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Siddiq MA, Duveau F, Wittkopp PJ. Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589130. [PMID: 38659876 PMCID: PMC11042213 DOI: 10.1101/2024.04.12.589130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Phenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeast Saccharomyces cerevisiae in four environments. Specifically, we measured how mutations in the promoter of the metabolic gene TDH3 modified its expression level and affected its growth on media with four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Genetic variants with similar effects on TDH3 expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. The set of mutants we examined also allowed us to compare the effects of mutations disrupting binding sites for key transcriptional regulators and the TATA box, which is part of the core promoter sequence. Mutations disrupting the binding sites for the transcription factors had more variable effects on expression among environments than mutations disrupting the TATA box, yet mutations with the most environmentally variable effects on fitness were located in the TATA box. This observation suggests that mutations affecting different molecular mechanisms are likely to contribute unequally to regulatory sequence evolution in changing environments.
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Affiliation(s)
- Mohammad A. Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
- Authors contributed equally to this work
| | - Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon, Université de Lyon, France
- Authors contributed equally to this work
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
- Department of Ecology and Evolutionary Biology, University of Michigan
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2
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Wittkopp PJ. Contributions of mutation and selection to regulatory variation: lessons from the Saccharomyces cerevisiae TDH3 gene. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220057. [PMID: 37004723 PMCID: PMC10067266 DOI: 10.1098/rstb.2022.0057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Heritable variation in gene expression is common within and among species and contributes to phenotypic diversity. Mutations affecting either cis- or trans-regulatory sequences controlling gene expression give rise to variation in gene expression, and natural selection acting on this variation causes some regulatory variants to persist in a population for longer than others. To understand how mutation and selection interact to produce the patterns of regulatory variation we see within and among species, my colleagues and I have been systematically determining the effects of new mutations on expression of the TDH3 gene in Saccharomyces cerevisiae and comparing them to the effects of polymorphisms segregating within this species. We have also investigated the molecular mechanisms by which regulatory variants act. Over the past decade, this work has revealed properties of cis- and trans-regulatory mutations including their relative frequency, effects, dominance, pleiotropy and fitness consequences. Comparing these mutational effects to the effects of polymorphisms in natural populations, we have inferred selection acting on expression level, expression noise and phenotypic plasticity. Here, I summarize this body of work and synthesize its findings to make inferences not readily discernible from the individual studies alone. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Patricia J. Wittkopp
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Azizoglu A, Brent R, Rudolf F. A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery. eLife 2021; 10:69549. [PMID: 34342575 PMCID: PMC8421071 DOI: 10.7554/elife.69549] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Conditional expression of genes and observation of phenotype remain central to biological discovery. Current methods enable either on/off or imprecisely controlled graded gene expression. We developed a 'well-tempered' controller, WTC846, for precisely adjustable, graded, growth condition independent expression of genes in Saccharomyces cerevisiae. Controlled genes are expressed from a strong semisynthetic promoter repressed by the prokaryotic TetR, which also represses its own synthesis; with basal expression abolished by a second, 'zeroing' repressor. The autorepression loop lowers cell-to-cell variation while enabling precise adjustment of protein expression by a chemical inducer. WTC846 allelic strains in which the controller replaced the native promoters recapitulated known null phenotypes (CDC42, TPI1), exhibited novel overexpression phenotypes (IPL1), showed protein dosage-dependent growth rates and morphological phenotypes (CDC28, TOR2, PMA1 and the hitherto uncharacterized PBR1), and enabled cell cycle synchronization (CDC20). WTC846 defines an 'expression clamp' allowing protein dosage to be adjusted by the experimenter across the range of cellular protein abundances, with limited variation around the setpoint.
