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Ganda E, Chakrabarti A, Sardi M, Bobel JM, Kozlowicz B, Norton SA, Warren LK, Khafipour E. PSXV-11 A Postbiotic from Saccharomyces Cerevisiae Fermentation Improves Microbiome Robustness in Young Stress-Challenged Horses in Training. J Anim Sci 2022. [DOI: 10.1093/jas/skac247.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Nutritional and environmental stressors can disturb the gut microbiome of horses which may ultimately decrease their health and performance. In this study, we hypothesized that a Saccharomyces cerevisiae fermentation postbiotic (SCFP) improves the robustness of the gut microbiome in stress-challenged horses. Quarter horses (n=20) were randomized based on sex, age (22 ± 3 mo) and body weight (439 ± 3 kg) to receive a basal diet (60% forage:40% concentrate) supplemented without (CON) or with SCFP (21g/d, TruEquine, Diamond V, Cedar Rapids, IA). Treatments were implemented for 60 d. On d 57, horses were tethered with their heads elevated 35 cm above wither height for 12 h to mimic long-distance transport stress. Fecal samples were collected on d 0, 28, and 56 pre-challenge and at 0, 12, 24 and 72 h post-challenge and subjected to DNA extraction and Nanopore shotgun metagenomics. Alpha-diversity and microbial abundances were compared using non-parametric Wilcoxon-Rank-Sum test with Benjamini-Hochberg FDR correction. The SCFP stabilized alpha-diversity across all time points, whereas CON horses had more fluctuation (P < 0.05) at 12, 24 and 72 h post-challenge compared to d 56. This resulted in a significant difference between CON and SCFP at 0 and 12 h. There was no difference in beta-diversity between SCFP and CON on d 56, however, treatments grouped separately (PERMANOVA, P < 0.05) within the 12 h post-challenge showing SCFP horses maintained higher abundances (P < 0.05) of fibrolytic taxa such as Fibrobacter succinogenes, Ruminococcus species and several members of Prevotellaceae and Lachnospiraceae among others. During the post-challenge period compositional clusters in the microbiome of CON horses were characterized by low abundances (P < 0.05) of Butyrivibrio, Pseudobutyrivibrio and Blautia species versus SCFP. Overall, treatments were similar in microbiome diversity and composition pre-challenge, however, post-challenge, SCFP supplementation improved microbiome robustness indicating an ability to resist change due to stress.
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Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 2018; 210:219-234. [PMID: 30045857 PMCID: PMC6116967 DOI: 10.1534/genetics.118.301161] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/23/2018] [Indexed: 01/20/2023] Open
Abstract
Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C2C1im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C2C1im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C2C1im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.
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Affiliation(s)
- Douglas A Higgins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Megan K M Young
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Mary Tremaine
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Maria Sardi
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Jenna M Fletcher
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Margaret Agnew
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Lisa Liu
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Quinn Dickinson
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - David Peris
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Russell L Wrobel
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Chris Todd Hittinger
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Audrey P Gasch
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Steven W Singer
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, California 94720
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Robert Landick
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53726
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53726
| | - Michael P Thelen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Trey K Sato
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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Abstract
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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4
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Sardi M, Gasch AP. Genetic background effects in quantitative genetics: gene-by-system interactions. Curr Genet 2018; 64:1173-1176. [PMID: 29644456 DOI: 10.1007/s00294-018-0835-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/18/2023]
Abstract
Proper cell function depends on networks of proteins that interact physically and functionally to carry out physiological processes. Thus, it seems logical that the impact of sequence variation in one protein could be significantly influenced by genetic variants at other loci in a genome. Nonetheless, the importance of such genetic interactions, known as epistasis, in explaining phenotypic variation remains a matter of debate in genetics. Recent work from our lab revealed that genes implicated from an association study of toxin tolerance in Saccharomyces cerevisiae show extensive interactions with the genetic background: most implicated genes, regardless of allele, are important for toxin tolerance in only one of two tested strains. The prevalence of background effects in our study adds to other reports of widespread genetic-background interactions in model organisms. We suggest that these effects represent many-way interactions with myriad features of the cellular system that vary across classes of individuals. Such gene-by-system interactions may influence diverse traits and require new modeling approaches to accurately represent genotype-phenotype relationships across individuals.