of chromosomes with differences between parasites recovered from a recrudescent infection from a previously treated individual. The results demonstrate that recombination is a significant feature of natural populations and contributes to the growing body of data that shows how recombination, and gene flow, shape natural populations of Leishmania.
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Affiliation(s)
| | | | | | - Tesfaye Gelanew
- Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Asrat Hailu
- Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - David Mateus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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146
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Abstract
Polyploids generated by natural whole genome duplication have served as a dynamic force in vertebrate evolution. As evidence for evolution, polyploid organisms exist generally, however there have been no reports of polyploid organisms in mammals. In mice, polyploid embryos under normal culture conditions normally develop to the blastocyst stage. Nevertheless, most tetraploid embryos degenerate after implantation, indicating that whole genome duplication produces harmful effects on normal development in mice. Most previous research on polyploidy has mainly focused on tetraploid embryos. Analysis of various ploidy outcomes is important to comprehend the effects of polyploidization on embryo development. The purpose of this present study was to discover the extent of the polyploidization effect on implantation and development in post-implantation embryos. This paper describes for the first time an octaploid embryo implanted in mice despite hyper-polyploidization, and indicates that these mammalian embryos have the ability to implant, and even develop, despite the harmfulness of extreme whole genome duplication.
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147
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Chance and necessity in the pleiotropic consequences of adaptation for budding yeast. Nat Ecol Evol 2020; 4:601-611. [PMID: 32152531 PMCID: PMC8063891 DOI: 10.1038/s41559-020-1128-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/28/2020] [Indexed: 12/12/2022]
Abstract
Mutations that a population accumulates during evolution in one 'home' environment may cause fitness gains or losses in other environments. Such pleiotropic fitness effects determine the evolutionary fate of the population in variable environments and can lead to ecological specialization. It is unclear how the pleiotropic outcomes of evolution are shaped by the intrinsic randomness of the evolutionary process and by the deterministic variation in selection pressures across environments. Here, to address this question, we evolved 20 replicate populations of the yeast Saccharomyces cerevisiae in 11 laboratory environments and measured their fitness across multiple conditions. We found that evolution led to diverse pleiotropic fitness gains and losses, driven by multiple types of mutations. Approximately 60% of this variation is explained by the home environment of a clone and the most common parallel genetic changes, whereas about 40% is attributed to the stochastic accumulation of mutations whose pleiotropic effects are unpredictable. Although populations are typically specialized to their home environment, generalists also evolved in almost all of the conditions. Our results suggest that the mutations that accumulate during evolution incur a variety of pleiotropic costs and benefits with different probabilities. Thus, whether a population evolves towards a specialist or a generalist phenotype is heavily influenced by chance.
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148
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Molecular signatures of aneuploidy-driven adaptive evolution. Nat Commun 2020; 11:588. [PMID: 32001709 PMCID: PMC6992709 DOI: 10.1038/s41467-019-13669-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
Alteration of normal ploidy (aneuploidy) can have a number of opposing effects, such as unbalancing protein abundances and inhibiting cell growth but also accelerating genetic diversification and rapid adaptation. The interplay of these detrimental and beneficial effects remains puzzling. Here, to understand how cells develop tolerance to aneuploidy, we subject disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution under strong selection, by forcing disomy maintenance and daily population dilution. We characterize mutations, karyotype alterations and gene expression changes, and dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates and displayed diverse adaptive events. They tended to evolve towards normal ploidy through chromosomal DNA loss and gene expression changes. We identify genes with recurrent mutations and altered expression in multiple lines, revealing a variant that improves growth under genotoxic stresses. These findings support rapid evolvability of disomic strains that can be used to characterize fitness effects of mutations under different stress conditions. Aneuploidy (abnormal chromosome number) can enable rapid adaptation to stress conditions, but it also entails fitness costs from gene imbalance. Here, the authors experimentally evolve yeast while forcing maintenance of aneuploidy to identify the mechanisms that promote tolerance of aneuploidy.
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149
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Birkbak NJ, McGranahan N. Cancer Genome Evolutionary Trajectories in Metastasis. Cancer Cell 2020; 37:8-19. [PMID: 31935374 DOI: 10.1016/j.ccell.2019.12.004] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/12/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023]
Abstract
Metastatic cancer is a major cause of death and remains largely incurable. A better understanding of metastasis is therefore desperately needed to improve prognosis for late-stage disease. Here we survey the landscape of studies exploring the genomics of metastatic cancer. We consider evidence for genomic drivers of metastasis and explore studies investigating modes of metastatic spread.
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Affiliation(s)
- Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
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150
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Designing New Yeasts for Craft Brewing: When Natural Biodiversity Meets Biotechnology. BEVERAGES 2020. [DOI: 10.3390/beverages6010003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Beer is a fermented beverage with a history as old as human civilization. Ales and lagers are by far the most common beers; however, diversification is becoming increasingly important in the brewing market and the brewers are continuously interested in improving and extending the range of products, especially in the craft brewery sector. Fermentation is one of the widest spaces for innovation in the brewing process. Besides Saccharomyces cerevisiae ale and Saccharomyces pastorianus lager strains conventionally used in macro-breweries, there is an increasing demand for novel yeast starter cultures tailored for producing beer styles with diversified aroma profiles. Recently, four genetic engineering-free approaches expanded the genetic background and the phenotypic biodiversity of brewing yeasts and allowed novel costumed-designed starter cultures to be developed: (1) the research for new performant S. cerevisiae yeasts from fermented foods alternative to beer; (2) the creation of synthetic hybrids between S. cerevisiae and Saccharomyces non-cerevisiae in order to mimic lager yeasts; (3) the exploitation of evolutionary engineering approaches; (4) the usage of non-Saccharomyces yeasts. Here, we summarized the pro and contra of these approaches and provided an overview on the most recent advances on how brewing yeast genome evolved and domestication took place. The resulting correlation maps between genotypes and relevant brewing phenotypes can assist and further improve the search for novel craft beer starter yeasts, enhancing the portfolio of diversified products offered to the final customer.
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