1
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De Guidi I, Serre C, Noble J, Ortiz-Julien A, Blondin B, Legras JL. QTL mapping reveals novel genes and mechanisms underlying variations in H2S production during alcoholic fermentation in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foad050. [PMID: 38124683 PMCID: PMC11090286 DOI: 10.1093/femsyr/foad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Saccharomyces cerevisiae requirement for reduced sulfur to synthesize methionine and cysteine during alcoholic fermentation, is mainly fulfilled through the sulfur assimilation pathway. Saccharomyces cerevisiae reduces sulfate into sulfur dioxide (SO2) and sulfide (H2S), whose overproduction is a major issue in winemaking, due to its negative impact on wine aroma. The amount of H2S produced is highly strain-specific and also depends on SO2 concentration, often added to grape must. Applying a bulk segregant analysis to a 96-strain-progeny derived from two strains with different abilities to produce H2S, and comparing allelic frequencies along the genome of pools of segregants producing contrasting H2S quantities, we identified two causative regions involved in H2S production in the presence of SO2. A functional genetic analysis allowed the identification of variants in four genes able to impact H2S formation, viz; ZWF1, ZRT2, SNR2, and YLR125W, and involved in functions and pathways not associated with sulfur metabolism until now. These data point out that, in wine fermentation conditions, redox status, and zinc homeostasis are linked to H2S formation while providing new insights into the regulation of H2S production, and a new vision of the interplay between the sulfur assimilation pathway and cell metabolism.
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Affiliation(s)
- Irene De Guidi
- SPO, Université de Montpellier, INRAE, Institut Agro, Montpellier 34060, France
| | - Céline Serre
- SPO, Université de Montpellier, INRAE, Institut Agro, Montpellier 34060, France
| | | | | | - Bruno Blondin
- SPO, Université de Montpellier, INRAE, Institut Agro, Montpellier 34060, France
| | - Jean-Luc Legras
- SPO, Université de Montpellier, INRAE, Institut Agro, Montpellier 34060, France
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2
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Cairo G, MacKenzie A, Tsuchiya D, Lacefield S. Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. Cerevisiae. J Vis Exp 2022:10.3791/64580. [PMID: 36314815 PMCID: PMC10114469 DOI: 10.3791/64580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Time-lapse fluorescence microscopy has revolutionized the understanding of meiotic cell-cycle events by providing temporal and spatial data that is often not seen by imaging fixed cells. Budding yeast has proved to be an important model organism to study meiotic chromosome segregation because many meiotic genes are highly conserved. Time-lapse microscopy of meiosis in budding yeast allows the monitoring of different meiotic mutants to show how the mutation disrupts meiotic processes. However, many proteins function at multiple points in meiosis. The use of loss-of-function or meiotic null mutants can therefore disrupt an early process, blocking or disturbing the later process and making it difficult to determine the phenotypes associated with each individual role. To circumvent this challenge, this protocol describes how the proteins can be conditionally depleted from the nucleus at specific stages of meiosis while monitoring meiotic events using time-lapse microscopy. Specifically, this protocol describes how the cells are synchronized in prophase I, how the anchor away technique is used to deplete proteins from the nucleus at specific meiotic stages, and how time-lapse imaging is used to monitor meiotic chromosome segregation. As an example of the usefulness of the technique, the kinetochore protein Ctf19 was depleted from the nucleus at different time points during meiosis, and the number of chromatin masses was analyzed at the end of meiosis II. Overall, this protocol can be adapted to deplete different nuclear proteins from the nucleus while monitoring the meiotic divisions.
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Affiliation(s)
| | | | - Dai Tsuchiya
- Department of Biology, Indiana University; Stowers Institute for Biomedical Research
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3
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Sing TL, Conlon K, Lu SH, Madrazo N, Morse K, Barker JC, Hollerer I, Brar GA, Sudmant PH, Ünal E. Meiotic cDNA libraries reveal gene truncations and mitochondrial proteins important for competitive fitness in Saccharomyces cerevisiae. Genetics 2022; 221:iyac066. [PMID: 35471663 PMCID: PMC9157139 DOI: 10.1093/genetics/iyac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/13/2022] [Indexed: 01/16/2023] Open
Abstract
Gametogenesis is an evolutionarily conserved developmental program whereby a diploid progenitor cell undergoes meiosis and cellular remodeling to differentiate into haploid gametes, the precursors for sexual reproduction. Even in the simple eukaryotic organism Saccharomyces cerevisiae, the meiotic transcriptome is very rich and complex, thereby necessitating new tools for functional studies. Here, we report the construction of 5 stage-specific, inducible complementary DNA libraries from meiotic cells that represent over 84% of the genes found in the budding yeast genome. We employed computational strategies to detect endogenous meiotic transcript isoforms as well as library-specific gene truncations. Furthermore, we developed a robust screening pipeline to test the effect of each complementary DNA on competitive fitness. Our multiday proof-of-principle time course revealed 877 complementary DNAs that were detrimental for competitive fitness when overexpressed. The list included mitochondrial proteins that cause dose-dependent disruption of cellular respiration as well as library-specific gene truncations that expose a dominant negative effect on competitive growth. Together, these high-quality complementary DNA libraries provide an important tool for systematically identifying meiotic genes, transcript isoforms, and protein domains that are important for a specific biological function.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Katie Conlon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie H Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicole Madrazo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kaitlin Morse
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Juliet C Barker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ina Hollerer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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4
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De Chiara M, Barré BP, Persson K, Irizar A, Vischioni C, Khaiwal S, Stenberg S, Amadi OC, Žun G, Doberšek K, Taccioli C, Schacherer J, Petrovič U, Warringer J, Liti G. Domestication reprogrammed the budding yeast life cycle. Nat Ecol Evol 2022; 6:448-460. [PMID: 35210580 DOI: 10.1038/s41559-022-01671-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.
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Affiliation(s)
| | - Benjamin P Barré
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Karl Persson
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | | | - Chiara Vischioni
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Sakshi Khaiwal
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden
| | - Onyetugo Chioma Amadi
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden.,Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Gašper Žun
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Doberšek
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | | | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg, Sweden.
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
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5
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Travers Cook TJ, Skirgaila C, Martin OY, Buser CC. Infection by dsRNA viruses is associated with enhanced sporulation efficiency in Saccharomyces cerevisiae. Ecol Evol 2022; 12:e8558. [PMID: 35127053 PMCID: PMC8794758 DOI: 10.1002/ece3.8558] [Citation(s) in RCA: 3] [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: 11/02/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 01/07/2023] Open
Abstract
Upon starvation diploid cells of the facultative sexual yeast Saccharomyces cerevisiae undergo sporulation, forming four metabolically quiescent and robust haploid spores encased in a degradable ascus. All endosymbionts, whether they provide net benefits or costs, utilize host resources; in yeast, this should induce an earlier onset of sporulation. Here, we tested whether the presence of endosymbiotic dsRNA viruses (M satellite and L-A helper) correspond with higher sporulation rate of their host, S. cerevisiae. We find that S. cerevisiae hosting both the M and L-A viruses (so-called "killer yeasts") have significantly higher sporulation efficiency than those without. We also found that the removal of the M virus did not reduce sporulation frequency, possibly because the L-A virus still utilizes host resources with and without the M virus. Our findings indicate that either virulent resource use by endosymbionts induces sporulation, or that viruses are spread more frequently to sporulating strains. Further exploration is required to distinguish cause from effect.