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Cargill, Incorporated, Minneapolis, MN, 55440, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Ariagno JI, Mendeluk GR, Furlan MJ, Sardi M, Chenlo P, Curi SM, Pugliese MN, Repetto HE, Cohen M. Computer-aided sperm analysis: a useful tool to evaluate patient's response to varicocelectomy. Asian J Androl 2018; 19:449-452. [PMID: 27101803 PMCID: PMC5507091 DOI: 10.4103/1008-682x.173441] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Preoperative and postoperative sperm parameter values from infertile men with varicocele were analyzed by computer-aided sperm analysis (CASA) to assess if sperm characteristics improved after varicocelectomy. Semen samples of men with proven fertility (n = 38) and men with varicocele-related infertility (n = 61) were also analyzed. Conventional semen analysis was performed according to WHO (2010) criteria and a CASA system was employed to assess kinetic parameters and sperm concentration. Seminal parameters values in the fertile group were very far above from those of the patients, either before or after surgery. No significant improvement in the percentage normal sperm morphology (P = 0.10), sperm concentration (P = 0.52), total sperm count (P = 0.76), subjective motility (%) (P = 0.97) nor kinematics (P = 0.30) was observed after varicocelectomy when all groups were compared. Neither was significant improvement found in percentage normal sperm morphology (P = 0.91), sperm concentration (P = 0.10), total sperm count (P = 0.89) or percentage motility (P = 0.77) after varicocelectomy in paired comparisons of preoperative and postoperative data. Analysis of paired samples revealed that the total sperm count (P = 0.01) and most sperm kinetic parameters: curvilinear velocity (P = 0.002), straight-line velocity (P = 0.0004), average path velocity (P = 0.0005), linearity (P = 0.02), and wobble (P = 0.006) improved after surgery. CASA offers the potential for accurate quantitative assessment of each patient's response to varicocelectomy.
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Affiliation(s)
- Julia I Ariagno
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - Gabriela R Mendeluk
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - María J Furlan
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - M Sardi
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - P Chenlo
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - Susana M Curi
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - Mercedes N Pugliese
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - Herberto E Repetto
- Clinical Biochemistry Department, Male Fertility Laboratory, Faculty of Pharmacy and Biochemetry, University of Buenos Aires, Argentina
| | - Mariano Cohen
- Urology Department, "José de San Martín" Clinical Hospital, University of Buenos Aires, Buenos Aires, Argentina (CP1120)
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Sardi M, Paithane V, Place M, Robinson DE, Hose J, Wohlbach DJ, Gasch AP. Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. PLoS Genet 2018; 14:e1007217. [PMID: 29474395 PMCID: PMC5849340 DOI: 10.1371/journal.pgen.1007217] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/13/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cellulosic plant biomass is a promising sustainable resource for generating alternative biofuels and biochemicals with microbial factories. But a remaining bottleneck is engineering microbes that are tolerant of toxins generated during biomass processing, because mechanisms of toxin defense are only beginning to emerge. Here, we exploited natural diversity in 165 Saccharomyces cerevisiae strains isolated from diverse geographical and ecological niches, to identify mechanisms of hydrolysate-toxin tolerance. We performed genome-wide association (GWA) analysis to identify genetic variants underlying toxin tolerance, and gene knockouts and allele-swap experiments to validate the involvement of implicated genes. In the process of this work, we uncovered a surprising difference in genetic architecture depending on strain background: in all but one case, knockout of implicated genes had a significant effect on toxin tolerance in one strain, but no significant effect in another strain. In fact, whether or not the gene was involved in tolerance in each strain background had a bigger contribution to strain-specific variation than allelic differences. Our results suggest a major difference in the underlying network of causal genes in different strains, suggesting that mechanisms of hydrolysate tolerance are very dependent on the genetic background. These results could have significant implications for interpreting GWA results and raise important considerations for engineering strategies for industrial strain improvement. Understanding the genetic architecture of complex traits is important for elucidating the genotype-phenotype relationship. Many studies have sought genetic variants that underlie phenotypic variation across individuals, both to implicate causal variants and to inform on architecture. Here we used genome-wide association analysis to identify genes and processes involved in tolerance of toxins found in plant-biomass hydrolysate, an important substrate for sustainable biofuel production. We found substantial variation in whether or not individual genes were important for tolerance across genetic backgrounds. Whether or not a gene was important in a given strain background explained more variation than the alleleic differences in the gene. These results suggest substantial variation in gene contributions, and perhaps underlying mechanisms, of toxin tolerance.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.,Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Vaishnavi Paithane