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Affiliation(s)
| | - Roger Brent
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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4
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Cámara E, Lenitz I, Nygård Y. A CRISPR activation and interference toolkit for industrial Saccharomyces cerevisiae strain KE6-12. Sci Rep 2020; 10:14605. [PMID: 32884066 PMCID: PMC7471924 DOI: 10.1038/s41598-020-71648-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/10/2020] [Indexed: 01/17/2023] Open
Abstract
Recent advances in CRISPR/Cas9 based genome editing have considerably advanced genetic engineering of industrial yeast strains. In this study, we report the construction and characterization of a toolkit for CRISPR activation and interference (CRISPRa/i) for a polyploid industrial yeast strain. In the CRISPRa/i plasmids that are available in high and low copy variants, dCas9 is expressed alone, or as a fusion with an activation or repression domain; VP64, VPR or Mxi1. The sgRNA is introduced to the CRISPRa/i plasmids from a double stranded oligonucleotide by in vivo homology-directed repair, allowing rapid transcriptional modulation of new target genes without cloning. The CRISPRa/i toolkit was characterized by alteration of expression of fluorescent protein-encoding genes under two different promoters allowing expression alterations up to ~ 2.5-fold. Furthermore, we demonstrated the usability of the CRISPRa/i toolkit by improving the tolerance towards wheat straw hydrolysate of our industrial production strain. We anticipate that our CRISPRa/i toolkit can be widely used to assess novel targets for strain improvement and thus accelerate the design-build-test cycle for developing various industrial production strains.
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Affiliation(s)
- Elena Cámara
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Ibai Lenitz
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Yvonne Nygård
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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5
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Effects of mutation and selection on plasticity of a promoter activity in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2017; 114:E11218-E11227. [PMID: 29259117 DOI: 10.1073/pnas.1713960115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Phenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single-nucleotide mutations in the Saccharomyces cerevisiae TDH3 promoter (PTDH3 ) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild-type allele. Comparing the effects of these mutations with the effects of 30 PTDH3 polymorphisms on expression plasticity in the same environments provided evidence of natural selection acting to prevent the plastic response in PTDH3 activity between glucose and galactose from becoming larger. The largest changes in expression plasticity were observed between fermentable (glucose or galactose) and nonfermentable (glycerol) carbon sources and were caused by mutations located in the RAP1 and GCR1 transcription factor binding sites. Mutations altered expression plasticity most frequently between the two fermentable environments, with mutations causing significant changes in plasticity between glucose and galactose distributed throughout the promoter, suggesting they might affect chromatin structure. Taken together, these results provide insight into the molecular mechanisms underlying gene-by-environment interactions affecting gene expression as well as the evolutionary dynamics affecting natural variation in plasticity of gene expression.
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Nakagawa Y, Ogihara H, Mochizuki C, Yamamura H, Iimura Y, Hayakawa M. Development of intra-strain self-cloning procedure for breeding baker's yeast strains. J Biosci Bioeng 2017; 123:319-326. [DOI: 10.1016/j.jbiosc.2016.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/09/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
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7
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Nakagawa Y, Arai Y, Toda Y, Yamamura H, Okuda T, Hayakawa M, Iimura Y. Glucose repression of FLO11 gene expression regulates pellicle formation by a wild pellicle-forming yeast strain isolated from contaminated wine. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1246203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Youji Nakagawa
- Division of Life and Agricultural Sciences, Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Yukari Arai
- Division of Biotechnology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Yasuhiro Toda
- Department of Biotechnology, Faculty of Engineering, University of Yamanashi, Kofu, Japan
| | - Hideki Yamamura
- Division of Life and Agricultural Sciences, Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Tohru Okuda
- The Institute of Enology and Viticulture, University of Yamanashi, Kofu, Japan
| | - Masayuki Hayakawa
- Division of Life and Agricultural Sciences, Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Yuzuru Iimura
- Division of Biotechnology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
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8
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Patel A, Pruthi V, Singh RP, Pruthi PA. Synergistic effect of fermentable and non-fermentable carbon sources enhances TAG accumulation in oleaginous yeast Rhodosporidium kratochvilovae HIMPA1. BIORESOURCE TECHNOLOGY 2015; 188:136-44. [PMID: 25769691 DOI: 10.1016/j.biortech.2015.02.062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/23/2023]
Abstract
Novel strategy for enhancing TAG accumulation by simultaneous utilization of fermentable and non-fermentable carbon sources as substrate for cultivation of oleaginous yeast Rhodosporidium kratochvilovae HIMPA1 were undertaken in this investigation. The yeast strain showed direct correlation between the size of lipid bodies, visualized by BODIPY stain (493-515 nm) and TAG accumulation when examined on individual fermenting and non-fermenting carbon sources and their mixtures. Maximum TAG accumulation (μm) in glucose (2.38 ± 0.52), fructose (4.03 ± 0.38), sucrose (4.24 ± 0.45), glycerol (4.35 ± 0.54), xylulose (3.94 ± 0.12), and arabinose (2.98 ± 0.43) were observed. Synergistic effect of the above carbon sources (fermentable and non-fermentable) in equimolar concentration revealed maximum lipid droplet size of 5.35 ± 0.76 μm and cell size of 6.89 ± 0.97 μm. Total lipid content observed in mixed carbon sources was 9.26 g/l compared to glucose (6.2g/l). FAME profile revealed enhanced longer chain (C14:0-C24:0) fatty acids in mix carbon sources.