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Affiliation(s)
- Thomas J. Travers Cook
- Institute of Integrative BiologyETH ZürichZürichSwitzerland
- Department of Aquatic EcologyEawagDübendorfSwitzerland
| | | | - Oliver Y. Martin
- Institute of Integrative BiologyETH ZürichZürichSwitzerland
- Department of BiologyETH ZürichZürichSwitzerland
| | - Claudia C. Buser
- Institute of Integrative BiologyETH ZürichZürichSwitzerland
- Department of Aquatic EcologyEawagDübendorfSwitzerland
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6
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Melo do Nascimento L, Terrao M, Marucha KK, Liu B, Egler F, Clayton C. The RNA-associated proteins MKT1 and MKT1L form alternative PBP1-containing complexes in Trypanosoma brucei. J Biol Chem 2020; 295:10940-10955. [PMID: 32532821 DOI: 10.1074/jbc.ra120.013306] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/03/2020] [Indexed: 01/20/2023] Open
Abstract
Control of gene expression in kinetoplastids such as trypanosomes depends heavily on RNA-binding proteins that influence mRNA decay and translation. We previously showed that the trypanosome protein MKT1 forms a multicomponent protein complex: MKT1 interacts with PBP1, which in turn recruits LSM12 and poly(A)-binding protein. MKT1 is recruited to mRNAs by sequence-specific RNA-binding proteins, resulting in stabilization of the bound mRNA. We here show that PBP1, LSM12, and a 117-residue protein, XAC1 (Tb927.7.2780), are present in complexes that contain either MKT1 or an MKT1-like protein, MKT1L (Tb927.10.1490). All five proteins are present predominantly in the complexes, and we found evidence for a minor subset of complexes containing both MKT1 and MKT1L. XAC1-containing complexes reproducibly contained RNA-binding proteins that were previously found associated with MKT1. Moreover, XAC1- or MKT1-containing complexes specifically recruited one of the two poly(A)-binding proteins, PABP2, and one of the six cap-binding translation initiation complexes, EIF4E6-EIF4G5. Yeast two-hybrid assay results indicated that MKT1 directly interacts with EIF4G5. MKT1-PBP1 complexes can therefore interact with mRNAs via their poly(A) tails and caps, as well as through sequence-specific RNA-binding proteins. Correspondingly, MKT1 is associated with many mRNAs, although not with those encoding ribosomal proteins. Meanwhile, MKT1L resembles MKT1 at the C terminus but additionally features an N-terminal extension with low-complexity regions. Although MKT1L depletion inhibited cell proliferation, we found no evidence that it specifically interacts with RNA-binding proteins or mRNA. We speculate that MKT1L may compete with MKT1 for PBP1 binding and thereby modulate the function of MKT1-containing complexes.
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Affiliation(s)
| | - Monica Terrao
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | | | - Bin Liu
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Franziska Egler
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
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7
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Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. Mol Cell 2019; 77:266-278.e6. [PMID: 31757756 DOI: 10.1016/j.molcel.2019.10.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/29/2019] [Accepted: 10/17/2019] [Indexed: 02/08/2023]
Abstract
Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.
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8
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Bushkin GG, Pincus D, Morgan JT, Richardson K, Lewis C, Chan SH, Bartel DP, Fink GR. m 6A modification of a 3' UTR site reduces RME1 mRNA levels to promote meiosis. Nat Commun 2019; 10:3414. [PMID: 31363087 PMCID: PMC6667471 DOI: 10.1038/s41467-019-11232-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 06/28/2019] [Indexed: 01/23/2023] Open
Abstract
Despite the vast number of modification sites mapped within mRNAs, known examples of consequential mRNA modifications remain rare. Here, we provide multiple lines of evidence to show that Ime4p, an N6-methyladenosine (m6A) methyltransferase required for meiosis in yeast, acts by methylating a site in the 3′ UTR of the mRNA encoding Rme1p, a transcriptional repressor of meiosis. Consistent with this mechanism, genetic analyses reveal that IME4 functions upstream of RME1. Transcriptome-wide, RME1 is the primary message that displays both increased methylation and reduced expression in an Ime4p-dependent manner. In yeast strains for which IME4 is dispensable for meiosis, a natural polymorphism in the RME1 promoter reduces RME1 transcription, obviating the requirement for methylation. Mutation of a single m6A site in the RME1 3′ UTR increases Rme1p repressor production and reduces meiotic efficiency. These results reveal the molecular and physiological consequences of a modification in the 3′ UTR of an mRNA. Ime4p is a yeast N6-methyladenosine (m6A) methyltransferase with an unknown role in meiosis. Rme1p is a repressor of meiosis. Here the authors show that Ime4p methylates RME1 3′ UTR to reduce its expression and enable meiosis, thus providing an example of an m6A site with a physiological role.
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Affiliation(s)
- G Guy Bushkin
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Molecular Genetics and Cell Biology and the Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, 60637, USA.
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Molecular Genetics and Cell Biology and the Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, 60637, USA
| | - Jeffrey T Morgan
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
| | - Kris Richardson
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Caroline Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
| | - Gerald R Fink
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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9
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Miles S, Li LH, Melville Z, Breeden LL. Ssd1 and the cell wall integrity pathway promote entry, maintenance, and recovery from quiescence in budding yeast. Mol Biol Cell 2019; 30:2205-2217. [PMID: 31141453 PMCID: PMC6743469 DOI: 10.1091/mbc.e19-04-0190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Wild Saccharomyces cerevisiae strains are typically diploid. When faced with glucose and nitrogen limitation they can undergo meiosis and sporulate. Diploids can also enter a protective, nondividing cellular state or quiescence. The ability to enter quiescence is highly reproducible but shows broad natural variation. Some wild diploids can only enter cellular quiescence, which indicates that there are conditions in which sporulation is lost or selected against. Others only sporulate, but if sporulation is disabled by heterozygosity at the IME1 locus, those diploids can enter quiescence. W303 haploids can enter quiescence, but their diploid counterparts cannot. This is the result of diploidy, not mating type regulation. Introduction of SSD1 to W303 diploids switches fate, in that it rescues cellular quiescence and disrupts the ability to sporulate. Ssd1 and another RNA-binding protein, Mpt5 (Puf5), have parallel roles in quiescence in haploids. The ability of these mutants to enter quiescence, and their long-term survival in the quiescent state, can be rescued by exogenously added trehalose. The cell wall integrity pathway also promotes entry, maintenance, and recovery from quiescence through the Rlm1 transcription factor.
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Affiliation(s)
- Shawna Miles
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Li Hong Li
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Zephan Melville
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
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10
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Meza-Gutierrez F, Simsek D, Toczyski DP. A genetic approach to study polyubiquitination in Saccharomyces cerevisiae. Methods Enzymol 2019; 618:49-72. [DOI: 10.1016/bs.mie.2018.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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12
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Peltier E, Sharma V, Martí Raga M, Roncoroni M, Bernard M, Jiranek V, Gibon Y, Marullo P. Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices. BMC Genomics 2018; 19:772. [PMID: 30409183 PMCID: PMC6225642 DOI: 10.1186/s12864-018-5145-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/05/2018] [Indexed: 11/17/2022] Open
Abstract
Background The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment. Industrial microbes such as Saccharomyces cerevisiae are also faced with a large range of fermentation conditions that affect their technological properties. Finding the molecular determinism of such variations is a critical task for better understanding the genetic bases of phenotypic plasticity and can also be helpful in order to improve breeding methods. Results In this study we implemented a QTL mapping program using two independent cross (~ 100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to whole genome sequencing approaches, both crosses were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the environmental conditions. Molecular dissection of a major QTL demonstrated that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits. Conclusions The detection of QTLs and their interactions with environment emphasizes the complexity of yeast industrial traits. The validation of the interaction of SSU1 allelic variants with the nature of the fermented juice increases knowledge about the impact of the sulfite pump during fermentation. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5145-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emilien Peltier
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France. .,Biolaffort, Bordeaux, France.