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - De Elegant Robinson
- Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dana J Wohlbach
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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7
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Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 2017; 10:78. [PMID: 28360936 PMCID: PMC5369230 DOI: 10.1186/s13068-017-0763-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/18/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. RESULTS To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, Saccharomyces mikatae strains have high innate tolerance to hydrolysate toxins, while some Saccharomyces species have a robust native capacity to consume xylose. CONCLUSIONS This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Ryan V. Moriarty
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - William G. Alexander
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - EmilyClare Baker
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Kayla Sylvester
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Maria Sardi
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro Argentina
| | - Qi-Ming Wang
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC Canada
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Guillaume Charron
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Christian R. Landry
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Katie E. Hyma
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Justin C. Fay
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Narasimhan RA, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Piotrowski JS, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R. Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet 2016; 12:e1006447. [PMID: 27828955 PMCID: PMC5102404 DOI: 10.1371/journal.pgen.1006447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLoS Genet 2016; 12:e1006372. [PMID: 27741250 PMCID: PMC5065143 DOI: 10.1371/journal.pgen.1006372] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022] Open
Abstract
The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy. Despite extensive knowledge of the regulatory networks controlling carbon metabolism in yeast, little is known about how to reprogram S. cerevisiae to ferment xylose at rates comparable to glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses to identify and characterize the responsible mutations in a series of evolved strains capable of metabolizing xylose aerobically or anaerobically. We report that rapid xylose conversion by engineered and evolved S. cerevisiae strains depends upon epistatic interactions among genes encoding a xylose reductase (GRE3), a component of MAP Kinase (MAPK) signaling (HOG1), a regulator of Protein Kinase A (PKA) signaling (IRA2), and a scaffolding protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis (ISU1). Interestingly, the mutation in IRA2 only impacted anaerobic xylose consumption and required the loss of ISU1 function, indicating a previously unknown connection between PKA signaling, Fe-S cluster biogenesis, and anaerobiosis. Proteomic and metabolomic comparisons revealed that the xylose-metabolizing mutant strains exhibit altered metabolic pathways relative to the parental strain when grown in xylose. Further analyses revealed that interacting mutations in HOG1 and ISU1 unexpectedly elevated mitochondrial respiratory proteins and enabled rapid aerobic respiration of xylose and other non-fermentable carbon substrates. Our findings suggest a surprising connection between Fe-S cluster biogenesis and signaling that facilitates aerobic respiration and anaerobic fermentation of xylose, underscoring how much remains unknown about the eukaryotic signaling systems that regulate carbon metabolism. The yeast Saccharomyces cerevisiae is being genetically engineered to produce renewable biofuels from sustainable plant material. Efficient biofuel production from plant material requires conversion of the complex suite of sugars found in plant material, including the five-carbon sugar xylose. Because it does not efficiently metabolize xylose, S. cerevisiae has been engineered with a minimal set of genes that should overcome this problem; however, additional genetic changes are required for optimal fermentative conversion of xylose into biofuel. Despite extensive knowledge of the regulatory networks controlling glucose metabolism, less is known about the regulation of xylose metabolism and how to rewire these networks for effective biofuel production. Here we report genetic mutations that enabled the conversion of xylose into bioethanol by a previously ineffective yeast strain. By comparing altered protein and metabolite abundance within yeast cells containing these mutations, we determined that the mutations synergistically alter metabolic pathways to improve the rate of xylose conversion. One change in a gene with well-characterized aerobic mitochondrial functions was found to play an unexpected role in anaerobic conversion of xylose into ethanol. The results of this work will allow others to rapidly generate yeast strains for the conversion of xylose into biofuels and other products.