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Affiliation(s)
- Alok Patel
- Molecular Microbiology Laboratory, Biotechnology Department, Indian Institute of Technology Roorkee (IIT R), Roorkee, Uttarakhand 247667, India
| | - Vikas Pruthi
- Molecular Microbiology Laboratory, Biotechnology Department, Indian Institute of Technology Roorkee (IIT R), Roorkee, Uttarakhand 247667, India
| | - Rajesh P Singh
- Molecular Microbiology Laboratory, Biotechnology Department, Indian Institute of Technology Roorkee (IIT R), Roorkee, Uttarakhand 247667, India
| | - Parul A Pruthi
- Molecular Microbiology Laboratory, Biotechnology Department, Indian Institute of Technology Roorkee (IIT R), Roorkee, Uttarakhand 247667, India.
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9
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Employing a combinatorial expression approach to characterize xylose utilization in Saccharomyces cerevisiae. Metab Eng 2014; 25:20-9. [DOI: 10.1016/j.ymben.2014.06.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/07/2014] [Accepted: 06/04/2014] [Indexed: 12/24/2022]
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Nakagawa Y, Hasebe T, Ishiai M, Yamamura H, Iimura Y, Hayakawa M. Forced expression of FLO11 confers pellicle-forming ability and furfural tolerance on Saccharomyces cerevisiae in ethanol production. Biosci Biotechnol Biochem 2014; 78:714-7. [PMID: 25036972 DOI: 10.1080/09168451.2014.895660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We constructed a plasmid that expresses FLO11 encoding a cell surface glycoprotein of Saccharomyces cerevisiae under the control of a constitutive promoter. This plasmid conferred pellicle-forming ability on the non-pellicle-forming industrial strain of S. cerevisiae at the air-liquid interface of the glucose-containing liquid medium. The induced pellicle-forming cells exhibited tolerance to furfural, which is a key toxin in lignocellulosic hydrolysates, in ethanol production.