| | - Vikas Sharma
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France
| | - Maria Martí Raga
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Departament de Bioquímica i Biotecnologia, Facultat d'Enologia de Tarragona, Tarragona, Spain
| | - Miguel Roncoroni
- Wine Science Programme, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Margaux Bernard
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, Bordeaux, France
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Urrbrae, South Australia, 5064, Australia
| | - Yves Gibon
- INRA, University of Bordeaux, UMR 1332 Fruit Biology and Pathology, F-33883, Villenave d'Ornon, France
| | - Philippe Marullo
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, Bordeaux, France
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13
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Yadav A, Sinha H. Gene-gene and gene-environment interactions in complex traits in yeast. Yeast 2018; 35:403-416. [PMID: 29322552 DOI: 10.1002/yea.3304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/11/2017] [Accepted: 12/23/2017] [Indexed: 01/05/2023] Open
Abstract
One of the fundamental questions in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that, in most cases, the effect of a genetic locus on the phenotype is context-dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects. This does not reflect an absence of the contribution of genetic interactions to phenotypic variation, but instead is a consequence of the technical limitations in mapping gene-gene interactions (GGI) and gene-environment interactions (GEI). Yeast, with its detailed molecular understanding, diverse population genomics and ease of genetic manipulation, is a unique and powerful resource to study the contributions of GGI and GEI in the regulation of phenotypic variation. Here we review studies in yeast that have identified GGI and GEI that regulate phenotypic variation, and discuss the contribution of these findings in explaining missing heritability of complex traits, and how observations from these GGI and GEI studies enhance our understanding of the mechanisms underlying genetic robustness and adaptability that shape the architecture of the genotype-phenotype map.
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Affiliation(s)
- Anupama Yadav
- Center for Cancer Systems Biology, and Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, 600036, India.,Robert Bosch Centre for Data Sciences and Artificial Intelligence, Indian Institute of Technology Madras, Chennai, 600036, India
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14
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Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses. G3-GENES GENOMES GENETICS 2017; 7:1693-1705. [PMID: 28592651 PMCID: PMC5473750 DOI: 10.1534/g3.117.042127] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.
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15
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Geng P, Zhang L, Shi GY. Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2017; 33:94. [PMID: 28405910 DOI: 10.1007/s11274-017-2259-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 04/01/2017] [Indexed: 12/31/2022]
Abstract
Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.
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Affiliation(s)
- Peng Geng
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
| | - Gui Yang Shi
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
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16
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García-Ríos E, Morard M, Parts L, Liti G, Guillamón JM. The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae. BMC Genomics 2017; 18:159. [PMID: 28196526 PMCID: PMC5310122 DOI: 10.1186/s12864-017-3572-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/09/2017] [Indexed: 12/25/2022] Open
Abstract
Background Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci. Results In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature. We detected four genomic regions involved in the adaptation at low temperature, three of them located in the subtelomeric regions (chromosomes XIII, XV and XVI) and one in the chromosome XIV. The QTL analysis revealed that subtelomeric regions play a key role in defining individual variation, which emphasizes the importance of these regions’ adaptive nature. Conclusions The reciprocal hemizygosity analysis (RHA), run to validate the genes involved in low-temperature fermentation, showed that genetic variation in mitochondrial proteins, maintenance of correct asymmetry and distribution of phospholipid in the plasma membrane are key determinants of low-temperature adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3572-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980-Paterna, Valencia, Spain
| | - Miguel Morard
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980-Paterna, Valencia, Spain.,Departament de Genètica, Facultat de Ciències Biològiques, Universitat de València, Dr. Moliner, 50, E-46100 Burjassot, València, Spain
| | - Leopold Parts
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Wellcome Trust Sanger Institute, Hinxton, CB101SA, UK
| | - Gianni Liti
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - José M Guillamón
- Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980-Paterna, Valencia, Spain.
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17
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Thompson DA, Cubillos FA. Natural gene expression variation studies in yeast. Yeast 2016; 34:3-17. [PMID: 27668700 DOI: 10.1002/yea.3210] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 11/06/2022] Open
Abstract
The rise of sequence information across different yeast species and strains is driving an increasing number of studies in the emerging field of genomics to associate polymorphic variants, mRNA abundance and phenotypic differences between individuals. Here, we gathered evidence from recent studies covering several layers that define the genotype-phenotype gap, such as mRNA abundance, allele-specific expression and translation efficiency to demonstrate how genetic variants co-evolve and define an individual's genome. Moreover, we exposed several antecedents where inter- and intra-specific studies led to opposite conclusions, probably owing to genetic divergence. Future studies in this area will benefit from the access to a massive array of well-annotated genomes and new sequencing technologies, which will allow the fine breakdown of the complex layers that delineate the genotype-phenotype map. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology.,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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18
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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19
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Amberg DC, Burke DJ. Classical Genetics with Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:2016/5/pdb.top077628. [PMID: 27140921 DOI: 10.1101/pdb.top077628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The budding yeast Saccharomyces cerevisiae is an outstanding experimental model organism that has been exploited since the early part of the twentieth century for studies in biochemistry and genetics. It has been the premiere experimental system for modern functional genomics and continues to make important contributions to many areas of biology. Here we discuss its many virtues as an organism for classical genetic research.
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Affiliation(s)
- David C Amberg
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Daniel J Burke
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0733
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20
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Laureau R, Loeillet S, Salinas F, Bergström A, Legoix-Né P, Liti G, Nicolas A. Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion. PLoS Genet 2016; 12:e1005781. [PMID: 26828862 PMCID: PMC4734685 DOI: 10.1371/journal.pgen.1005781] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
In somatic cells, recombination between the homologous chromosomes followed by equational segregation leads to loss of heterozygosity events (LOH), allowing the expression of recessive alleles and the production of novel allele combinations that are potentially beneficial upon Darwinian selection. However, inter-homolog recombination in somatic cells is rare, thus reducing potential genetic variation. Here, we explored the property of S. cerevisiae to enter the meiotic developmental program, induce meiotic Spo11-dependent double-strand breaks genome-wide and return to mitotic growth, a process known as Return To Growth (RTG). Whole genome sequencing of 36 RTG strains derived from the hybrid S288c/SK1 diploid strain demonstrates that the RTGs are bona fide diploids with mosaic recombined genome, derived from either parental origin. Individual RTG genome-wide genotypes are comprised of 5 to 87 homozygous regions due to the loss of heterozygous (LOH) events of various lengths, varying between a few nucleotides up to several hundred kilobases. Furthermore, we show that reiteration of the RTG process shows incremental increases of homozygosity. Phenotype/genotype analysis of the RTG strains for the auxotrophic and arsenate resistance traits validates the potential of this procedure of genome diversification to rapidly map complex traits loci (QTLs) in diploid strains without undergoing sexual reproduction.
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Affiliation(s)
- Raphaëlle Laureau
- Institut Curie, PSL Research University, CNRS, UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 3244, Paris, France
| | - Sophie Loeillet
- Institut Curie, PSL Research University, CNRS, UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 3244, Paris, France
| | - Francisco Salinas
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Anders Bergström
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Patricia Legoix-Né
- Institut Curie, PSL Research University, Next Generation Sequencing Platform, Paris, France
| | - Gianni Liti
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, CNRS, UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 3244, Paris, France
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21
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Malabat C, Saveanu C. Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM). Methods Mol Biol 2016; 1361:325-343. [PMID: 26483030 DOI: 10.1007/978-1-4939-3079-1_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The yeast systematic deletion collection offered the basis for a number of different strategies that establish functional links between genes by analyzing the phenotype of cells that combine two different deletions or mutations. A distinguishing feature of the collection is the presence of molecular barcodes at each deleted locus, which can be used to quantify the presence and abundance of cells bearing a given allele in a complex mix. As a result, a large number of mutants can be tested in batch cultures, replacing tedious manipulation of thousands of individual strains with a barcode microarray readout. Barcode-based genetic screens like Genetic Interaction Mapping (GIM) thus require little investment in terms of specific equipment, are fast to perform, and allow precise measurements of double mutant growth rates for both aggravating (synthetic sick) and alleviating (epistatic) effects. We describe here protocols for preparing the pools of haploid double mutant S. cerevisiae cells, testing their composition with barcode microarrays, and analyzing the results to extract useful functional information.