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Affiliation(s)
- Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (TKS); (APG); (RL)
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lucas S. Parreiras
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander S. Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin S. Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alan J. Higbee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Maria Sardi
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sean J. McIlwain
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M. Ong
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rebecca J. Breuer
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ragothaman Avanasi Narasimhan
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mick A. McGee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Quinn Dickinson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alex La Reau
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mingyuan Tian
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jennifer L. Reed
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P. Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (TKS); (APG); (RL)
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (TKS); (APG); (RL)
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Hose J, Yong CM, Sardi M, Wang Z, Newton MA, Gasch AP. Correction: Dosage compensation can buffer copy-number variation in wild yeast. eLife 2016; 5. [PMID: 27006204 PMCID: PMC4821797 DOI: 10.7554/elife.15743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 11/13/2022] Open
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11
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Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z. Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. eLife 2016; 5:e14409. [PMID: 26949252 PMCID: PMC4798956 DOI: 10.7554/elife.14409] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 12/19/2022] Open
Abstract
In our prior work by Hose et al., we performed a genome-sequencing survey and reported that aneuploidy was frequently observed in wild strains of S. cerevisiae. We also profiled transcriptome abundance in naturally aneuploid isolates compared to isogenic euploid controls and found that 10–30% of amplified genes, depending on the strain and affected chromosome, show lower-than-expected expression compared to gene copy number. In Hose et al., we argued that this gene group is enriched for genes subject to one or more modes of dosage compensation, where mRNA abundance is decreased in response to higher dosage of that gene. A recent manuscript by Torres et al. refutes our prior work. Here, we provide a response to Torres et al., along with additional analysis and controls to support our original conclusions. We maintain that aneuploidy is well tolerated in the wild strains of S. cerevisiae that we studied and that the group of genes enriched for those subject to dosage compensation show unique evolutionary signatures. DOI:http://dx.doi.org/10.7554/eLife.14409.001 Cells package their DNA into structures called chromosomes. Sometimes when a cell divides, it fails to allocate the right number of chromosomes to each new cell and so they end up with too many or too few chromosomes. The extra copies of the genes on an additional chromosome can be harmful to the cells, because the levels of the proteins encoded by those genes may rise abnormally. Some organisms counteract the harmful effect of having additional chromosomes through a process called dosage compensation. Proteins are produced using genetic information via two steps: first a gene’s DNA sequence is copied into a molecule of RNA, which is then translated into a protein. Dosage compensation can inactivate single genes or whole chromosomes via various means to ensure that the levels of RNA expressed remain normal, even in the presence of extra genes. In 2015, researchers from the University of Wisconsin-Madison reported that dosage compensation occurs in wild strains of budding yeast and effectively protects against the harmful effects of having extra chromosomes. However, these findings conflicted with earlier studies of laboratory strains of this yeast, and earlier in 2016, other researchers re-analysed the previous study’s data and challenged its findings. Now, Gasch et al. – who conducted the work reported in 2015 – provide additional controls and computational experiments that support their original analysis. The latest analysis confirmed that the genes identified in the first study are indeed commonly duplicated in wild yeast populations, yet the expression of these genes remains controlled. This is consistent with a model of dosage compensation, for at least some of duplicated genes. Gasch et al. believe that part of the difference in interpretation of the data relates to perspective. The challenging researchers tested to see if there was a mechanism of dosage compensation that acted across entire chromosomes, which is known to occur in the case of sex chromosomes in mammals. Gasch et al. on the other hand took a different approach and looked to identify effects at the level of individual genes. Together, the analyses show that, while there is no evidence for a widespread mechanism, the expression of a select set of genes in wild yeast is consistent with gene-specific dosage compensation. Future work will now undoubtedly test the mechanisms behind the gene-specific effects, and explore why wild yeast strains are more tolerant to extra chromosomes than laboratory strains. DOI:http://dx.doi.org/10.7554/eLife.14409.002
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Affiliation(s)
- Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
| | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Michael A Newton
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States.,Department of Statistics, University of Wisconsin-Madison, Madison, United States
| | - Maria Sardi
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Mun Yong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Zhishi Wang
- Department of Statistics, University of Wisconsin-Madison, Madison, United States
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12
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Wohlbach DJ, Rovinskiy N, Lewis JA, Sardi M, Schackwitz WS, Martin JA, Deshpande S, Daum CG, Lipzen A, Sato TK, Gasch AP. Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. Genome Biol Evol 2015; 6:2557-66. [PMID: 25364804 PMCID: PMC4202335 DOI: 10.1093/gbe/evu199] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Lignocellulosic plant material is a viable source of biomass to produce alternative energy including ethanol and other biofuels. However, several factors—including toxic byproducts from biomass pretreatment and poor fermentation of xylose and other pentose sugars—currently limit the efficiency of microbial biofuel production. To begin to understand the genetic basis of desirable traits, we characterized three strains of Saccharomyces cerevisiae with robust growth in a pretreated lignocellulosic hydrolysate or tolerance to stress conditions relevant to industrial biofuel production, through genome and transcriptome sequencing analysis. All stress resistant strains were highly mosaic, suggesting that genetic admixture may contribute to novel allele combinations underlying these phenotypes. Strain-specific gene sets not found in the lab strain were functionally linked to the tolerances of particular strains. Furthermore, genes with signatures of evolutionary selection were enriched for functional categories important for stress resistance and included stress-responsive signaling factors. Comparison of the strains’ transcriptomic responses to heat and ethanol treatment—two stresses relevant to industrial bioethanol production—pointed to physiological processes that were related to particular stress resistance profiles. Many of the genotype-by-environment expression responses occurred at targets of transcription factors with signatures of positive selection, suggesting that these strains have undergone positive selection for stress tolerance. Our results generate new insights into potential mechanisms of tolerance to stresses relevant to biofuel production, including ethanol and heat, present a backdrop for further engineering, and provide glimpses into the natural variation of stress tolerance in wild yeast strains.
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Affiliation(s)
- Dana J. Wohlbach
- Laboratory of Genetics, University of Wisconsin, Madison
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison
- Present address: Biology Department, Dickinson College, Carlisle, PA
| | - Nikolay Rovinskiy
- Laboratory of Genetics, University of Wisconsin, Madison
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison
| | - Jeffrey A. Lewis
- Laboratory of Genetics, University of Wisconsin, Madison
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison
- Present address: Department of Biological Sciences, University of Arkansas, Fayetteville, AR
| | - Maria Sardi
- Laboratory of Genetics, University of Wisconsin, Madison
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison
| | | | - Joel A. Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, California
| | - Shweta Deshpande
- US Department of Energy Joint Genome Institute, Walnut Creek, California
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, California
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin, Madison
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison
- *Corresponding author: E-mail:
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13
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Hose J, Yong CM, Sardi M, Wang Z, Newton MA, Gasch AP. Dosage compensation can buffer copy-number variation in wild yeast. eLife 2015; 4. [PMID: 25955966 PMCID: PMC4448642 DOI: 10.7554/elife.05462] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 05/07/2015] [Indexed: 12/22/2022] Open
Abstract
Aneuploidy is linked to myriad diseases but also facilitates organismal evolution. It remains unclear how cells overcome the deleterious effects of aneuploidy until new phenotypes evolve. Although laboratory strains are extremely sensitive to aneuploidy, we show here that aneuploidy is common in wild yeast isolates, which show lower-than-expected expression at many amplified genes. We generated diploid strain panels in which cells carried two, three, or four copies of the affected chromosomes, to show that gene-dosage compensation functions at >30% of amplified genes. Genes subject to dosage compensation are under higher expression constraint in wild populations—but they show elevated rates of gene amplification, suggesting that copy-number variation is buffered at these genes. We find that aneuploidy provides a clear ecological advantage to oak strain YPS1009, by amplifying a causal gene that escapes dosage compensation. Our work presents a model in which dosage compensation buffers gene amplification through aneuploidy to provide a natural, but likely transient, route to rapid phenotypic evolution. DOI:http://dx.doi.org/10.7554/eLife.05462.001 Evolution is driven by changes to the genes and other genetic information found in the DNA of an organism. These changes might, for example, alter the physical characteristics of the organism, or change how efficiently crucial tasks are carried out inside cells. Whatever the change, if it makes it easier for the organism to survive and reproduce, it