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Affiliation(s)
- Youji Nakagawa
- a Division of Biotechnology, Interdisciplinary Graduate School of Medicine and Engineering , University of Yamanashi , 4-3-11 Takeda, Kofu, Yamanashi, 400-8511 , Japan
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11
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Use of the glyceraldehyde-3-phosphate dehydrogenase promoter from a thermotolerant yeast, Pichia thermomethanolica, for heterologous gene expression, especially at elevated temperature. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0765-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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12
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Fukunaga T, Cha-aim K, Hirakawa Y, Sakai R, Kitagawa T, Nakamura M, Nonklang S, Hoshida H, Akada R. Designed construction of recombinant DNA at theura3Δ0locus in the yeastSaccharomyces cerevisiae. Yeast 2013; 30:243-53. [DOI: 10.1002/yea.2957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/08/2013] [Accepted: 04/15/2013] [Indexed: 11/08/2022] Open
Affiliation(s)
- Tomoaki Fukunaga
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Kamonchai Cha-aim
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Yuki Hirakawa
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Ryota Sakai
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Takao Kitagawa
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Mikiko Nakamura
- Innovation Centre; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Sanom Nonklang
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai; Ube; Japan
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13
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Overexpression of stress-related genes enhances cell viability and velum formation in Sherry wine yeasts. Appl Microbiol Biotechnol 2013; 97:6867-81. [DOI: 10.1007/s00253-013-4850-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/06/2013] [Accepted: 03/10/2013] [Indexed: 11/25/2022]
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14
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Gruber JD, Vogel K, Kalay G, Wittkopp PJ. Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance. PLoS Genet 2012; 8:e1002497. [PMID: 22346762 PMCID: PMC3276545 DOI: 10.1371/journal.pgen.1002497] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Accepted: 12/08/2011] [Indexed: 12/18/2022] Open
Abstract
Genetic variation within and between species can be shaped by population-level processes and mutation; however, the relative impact of “survival of the fittest” and “arrival of the fittest” on phenotypic evolution remains unclear. Assessing the influence of mutation on evolution requires understanding the relative rates of different types of mutations and their genetic properties, yet little is known about the functional consequences of new mutations. Here, we examine the spectrum of mutations affecting a focal gene in Saccharomyces cerevisiae by characterizing 231 novel haploid genotypes with altered activity of a fluorescent reporter gene. 7% of these genotypes had a nonsynonymous mutation in the coding sequence for the fluorescent protein and were classified as “coding” mutants; 2% had a change in the S. cerevisiae TDH3 promoter sequence controlling expression of the fluorescent protein and were classified as “cis-regulatory” mutants; 10% contained two copies of the reporter gene and were classified as “copy number” mutants; and the remaining 81% showed altered fluorescence without a change in the reporter gene itself and were classified as “trans-acting” mutants. As a group, coding mutants had the strongest effect on reporter gene activity and always decreased it. By contrast, 50%–95% of the mutants in each of the other three classes increased gene activity, with mutants affecting copy number and cis-regulatory sequences having larger median effects on gene activity than trans-acting mutants. When made heterozygous in diploid cells, coding, cis-regulatory, and copy number mutant genotypes all had significant effects on gene activity, whereas 88% of the trans-acting mutants appeared to be recessive. These differences in the frequency, effects, and dominance among functional classes of mutations might help explain why some types of mutations are found to be segregating within or fixed between species more often than others. Genetic dissection of phenotypic differences within and between species has shown that mutations affecting either the expression or function of a gene product can contribute to phenotypic evolution; mutations that alter gene copy number have also been shown to be an important source of phenotypic variation. Predicting when and why one type of mutation is more likely to underlie a phenotypic change than another remains a pressing challenge for evolution biology. Understanding the relative frequency and properties of different types of mutations will help resolve this issue. To this end, we isolated 231 mutants with altered activity of a focal gene. Mutants were classified into one of four functional classes (i.e., coding, cis-regulatory, trans-acting, or copy number) based on the location and nature of mutation(s), or lack thereof, within the focal gene. Mutant effects on focal gene activity were assessed in both haploid and diploid cells. These data identified differences in the frequency, effects, and dominance (relative to the wild-type allele) among functional classes of mutants that help explain patterns of genetic variation within and between species.