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Affiliation(s)
- Christophe Malabat
- Génétique des Interactions Macromoléculaires (UMR3525-CNRS), Institut Pasteur, 25 rue du Docteur ROUX, 75015, Paris, France
| | - Cosmin Saveanu
- Génétique des Interactions Macromoléculaires (UMR3525-CNRS), Institut Pasteur, 25 rue du Docteur ROUX, 75015, Paris, France.
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22
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Kaboli S, Miyamoto T, Sunada K, Sasano Y, Sugiyama M, Harashima S. Improved stress resistance and ethanol production by segmental haploidization of the diploid genome in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 121:638-644. [PMID: 26690924 DOI: 10.1016/j.jbiosc.2015.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/25/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
Saccharomyces cerevisiae strains from industrial and natural geographical environments are reported to show great variation in copy number of chromosomal regions. Such variation contributes to the mechanisms underlying adaptation to different environments. Here, we created and phenotypically analyzed segmentally haploidized strains, each harboring a deletion of one copy of approximately 100-300 kb of the left or right terminal region of 16 chromosomes in a diploid strain by using a PCR-mediated chromosomal deletion method. No haploidized strain of the 158-kb deleted right terminal region of chromosome III or the 172-kb deleted right terminal region of chromosome VI was produced; however, segmentally haploidized strains of the remaining 30 terminal regions were obtained. Among these 30 strains, two exhibited higher lactic acid resistance and two displayed higher thermo-tolerance at 41°C versus the host diploid strain. By contrast, four and two segmentally haploidized strains showed sensitivity to 6% lactic acid and low temperature at 13°C, respectively. The effect of the decreased copy number of the chromosomal terminal regions on ethanol production was analyzed. As compared with the host diploid strain, a 3.8% and 4.3% improvement in ethanol production in 10% glucose medium was observed for two strains in which one of two copies of the 197-kb left terminal region of chromosome V and one of two copies of the 195-kb left terminal region of chromosome X was deleted, respectively. These results indicate that artificial segmental haploidization might contribute to improvement of industrially important phenotypes and provide a new approach to breeding superior yeast strains.
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Affiliation(s)
- Saeed Kaboli
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Miyamoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Sunada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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23
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Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae. Genetics 2015; 201:599-612. [PMID: 26281848 DOI: 10.1534/genetics.115.181164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Studies of natural populations of many organisms have shown that traits are often complex, caused by contributions of mutations in multiple genes. In contrast, genetic studies in the laboratory primarily focus on studying the phenotypes caused by mutations in a single gene. However, the single mutation approach may be limited with respect to the breadth and degree of new phenotypes that can be found. We have taken the approach of isolating complex, or polygenic mutants in the lab to study the regulation of transcriptional activation distance in yeast. While most aspects of eukaryotic transcription are conserved from yeast to human, transcriptional activation distance is not. In Saccharomyces cerevisiae, the upstream activating sequence (UAS) is generally found within 450 base pairs of the transcription start site (TSS) and when the UAS is moved too far away, activation no longer occurs. In contrast, metazoan enhancers can activate from as far as several hundred kilobases from the TSS. Previously, we identified single mutations that allow transcription activation to occur at a greater-than-normal distance from the GAL1 UAS. As the single mutant phenotypes were weak, we have now isolated polygenic mutants that possess strong long-distance phenotypes. By identification of the causative mutations we have accounted for most of the heritability of the phenotype in each strain and have provided evidence that the Mediator coactivator complex plays both positive and negative roles in the regulation of transcription activation distance.
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24
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Gupta R, Sadhale PP, Vijayraghavan U. SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae. PLoS One 2015; 10:e0132350. [PMID: 26147804 PMCID: PMC4492983 DOI: 10.1371/journal.pone.0132350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/14/2015] [Indexed: 01/29/2023] Open
Abstract
Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1Δ cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1Δ sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation.
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Affiliation(s)
- Ritu Gupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Parag P. Sadhale
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
- * E-mail:
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25
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Fulcher N, Teubenbacher A, Kerdaffrec E, Farlow A, Nordborg M, Riha K. Genetic architecture of natural variation of telomere length in Arabidopsis thaliana. Genetics 2015; 199:625-35. [PMID: 25488978 PMCID: PMC4317667 DOI: 10.1534/genetics.114.172163] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/25/2014] [Indexed: 11/18/2022] Open
Abstract
Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.
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Affiliation(s)
- Nick Fulcher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Astrid Teubenbacher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Envel Kerdaffrec
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Karel Riha
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, Czech Republic
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26
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Rawi R, El Anbari M, Bensmail H. Model selection emphasises the importance of non-chromosomal information in genetic studies. PLoS One 2015; 10:e0117014. [PMID: 25626013 PMCID: PMC4308103 DOI: 10.1371/journal.pone.0117014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 12/17/2014] [Indexed: 12/05/2022] Open
Abstract
Ever since the case of the missing heritability was highlighted some years ago, scientists have been investigating various possible explanations for the issue. However, none of these explanations include non-chromosomal genetic information. Here we describe explicitly how chromosomal and non-chromosomal modifiers collectively influence the heritability of a trait, in this case, the growth rate of yeast. Our results show that the non-chromosomal contribution can be large, adding another dimension to the estimation of heritability. We also discovered, combining the strength of LASSO with model selection, that the interaction of chromosomal and non-chromosomal information is essential in describing phenotypes.
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Affiliation(s)
- Reda Rawi
- Computational Science and Engineering Center, Qatar Computing Research Institute, Doha, Qatar
| | - Mohamed El Anbari
- Computational Science and Engineering Center, Qatar Computing Research Institute, Doha, Qatar
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha, Qatar
| | - Halima Bensmail
- Computational Science and Engineering Center, Qatar Computing Research Institute, Doha, Qatar
- * E-mail:
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Bergman J, Mitrikeski PT, Brčić-Kostić K. Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae. Food Technol Biotechnol 2015; 53:367-378. [PMID: 27904371 DOI: 10.17113/ftb.53.04.15.3998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait.
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Affiliation(s)
- Juraj Bergman
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute,
Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Petar T Mitrikeski
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute,
Bijenička cesta 54, HR-10000 Zagreb, Croatia; Institute for Research and Development of Sustainable Ecosystems, Faculty of Veterinary Medicine, Heinzelova 55, HR-10000 Zagreb, Croatia
| | - Krunoslav Brčić-Kostić
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute,
Bijenička cesta 54, HR-10000 Zagreb, Croatia
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Abstract
Copper is a micronutrient essential for growth due to its role as a cofactor in enzymes involved in respiration, defense against oxidative damage, and iron uptake. Yet too much of a good thing can be lethal, and yeast cells typically do not have tolerance to copper levels much beyond the concentration in their ancestral environment. Here, we report a short-term evolutionary study of Saccharomyces cerevisiae exposed to levels of copper sulfate that are inhibitory to the initial strain. We isolated and identified adaptive mutations soon after they arose, reducing the number of neutral mutations, to determine the first genetic steps that yeast take when adapting to copper. We analyzed 34 such strains through whole-genome sequencing and by assaying fitness within different environments; we also isolated a subset of mutations through tetrad analysis of four lines. We identified a multilayered evolutionary response. In total, 57 single base-pair mutations were identified across the 34 lines. In addition, gene amplification of the copper metallothionein protein, CUP1-1, was rampant, as was chromosomal aneuploidy. Four other genes received multiple, independent mutations in different lines (the vacuolar transporter genes VTC1 and VTC4; the plasma membrane H+-ATPase PMA1; and MAM3, a protein required for normal mitochondrial morphology). Analyses indicated that mutations in all four genes, as well as CUP1-1 copy number, contributed significantly to explaining variation in copper tolerance. Our study thus finds that evolution takes both common and less trodden pathways toward evolving tolerance to an essential, but highly toxic, micronutrient.