is more likely to be passed on to future generations. DNA is organized inside cells in structures called chromosomes. Most of the cells in animals, plants, and fungi contain two copies of each chromosome. However, sometimes mistakes happen during cell division and extra copies of a chromosome—and hence the genes contained within it—may end up in a cell. These extra copies of genes might help to speed up the rate at which a species evolves, as the ‘spare’ copies are free to adapt to new roles. However, having extra copies of genes can also often be harmful, and in humans can cause genetic disorders such as Down syndrome. In the laboratory, chromosomes are commonly studied in a species of yeast called Saccharomyces cerevisiae. This species consists of several groups—or strains—that are genetically distinct from each other. Over the years, breeding the yeast for experiments has created laboratory strains that have lost some of the characteristics seen in wild strains. Earlier studies suggested that these cells fail to grow properly if they contain extra copies of chromosomes. Now, Hose et al. have studied nearly 50 wild strains of Saccharomyces cerevisiae. In these, extra copies of chromosomes are commonplace, and seemingly have no detrimental effect on growth. Instead, Hose et al. found that cells with too many copies of a gene use many of those genes less often than would be expected. This process is known as ‘dosage compensation’. This dosage compensation has not been observed in laboratory strains, in part because the extra gene copies make them sickly and hard to study. Together, the results provide examples of how dosage compensation could help new traits to evolve in a species by reducing the negative effects of duplicated genes. This knowledge may have broad application, from suggesting methods to alleviate human disorders to implicating new ways to engineer useful traits in yeast and other microbes. DOI:http://dx.doi.org/10.7554/eLife.05462.002
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Affiliation(s)
- James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Chris Mun Yong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Maria Sardi
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
| | - Zhishi Wang
- Department of Statistics, University of Wisconsin-Madison, Madison, United States
| | - Michael A Newton
- Department of Statistics, University of Wisconsin-Madison, Madison, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States
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Prentki Santos E, López-Costa S, Chenlo P, Pugliese MN, Curi S, Ariagno J, Repetto H, Sardi M, Palaoro L, Mendeluk G. Impact of spontaneous smoking cessation on sperm quality: case report. Andrologia 2011; 43:431-5. [DOI: 10.1111/j.1439-0272.2010.01089.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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15
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Sardi M, Haldemann Y, Nordmann H, Bottex B, Safford B, Smith B, Tennant D, Howlett J, Jasti P. Use of retailer fidelity card schemes in the assessment of food additive intake: Sunset Yellow a case study. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2010; 27:1507-15. [DOI: 10.1080/19440049.2010.495728] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Curi S, Ariagno J, Repetto H, Chenlo P, Mendeluk G, Pugliese N, Sardi M, Blanco A. Laboratory methods for the diagnosis of asthenozoospermia. Arch Androl 2002; 48:177-80. [PMID: 11964209 DOI: 10.1080/01485010252869252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Human sperm samples from 46 men were evaluated for standard semen parameters by two trained technicians, according to WHO criteria. A computer-aided semen analyzer (CASA, HTM-IVOS) was employed. The overall mean coefficient of variation for the 2 participants and the 46 samples studied was 17% for the percentage of progressive motile spermatozoa (r = 0.77). Twenty-nine (63%) samples were classified as asthenozoospermia by both methods. From the studied samples, 12 (26%) were classified as asthenozoospermia by the subjective method and 2 (4.3%) by CASA (p =.01). The two methods do not provide directly comparable data.
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Affiliation(s)
- S Curi
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Male Fertility Laboratory, Department of Clinical Biochemistry, University Clinical Hospital José de San Martin, Argentina
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Abstract
The immature germ cells (IGC) constitute the highest percentage (90%) of nonsperm cells (NSpC) in ejaculates from fertile or infertile men. The objective of this study was to evaluate IGC concentration and the IGC/(IGC + Sp) ratio, in normozoospermia and dispermia. Normozoospermia from men with proven fertility (NPF). nonproven fertility (NNPF). dispermia (D) and semen samples with excessive shedding of immature germ cells (GI 1.7 x 10(6) to 5 x 10(6) IGC/mL and GII > 5.0 x 10(6) IGC/mL) were used in this study. The mean value +2 SD for the NNPF (1.7 x 10(6)/mL) and the value proposed by WHO (5 x 10(6)/mL) were employed to define GI and GII groups. IGC concentration is statistically different in the studied groups. The IGC/Sp ratio showed a significant difference only between the NNPF and the D. When comparing semen parameters (Sp/ejaculate. grade (a) motility and morphology) there was a highly significant difference between NNPF and GI and GII: no difference was found between GI and GII. While studying 200 cases of dispermias 83% showed a high shedding of immature germ cells. The cytological study of nonsperm cells and the count and identification of the immature germ cells could be used to evaluate the dispermic disorders.