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Affiliation(s)
- Jonathan D. Gruber
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kara Vogel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gizem Kalay
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patricia J. Wittkopp
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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15
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Tochigi Y, Sato N, Sahara T, Wu C, Saito S, Irie T, Fujibuchi W, Goda T, Yamaji R, Ogawa M, Ohmiya Y, Ohgiya S. Sensitive and Convenient Yeast Reporter Assay for High-Throughput Analysis by Using a Secretory Luciferase from Cypridina noctiluca. Anal Chem 2010; 82:5768-76. [DOI: 10.1021/ac100832b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Tochigi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Natsuko Sato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Takehiko Sahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Chun Wu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Shinya Saito
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Tsutomu Irie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Wataru Fujibuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Takako Goda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Ryoichi Yamaji
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Masahiro Ogawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Yoshihiro Ohmiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
| | - Satoru Ohgiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan, Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda 563-8577, Japan, ATTO Corporation, 1-5-32
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16
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Anderlund M, Nissen TL, Nielsen J, Villadsen J, Rydström J, Hahn-Hägerdal B, Kielland-Brandt MC. Expression of the Escherichia coli pntA and pntB genes, encoding nicotinamide nucleotide transhydrogenase, in Saccharomyces cerevisiae and its effect on product formation during anaerobic glucose fermentation. Appl Environ Microbiol 1999; 65:2333-40. [PMID: 10347010 PMCID: PMC91345 DOI: 10.1128/aem.65.6.2333-2340.1999] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the physiological effect of the interconversion between the NAD(H) and NADP(H) coenzyme systems in recombinant Saccharomyces cerevisiae expressing the membrane-bound transhydrogenase from Escherichia coli. Our objective was to determine if the membrane-bound transhydrogenase could work in reoxidation of NADH to NAD+ in S. cerevisiae and thereby reduce glycerol formation during anaerobic fermentation. Membranes isolated from the recombinant strains exhibited reduction of 3-acetylpyridine-NAD+ by NADPH and by NADH in the presence of NADP+, which demonstrated that an active enzyme was present. Unlike the situation in E. coli, however, most of the transhydrogenase activity was not present in the yeast plasma membrane; rather, the enzyme appeared to remain localized in the membrane of the endoplasmic reticulum. During anaerobic glucose fermentation we observed an increase in the formation of 2-oxoglutarate, glycerol, and acetic acid in a strain expressing a high level of transhydrogenase, which indicated that increased NADPH consumption and NADH production occurred. The intracellular concentrations of NADH, NAD+, NADPH, and NADP+ were measured in cells expressing transhydrogenase. The reduction of the NADPH pool indicated that the transhydrogenase transferred reducing equivalents from NADPH to NAD+.
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Affiliation(s)
- M Anderlund
- Department of Yeast Genetics, Carlsberg Laboratory, DK-2500 Copenhagen Valby, Denmark
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17
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Shen H, Dowhan W. Regulation of phosphatidylglycerophosphate synthase levels in Saccharomyces cerevisiae. J Biol Chem 1998; 273:11638-42. [PMID: 9565583 DOI: 10.1074/jbc.273.19.11638] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PGS1 gene of Saccharomyces cerevisiae encodes phosphatidylglycerophosphate (PG-P) synthase. PG-P synthase activity is regulated by factors affecting mitochondrial development and through cross-pathway control by inositol. The molecular mechanism of this regulation was examined by using a reporter gene under control of the PGS1 gene promoter (PPGS1-lacZ). Gene expression subject to carbon source regulation was monitored both at steady-state level and during the switch between different carbon sources. Cells grown in a non-fermentable carbon source had beta-galactosidase levels 3-fold higher than those grown in glucose. A shift from glucose to lactate rapidly raised the level of gene expression, whereas a shift back to glucose had the opposite effect. In either a pgs1 null mutant or a rho mutant grown in glucose, PPGS1-lacZ expression was 30-50% of the level in wild type cells. Addition of inositol to the growth medium resulted in a 2-3-fold reduction in gene expression in wild type cells. In ino2 and ino4 mutants, gene expression was greatly reduced and was not subject to inositol regulation consistent with inositol repression being dependent on the INO2 and INO4 regulatory genes. PPGS1-lacZ expression was elevated in a cds1 null mutant in the presence or absence of inositol, indicating that the capacity to synthesize CDP-diacylglycerol affects gene expression. Lack of cardiolipin synthesis (cls1 null mutant) had no effect on reporter gene expression.
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Affiliation(s)
- H Shen
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77225, USA
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18
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Chambers A, Packham EA, Graham IR. Control of glycolytic gene expression in the budding yeast (Saccharomyces cerevisiae). Curr Genet 1995; 29:1-9. [PMID: 8595651 DOI: 10.1007/bf00313187] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- A Chambers
- Department of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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