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Stern DL. Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test. Trends Genet 2014; 30:547-54. [PMID: 25278102 DOI: 10.1016/j.tig.2014.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 12/18/2022]
Abstract
The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.
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Affiliation(s)
- David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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Lorenz K, Cohen BA. Causal variation in yeast sporulation tends to reside in a pathway bottleneck. PLoS Genet 2014; 10:e1004634. [PMID: 25211152 PMCID: PMC4161353 DOI: 10.1371/journal.pgen.1004634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 07/29/2014] [Indexed: 12/31/2022] Open
Abstract
There has been extensive debate over whether certain classes of genes are more likely than others to contain the causal variants responsible for phenotypic differences in complex traits between individuals. One hypothesis states that input/output genes positioned in signal transduction bottlenecks are more likely than other genes to contain causal natural variation. The IME1 gene resides at such a signaling bottleneck in the yeast sporulation pathway, suggesting that it may be more likely to contain causal variation than other genes in the sporulation pathway. Through crosses between natural isolates of yeast, we demonstrate that the specific causal nucleotides responsible for differences in sporulation efficiencies reside not only in IME1 but also in the genes that surround IME1 in the signaling pathway, including RME1, RSF1, RIM15, and RIM101. Our results support the hypothesis that genes at the critical decision making points in signaling cascades will be enriched for causal variants responsible for phenotypic differences. Distinguishing the small number of genetic variants that impact phenotypes from the huge number of innocuous variants within an individual's genome is a difficult problem. Several hypotheses concerning the location of causal variants have been put forward based on the fact that genes are often organized into signaling cascades where the activation of a gene at the top of a pathway in turn activates large numbers of downstream genes. One hypothesis states that causal variations are more likely to reside in the genes at the top of these pathways because their effects are amplified by the signaling cascade. Here we provide support for this hypothesis by showing that causal genetic variants in yeast sporulation cluster around a gene at the top of the sporulation signaling cascade. Our result suggests a way to focus the search for causal genetic variants, including those that cause disease, on a smaller number of genes that are more likely to harbor important variations.
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Affiliation(s)
- Kim Lorenz
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barak A. Cohen
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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31
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Brice C, Sanchez I, Bigey F, Legras JL, Blondin B. A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling. BMC Genomics 2014; 15:495. [PMID: 24947828 PMCID: PMC4073503 DOI: 10.1186/1471-2164-15-495] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background In conditions of nitrogen limitation, Saccharomyces cerevisiae strains differ in their fermentation capacities, due to differences in their nitrogen requirements. The mechanisms ensuring the maintenance of glycolytic flux in these conditions are unknown. We investigated the genetic basis of these differences, by studying quantitative trait loci (QTL) in a population of 133 individuals from the F2 segregant population generated from a cross between two strains with different nitrogen requirements for efficient fermentation. Results By comparing two bulks of segregants with low and high nitrogen requirements, we detected four regions making a quantitative contribution to these traits. We identified four polymorphic genes, in three of these four regions, for which involvement in the phenotype was validated by hemizygote comparison. The functions of the four validated genes, GCN1, MDS3, ARG81 and BIO3, relate to key roles in nitrogen metabolism and signaling, helping to maintain fermentation performance. Conclusions This study reveals that differences in nitrogen requirement between yeast strains results from a complex allelic combination. The identification of three genes involved in sensing and signaling nitrogen and specially one from the TOR pathway as affecting nitrogen requirements suggests a role for this pathway in regulating the fermentation rate in starvation through unknown mechanisms linking nitrogen signaling to glycolytic flux. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-495) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Bruno Blondin
- INRA, UMR1083 Science pour l'Œnologie, 2 Place Viala, F-34060 Montpellier, France.
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Interactions between chromosomal and nonchromosomal elements reveal missing heritability. Proc Natl Acad Sci U S A 2014; 111:7719-22. [PMID: 24825890 DOI: 10.1073/pnas.1407126111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The measurement of any nonchromosomal genetic contribution to the heritability of a trait is often confounded by the inability to control both the chromosomal and nonchromosomal information in a population. We have designed a unique system in yeast where we can control both sources of information so that the phenotype of a single chromosomal polymorphism can be measured in the presence of different cytoplasmic elements. With this system, we have shown that both the source of the mitochondrial genome and the presence or absence of a dsRNA virus influence the phenotype of chromosomal variants that affect the growth of yeast. Moreover, by considering this nonchromosomal information that is passed from parent to offspring and by allowing chromosomal and nonchromosomal information to exhibit nonadditive interactions, we are able to account for much of the heritability of growth traits. Taken together, our results highlight the importance of including all sources of heritable information in genetic studies and suggest a possible avenue of attack for finding additional missing heritability.
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Sudarsanam P, Cohen BA. Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. PLoS Genet 2014; 10:e1004325. [PMID: 24784239 PMCID: PMC4006743 DOI: 10.1371/journal.pgen.1004325] [Citation(s) in RCA: 13] [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: 12/06/2013] [Accepted: 03/10/2014] [Indexed: 01/22/2023] Open
Abstract
Mapping the polymorphisms responsible for variation in gene expression, known as Expression Quantitative Trait Loci (eQTL), is a common strategy for investigating the molecular basis of disease. Despite numerous eQTL studies, the relationship between the explanatory power of variants on gene expression versus their power to explain ultimate phenotypes remains to be clarified. We addressed this question using four naturally occurring Quantitative Trait Nucleotides (QTN) in three transcription factors that affect sporulation efficiency in wild strains of the yeast, Saccharomyces cerevisiae. We compared the ability of these QTN to explain the variation in both gene expression and sporulation efficiency. We find that the amount of gene expression variation explained by the sporulation QTN is not predictive of the amount of phenotypic variation explained. The QTN are responsible for 98% of the phenotypic variation in our strains but the median gene expression variation explained is only 49%. The alleles that are responsible for most of the variation in sporulation efficiency do not explain most of the variation in gene expression. The balance between the main effects and gene-gene interactions on gene expression variation is not the same as on sporulation efficiency. Finally, we show that nucleotide variants in the same transcription factor explain the expression variation of different sets of target genes depending on whether the variant alters the level or activity of the transcription factor. Our results suggest that a subset of gene expression changes may be more predictive of ultimate phenotypes than the number of genes affected or the total fraction of variation in gene expression variation explained by causative variants, and that the downstream phenotype is buffered against variation in the gene expression network.
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Affiliation(s)
- Priya Sudarsanam
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barak A Cohen
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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34
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Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014; 12:355-67. [DOI: 10.1038/nrmicro3240] [Citation(s) in RCA: 461] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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35
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Abstract
Sexual reproduction is a nearly universal feature of eukaryotic organisms. Given its ubiquity and shared core features, sex is thought to have arisen once in the last common ancestor to all eukaryotes. Using the perspectives of molecular genetics and cell biology, we consider documented and hypothetical scenarios for the instantiation and evolution of meiosis, fertilization, sex determination, uniparental inheritance of organelle genomes, and speciation.