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Affiliation(s)
- J Ariagno
- Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Department of Clinical Biochemistry, University Clinical Hospital José de San Martin, Argentina.
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Abstract
Objective spermatic motility (Hamilton Thorne Research), the rapid progressive spermatozoa (grade A) recovery after swim-up, and the spermatozoa ATP content (bioluminescence) were studied in normoviscous and hyperviscous asthenospermic samples. The amplitude of lateral head displacement (ALH) was significantly lower in hyperviscous semen (normal: 4.6 +/- 0.7 microns [n = 20], high: 3.5 +/- 1.2 microns [n = 16]; p < .05). The grade A recovery percentage after swim-up was significantly higher in semens with high consistency (normal: 71.0 +/- 38.0 [n = 14], high: 181.3 +/- 108.9 [n = 6]; p < .05). The ATP content per living spermatozoa was in the normal consistency group 449.4 +/- 65.1 pmol per million living spermatozoa (n = 29) and in the high consistency batch 605.1 +/- 242.8 (n = 9), p < .05. In asthenospermia, the spermatozoa from hyperviscous samples have minor ALH values, better response to swim-up, and high ATP content than those from normoviscous ejaculates.
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Affiliation(s)
- G R Mendeluk
- Departamentos de Bioquímica Clínica y Tecnología Farmacéutica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
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Roca E, Pennella E, Sardi M, Carraro S, Barugel M, Milano C, Fiorini A, Giglio R, Gonzalez G, Kneitschel R, Aman E, Jarentchuk A, Blajman C, Nadal J, Santarelli MT, Navigante A. Combined intensive chemoradiotherapy for organ preservation in patients with resectable and non-resectable oesophageal cancer. Eur J Cancer 1996; 32A:429-32. [PMID: 8814686 DOI: 10.1016/0959-8049(95)00524-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
From January 1990 to April 1993, 60 oesophageal cancer patients were enrolled in a protocol of non-surgical treatment that consisted of induction chemotherapy followed by concurrent chemoradiotherapy. Induction chemotherapy consisted of cisplatin 40 mg/m2 intravenous bolus days 1, 2, 14, 15; 24 h continuous infusion of 5-fluorouracil (5-FU) 1000 mg/m2 days 1 and 14; leucovorin 20 mg/m2 days 1 and 14 given before and with 5-FU; bleomycin 30 UI days 1 and 14; mitomycin C 10 mg/m2 day 14. Concurrent chemoradiotherapy consisted of 60 Gy (6 weeks) from day 21 and cisplatin 70 mg/m2 days 28, 42 and 56; leucovorin 20 mg/m2 followed by 5-FU 425 mg/m2 days 28, 35, 42, 49 and 56. Complete response occurred in 44 of 55 evaluable patients (80%). The median survival is 32 months; the actuarial survival at 40 months is 35% (CI 18-53). These results appear improved over those reported with surgery or radiation alone, and suggest that organ preservation as a secondary treatment goal should be vigorously investigated.
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Affiliation(s)
- E Roca
- Hospital Municipal de Gastroenterologia, Caseros, Argentina
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20
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Sardi M. [Practical models in dentistry in Venezuela for the last forty years]. Acta Odontol Venez 1980; 18:37-66. [PMID: 6948495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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21
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Sardi M. [Odontologic research: methods and problems. Consulting the sources of information]. Acta Odontol Venez 1978; 16:339-45. [PMID: 95869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Sardi M. [Experiences in planning and evaluation of teaching dentistry]. Acta Odontol Venez 1974; 12:22-113. [PMID: 4535199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Sardi M. [Education of the patient in the dentist's office; commentary]. ALAFO 1969; 4:45-9. [PMID: 5250980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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24
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Sardi M. [Analysis of selective tests employed in the School of Dentistry of the Central University of Venezuela during the years 1963-1966]. Acta Odontol Venez 1968; 6:166-226. [PMID: 5266191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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25
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Sardi M. [The university structure and professional practice]. Acta Odontol Venez 1967; 1:89-93. [PMID: 5236271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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