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Affiliation(s)
- Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri 63130
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36
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Pardo-Diaz C, Jiggins CD. Neighboring genes shaping a single adaptive mimetic trait. Evol Dev 2014; 16:3-12. [DOI: 10.1111/ede.12058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Carolina Pardo-Diaz
- Department of Zoology; University of Cambridge; Downing Street Cambridge CB2 3EJ United Kingdom
| | - Chris D. Jiggins
- Department of Zoology; University of Cambridge; Downing Street Cambridge CB2 3EJ United Kingdom
- Smithsonian Tropical Research Institute; Balboa AA2072 Panama
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37
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Abstract
Dissecting the molecular basis of quantitative traits is a significant challenge and is essential for understanding complex diseases. Even in model organisms, precisely determining causative genes and their interactions has remained elusive, due in part to difficulty in narrowing intervals to single genes and in detecting epistasis or linked quantitative trait loci. These difficulties are exacerbated by limitations in experimental design, such as low numbers of analyzed individuals or of polymorphisms between parental genomes. We address these challenges by applying three independent high-throughput approaches for QTL mapping to map the genetic variants underlying 11 phenotypes in two genetically distant Saccharomyces cerevisiae strains, namely (1) individual analysis of >700 meiotic segregants, (2) bulk segregant analysis, and (3) reciprocal hemizygosity scanning, a new genome-wide method that we developed. We reveal differences in the performance of each approach and, by combining them, identify eight polymorphic genes that affect eight different phenotypes: colony shape, flocculation, growth on two nonfermentable carbon sources, and resistance to two drugs, salt, and high temperature. Our results demonstrate the power of individual segregant analysis to dissect QTL and address the underestimated contribution of interactions between variants. We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies.
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38
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Fay JC. The molecular basis of phenotypic variation in yeast. Curr Opin Genet Dev 2013; 23:672-7. [PMID: 24269094 DOI: 10.1016/j.gde.2013.10.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/19/2013] [Accepted: 10/24/2013] [Indexed: 11/19/2022]
Abstract
The power of yeast genetics has now been extensively applied to phenotypic variation among strains of Saccharomyces cerevisiae. As a result, over 100 genes and numerous sequence variants have been identified, providing us with a general characterization of mutations underlying quantitative trait variation. Most quantitative trait alleles exert considerable phenotypic effects and alter conserved amino acid positions within protein coding sequences. When examined, quantitative trait alleles influence the expression of numerous genes, most of which are unrelated to an allele's phenotypic effect. The profile of quantitative trait alleles has proven useful to reverse quantitative genetics approaches and supports the use of systems genetics approaches to synthesize the molecular basis of trait variation across multiple strains.
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Affiliation(s)
- Justin C Fay
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St. Louis, MO, United States.
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39
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Yang Y, Foulquié-Moreno MR, Clement L, Erdei É, Tanghe A, Schaerlaekens K, Dumortier F, Thevelein JM. QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing. PLoS Genet 2013; 9:e1003693. [PMID: 23966873 PMCID: PMC3744412 DOI: 10.1371/journal.pgen.1003693] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 06/18/2013] [Indexed: 11/18/2022] Open
Abstract
Revealing QTLs with a minor effect in complex traits remains difficult. Initial strategies had limited success because of interference by major QTLs and epistasis. New strategies focused on eliminating major QTLs in subsequent mapping experiments. Since genetic analysis of superior segregants from natural diploid strains usually also reveals QTLs linked to the inferior parent, we have extended this strategy for minor QTL identification by eliminating QTLs in both parent strains and repeating the QTL mapping with pooled-segregant whole-genome sequence analysis. We first mapped multiple QTLs responsible for high thermotolerance in a natural yeast strain, MUCL28177, compared to the laboratory strain, BY4742. Using single and bulk reciprocal hemizygosity analysis we identified MKT1 and PRP42 as causative genes in QTLs linked to the superior and inferior parent, respectively. We subsequently downgraded both parents by replacing their superior allele with the inferior allele of the other parent. QTL mapping using pooled-segregant whole-genome sequence analysis with the segregants from the cross of the downgraded parents, revealed several new QTLs. We validated the two most-strongly linked new QTLs by identifying NCS2 and SMD2 as causative genes linked to the superior downgraded parent and we found an allele-specific epistatic interaction between PRP42 and SMD2. Interestingly, the related function of PRP42 and SMD2 suggests an important role for RNA processing in high thermotolerance and underscores the relevance of analyzing minor QTLs. Our results show that identification of minor QTLs involved in complex traits can be successfully accomplished by crossing parent strains that have both been downgraded for a single QTL. This novel approach has the advantage of maintaining all relevant genetic diversity as well as enough phenotypic difference between the parent strains for the trait-of-interest and thus maximizes the chances of successfully identifying additional minor QTLs that are relevant for the phenotypic difference between the original parents. Most traits of organisms are determined by an interplay of different genes interacting in a complex way. For instance, nearly all industrially-important traits of the yeast Saccharomyces cerevisiae are complex traits. We have analyzed high thermotolerance, which is important for industrial fermentations, reducing cooling costs and sustaining higher productivity. Whereas genetic analysis of complex traits has been cumbersome for many years, the development of pooled-segregant whole-genome sequence analysis now allows successful identification of underlying genetic loci with a major effect. On the other hand, identification of loci with a minor contribution remains a challenge. We now present a methodology for identifying minor loci, which is based on the finding that the inferior parent usually also harbours superior alleles. This allowed construction for the trait of high thermotolerance of two ‘downgraded parent strains’ by replacing in each parent a superior allele by the inferior allele from the other parent. Subsequent mapping with the downgraded parents revealed new minor loci, which we validated by identifying the causative genes. Hence, our results illustrate the power of this methodology for successfully identifying minor loci determining complex traits and with a high chance of being co-responsible for the phenotypic difference between the original parents.
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Affiliation(s)
- Yudi Yang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Flanders, Belgium
| | - Éva Erdei
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - An Tanghe
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Kristien Schaerlaekens
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Françoise Dumortier
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium
- Department of Molecular Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
- * E-mail:
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40
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Tomar P, Bhatia A, Ramdas S, Diao L, Bhanot G, Sinha H. Sporulation genes associated with sporulation efficiency in natural isolates of yeast. PLoS One 2013; 8:e69765. [PMID: 23874994 PMCID: PMC3714247 DOI: 10.1371/journal.pone.0069765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/13/2013] [Indexed: 11/19/2022] Open
Abstract
Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes - HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast.
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Affiliation(s)
- Parul Tomar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Aatish Bhatia
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, United States of America
| | - Shweta Ramdas
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Liyang Diao
- BioMaPS Institute for Quantitative Biology, Busch Campus, Rutgers University, Piscataway, New Jersey, United States of America
| | - Gyan Bhanot
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, United States of America
- BioMaPS Institute for Quantitative Biology, Busch Campus, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
| | - Himanshu Sinha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- * E-mail:
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41
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Abstract
Understanding the genetic mechanisms underlying complex traits is one of the next frontiers in biology. The budding yeast Saccharomyces cerevisiae has become an important model for elucidating the mechanisms that govern natural genetic and phenotypic variation. This success is partially due to its intrinsic biological features, such as the short sexual generation time, high meiotic recombination rate, and small genome size. Precise reverse genetics technologies allow the high throughput manipulation of genetic information with exquisite precision, offering the unique opportunity to experimentally measure the phenotypic effect of genetic variants. Population genomic and phenomic studies have revealed widespread variation between diverged populations, characteristic of man-made environments, as well as geographic clusters of wild strains along with naturally occurring recombinant strains (mosaics). Here, we review these recent studies and provide a perspective on how these previously unappreciated levels of variation can help to bridge our understanding of the genotype-phenotype gap, keeping budding yeast at the forefront of genetic studies. Not only are quantitative trait loci (QTL) being mapped with high resolution down to the nucleotide, for the first time QTLs of modest effect and complex interactions between these QTLs and between QTLs and the environment are being determined experimentally at unprecedented levels using next generation techniques of deep sequencing selected pools of individuals as well as multi-generational crosses.
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42
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A noncomplementation screen for quantitative trait alleles in saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2012; 2:753-60. [PMID: 22870398 PMCID: PMC3385981 DOI: 10.1534/g3.112.002550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 04/30/2012] [Indexed: 11/18/2022]
Abstract
Both linkage and linkage disequilibrium mapping provide well-defined approaches to mapping quantitative trait alleles. However, alleles of small effect are particularly difficult to refine to individual genes and causative mutations. Quantitative noncomplementation provides a means of directly testing individual genes for quantitative trait alleles in a fixed genetic background. Here, we implement a genome-wide noncomplementation screen for quantitative trait alleles that affect colony color or size by using the yeast deletion collection. As proof of principle, we find a previously known allele of CYS4 that affects colony color and a novel allele of CTT1 that affects resistance to hydrogen peroxide. To screen nearly 4700 genes in nine diverse yeast strains, we developed a high-throughput robotic plating assay to quantify colony color and size. Although we found hundreds of candidate alleles, reciprocal hemizygosity analysis of a select subset revealed that many of the candidates were false positives, in part the result of background-dependent haploinsufficiency or second-site mutations within the yeast deletion collection. Our results highlight the difficulty of identifying small-effect alleles but support the use of noncomplementation as a rapid means of identifying quantitative trait alleles of large effect.
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Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, Sontheimer EJ. Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA (NEW YORK, N.Y.) 2012; 18:1142-53. [PMID: 22539527 PMCID: PMC3358637 DOI: 10.1261/rna.030510.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Changes in transcript architecture can have powerful effects on protein expression. Regulation of the transcriptome is often dramatically revealed during dynamic conditions such as development. To examine changes in transcript architecture we analyzed the expression and transcript boundaries of protein-coding and noncoding RNAs over the developmental process of meiosis in Saccharomyces cerevisiae. Custom-designed, high-resolution tiling arrays were used to define the time-resolved transcriptome of cells undergoing meiosis and sporulation. These arrays were specifically designed for the S. cerevisiae strain SK1 that sporulates with high efficiency and synchrony. In addition, new methods were created to define transcript boundaries and to identify dynamic changes in transcript expression and architecture over time. Of 8407 total segments, 699 (8.3%) were identified by our algorithm as regions containing potential transcript architecture changes. Our analyses reveal extensive changes to both the coding and noncoding transcriptome, including altered 5' ends, 3' ends, and splice sites. Additionally, 3910 (46.5%) unannotated expressed segments were identified. Interestingly, subsets of unannotated RNAs are located across from introns (anti-introns) or across from the junction between two genes (anti-intergenic junctions). Many of these unannotated RNAs are abundant and exhibit sporulation-specific changes in expression patterns. All work, including heat maps of the tiling array, annotation for the SK1 strain, and phastCONS conservation analysis, is available at http://groups.molbiosci.northwestern.edu/sontheimer/sk1meiosis.php. Our high-resolution transcriptome analyses reveal that coding and noncoding transcript architectures are exceptionally dynamic in S. cerevisiae and suggest a vast array of novel transcriptional and post-transcriptional control mechanisms that are activated upon meiosis and sporulation.
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Affiliation(s)
- Karen S. Kim Guisbert
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Yong Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Jared Flatow
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Sara Hurtado
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Jonathan P. Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Simon Lin
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Erik J. Sontheimer
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
- Corresponding author.E-mail .
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Swinnen S, Schaerlaekens K, Pais T, Claesen J, Hubmann G, Yang Y, Demeke M, Foulquié-Moreno MR, Goovaerts A, Souvereyns K, Clement L, Dumortier F, Thevelein JM. Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. Genome Res 2012; 22:975-84. [PMID: 22399573 PMCID: PMC3337442 DOI: 10.1101/gr.131698.111] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 03/06/2012] [Indexed: 01/13/2023]
Abstract
High ethanol tolerance is an exquisite characteristic of the yeast Saccharomyces cerevisiae, which enables this microorganism to dominate in natural and industrial fermentations. Up to now, ethanol tolerance has only been analyzed in laboratory yeast strains with moderate ethanol tolerance. The genetic basis of the much higher ethanol tolerance in natural and industrial yeast strains is unknown. We have applied pooled-segregant whole-genome sequence analysis to map all quantitative trait loci (QTL) determining high ethanol tolerance. We crossed a highly ethanol-tolerant segregant of a Brazilian bioethanol production strain with a laboratory strain with moderate ethanol tolerance. Out of 5974 segregants, we pooled 136 segregants tolerant to at least 16% ethanol and 31 segregants tolerant to at least 17%. Scoring of SNPs using whole-genome sequence analysis of DNA from the two pools and parents revealed three major loci and additional minor loci. The latter were more pronounced or only present in the 17% pool compared to the 16% pool. In the locus with the strongest linkage, we identified three closely located genes affecting ethanol tolerance: MKT1, SWS2, and APJ1, with SWS2 being a negative allele located in between two positive alleles. SWS2 and APJ1 probably contained significant polymorphisms only outside the ORF, and lower expression of APJ1 may be linked to higher ethanol tolerance. This work has identified the first causative genes involved in high ethanol tolerance of yeast. It also reveals the strong potential of pooled-segregant sequence analysis using relatively small numbers of selected segregants for identifying QTL on a genome-wide scale.
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Affiliation(s)
- Steve Swinnen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Kristien Schaerlaekens
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Thiago Pais
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Jürgen Claesen
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, UHasselt and KU Leuven, B-3590 Flanders, Belgium
| | - Georg Hubmann
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Yudi Yang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Mekonnen Demeke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - María R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Annelies Goovaerts
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Kris Souvereyns
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Lieven Clement
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, UHasselt and KU Leuven, B-3590 Flanders, Belgium
| | - Françoise Dumortier
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIB, B-3001 Leuven-Heverlee, Flanders, Belgium
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Swinnen S, Thevelein JM, Nevoigt E. Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae. FEMS Yeast Res 2012; 12:215-27. [PMID: 22150948 DOI: 10.1111/j.1567-1364.2011.00777.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/01/2011] [Accepted: 12/05/2011] [Indexed: 12/13/2022] Open
Abstract
Saccharomyces cerevisiae has become a favorite production organism in industrial biotechnology presenting new challenges to yeast engineers in terms of introducing advantageous traits such as stress tolerances. Exploring subspecies diversity of S. cerevisiae has identified strains that bear industrially relevant phenotypic traits. Provided that the genetic basis of such phenotypic traits can be identified inverse engineering allows the targeted modification of production strains. Most phenotypic traits of interest in S. cerevisiae strains are quantitative, meaning that they are controlled by multiple genetic loci referred to as quantitative trait loci (QTL). A straightforward approach to identify the genetic basis of quantitative traits is QTL mapping which aims at the allocation of the genetic determinants to regions in the genome. The application of high-density oligonucleotide arrays and whole-genome re-sequencing to detect genetic variations between strains has facilitated the detection of large numbers of molecular markers thus allowing high-resolution QTL mapping over the entire genome. This review focuses on the basic principle and state of the art of QTL mapping in S. cerevisiae. Furthermore we discuss several approaches developed during the last decade that allow down-scaling of the regions identified by QTL mapping to the gene level. We also emphasize the particular challenges of QTL mapping in nonlaboratory strains of S. cerevisiae.
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Affiliation(s)
- Steve Swinnen
- School of Engineering and Science, Jacobs University gGmbH, Bremen, Germany
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Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci U S A 2012; 109:E111-8. [PMID: 22247290 DOI: 10.1073/pnas.1110740109] [Citation(s) in RCA: 475] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Malaria, caused by Plasmodium sp, results in almost one million deaths and over 200 million new infections annually. The World Health Organization has recommended that artemisinin-based combination therapies be used for treatment of malaria. Artemisinin is a sesquiterpene lactone isolated from the plant Artemisia annua. However, the supply and price of artemisinin fluctuate greatly, and an alternative production method would be valuable to increase availability. We describe progress toward the goal of developing a supply of semisynthetic artemisinin based on production of the artemisinin precursor amorpha-4,11-diene by fermentation from engineered Saccharomyces cerevisiae, and its chemical conversion to dihydroartemisinic acid, which can be subsequently converted to artemisinin. Previous efforts to produce artemisinin precursors used S. cerevisiae S288C overexpressing selected genes of the mevalonate pathway [Ro et al. (2006) Nature 440:940-943]. We have now overexpressed every enzyme of the mevalonate pathway to ERG20 in S. cerevisiae CEN.PK2, and compared production to CEN.PK2 engineered identically to the previously engineered S288C strain. Overexpressing every enzyme of the mevalonate pathway doubled artemisinic acid production, however, amorpha-4,11-diene production was 10-fold higher than artemisinic acid. We therefore focused on amorpha-4,11-diene production. Development of fermentation processes for the reengineered CEN.PK2 amorpha-4,11-diene strain led to production of > 40 g/L product. A chemical process was developed to convert amorpha-4,11-diene to dihydroartemisinic acid, which could subsequently be converted to artemisinin. The strains and procedures described represent a complete process for production of semisynthetic artemisinin.
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Camarasa C, Sanchez I, Brial P, Bigey F, Dequin S. Phenotypic landscape of Saccharomyces cerevisiae during wine fermentation: evidence for origin-dependent metabolic traits. PLoS One 2011; 6:e25147. [PMID: 21949874 PMCID: PMC3174997 DOI: 10.1371/journal.pone.0025147] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 08/29/2011] [Indexed: 01/01/2023] Open
Abstract
The species Saccharomyces cerevisiae includes natural strains, clinical isolates, and a large number of strains used in human activities. The aim of this work was to investigate how the adaptation to a broad range of ecological niches may have selectively shaped the yeast metabolic network to generate specific phenotypes. Using 72 S. cerevisiae strains collected from various sources, we provide, for the first time, a population-scale picture of the fermentative metabolic traits found in the S. cerevisiae species under wine making conditions. Considerable phenotypic variation was found suggesting that this yeast employs diverse metabolic strategies to face environmental constraints. Several groups of strains can be distinguished from the entire population on the basis of specific traits. Strains accustomed to growing in the presence of high sugar concentrations, such as wine yeasts and strains obtained from fruits, were able to achieve fermentation, whereas natural yeasts isolated from “poor-sugar” environments, such as oak trees or plants, were not. Commercial wine yeasts clearly appeared as a subset of vineyard isolates, and were mainly differentiated by their fermentative performances as well as their low acetate production. Overall, the emergence of the origin-dependent properties of the strains provides evidence for a phenotypic evolution driven by environmental constraints and/or human selection within S. cerevisiae.
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Ambroset C, Petit M, Brion C, Sanchez I, Delobel P, Guérin C, Chiapello H, Nicolas P, Bigey F, Dequin S, Blondin B. Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. G3 (BETHESDA, MD.) 2011; 1:263-81. [PMID: 22384338 PMCID: PMC3276144 DOI: 10.1534/g3.111.000422] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/20/2011] [Indexed: 12/31/2022]
Abstract
The genetic basis of the phenotypic diversity of yeast is still poorly understood. Wine yeast strains have specific abilities to grow and ferment under stressful conditions compared with other strains, but the genetic basis underlying these traits is unknown. Understanding how sequence variation influences such phenotypes is a major challenge to address adaptation mechanisms of wine yeast. We aimed to identify the genetic basis of fermentation traits and gain insight into their relationships with variations in gene expression among yeast strains. We combined fermentation trait QTL mapping and expression profiling of fermenting cells in a segregating population from a cross between a wine yeast derivative and a laboratory strain. We report the identification of QTL for various fermentation traits (fermentation rates, nitrogen utilization, metabolites production) as well as expression QTL (eQTL). We found that many transcripts mapped to several eQTL hotspots and that two of them overlapped with QTL for fermentation traits. A QTL controlling the maximal fermentation rate and nitrogen utilization overlapping with an eQTL hotspot was dissected. We functionally demonstrated that an allele of the ABZ1 gene, localized in the hotspot and involved in p-aminobenzoate biosynthesis, controls the fermentation rate through modulation of nitrogen utilization. Our data suggest that the laboratory strain harbors a defective ABZ1 allele, which triggers strong metabolic and physiological alterations responsible for the generation of the eQTL hotspot. They also suggest that a number of gene expression differences result from some alleles that trigger major physiological disturbances.
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Affiliation(s)
- Chloé Ambroset
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Maud Petit
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Christian Brion
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Isabelle Sanchez
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Pierre Delobel
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Cyprien Guérin
- INRA, UR1077 Mathématique Informatique et Génome, F-78352 Jouy-en-Josas, France
| | - Hélène Chiapello
- INRA, UR1077 Mathématique Informatique et Génome, F-78352 Jouy-en-Josas, France
| | - Pierre Nicolas
- INRA, UR1077 Mathématique Informatique et Génome, F-78352 Jouy-en-Josas, France
| | - Frédéric Bigey
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Sylvie Dequin
- Institut National de la Recherche Agronomique (INRA), UMR1083, and
| | - Bruno Blondin
- Montpellier SupAgro, UMR 1083 Sciences pour l'Oenologie, F-34060 Montpellier, and
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Oxidative stress survival in a clinical Saccharomyces cerevisiae isolate is influenced by a major quantitative trait nucleotide. Genetics 2011; 188:709-22. [PMID: 21515583 DOI: 10.1534/genetics.111.128256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One of the major challenges in characterizing eukaryotic genetic diversity is the mapping of phenotypes that are the cumulative effect of multiple alleles. We have investigated tolerance of oxidative stress in the yeast Saccharomyces cerevisiae, a trait showing phenotypic variation in the population. Initial crosses identified that this is a quantitative trait. Microorganisms experience oxidative stress in many environments, including during infection of higher eukaryotes. Natural variation in oxidative stress tolerance is an important aspect of response to oxidative stress exerted by the human immune system and an important trait in microbial pathogens. A clinical isolate of the usually benign yeast S. cerevisiae was found to survive oxidative stress significantly better than the laboratory strain. We investigated the genetic basis of increased peroxide survival by crossing those strains, phenotyping 1500 segregants, and genotyping of high-survival segregants by hybridization of bulk and single segregant DNA to microarrays. This effort has led to the identification of an allele of the transcription factor Rds2 as contributing to stress response. Rds2 has not previously been associated with the survival of oxidative stress. The identification of its role in the oxidative stress response here is an example of a specific trait that appears to be beneficial to Saccharomyces cerevisiae when growing as a pathogen. Understanding the role of this fungal-specific transcription factor in pathogenicity will be important in deciphering how fungi infect and colonize the human host and could eventually lead to a novel drug target.
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Nieduszynski CA, Liti G. From sequence to function: Insights from natural variation in budding yeasts. Biochim Biophys Acta Gen Subj 2011; 1810:959-66. [PMID: 21320572 PMCID: PMC3271348 DOI: 10.1016/j.bbagen.2011.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 02/03/2011] [Accepted: 02/08/2011] [Indexed: 12/18/2022]
Abstract
Background Natural variation offers a powerful approach for assigning function to DNA sequence—a pressing challenge in the age of high throughput sequencing technologies. Scope of Review Here we review comparative genomic approaches that are bridging the sequence–function and genotype–phenotype gaps. Reverse genomic approaches aim to analyse sequence to assign function, whereas forward genomic approaches start from a phenotype and aim to identify the underlying genotype responsible. Major Conclusions Comparative genomic approaches, pioneered in budding yeasts, have resulted in dramatic improvements in our understanding of the function of both genes and regulatory sequences. Analogous studies in other systems, including humans, demonstrate the ubiquity of comparative genomic approaches. Recently, forward genomic approaches, exploiting natural variation within yeast populations, have started to offer powerful insights into how genotype influences phenotype and even the ability to predict phenotypes. General Significance Comparative genomic experiments are defining the fundamental rules that govern complex traits in natural populations from yeast to humans. This article is part of a Special Issue entitled Systems Biology of Microorganisms.
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