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Sonal, Yuan AE, Yang X, Shou W. Collective production of hydrogen sulfide gas enables budding yeast lacking MET17 to overcome their metabolic defect. PLoS Biol 2023; 21:e3002439. [PMID: 38060626 PMCID: PMC10729969 DOI: 10.1371/journal.pbio.3002439] [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] [Received: 05/10/2023] [Revised: 12/19/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
Assimilation of sulfur is vital to all organisms. In S. cerevisiae, inorganic sulfate is first reduced to sulfide, which is then affixed to an organic carbon backbone by the Met17 enzyme. The resulting homocysteine can then be converted to all other essential organosulfurs such as methionine, cysteine, and glutathione. This pathway has been known for nearly half a century, and met17 mutants have long been classified as organosulfur auxotrophs, which are unable to grow on sulfate as their sole sulfur source. Surprisingly, we found that met17Δ could grow on sulfate, albeit only at sufficiently high cell densities. We show that the accumulation of hydrogen sulfide gas underpins this density-dependent growth of met17Δ on sulfate and that the locus YLL058W (HSU1) enables met17Δ cells to assimilate hydrogen sulfide. Hsu1 protein is induced during sulfur starvation and under exposure to high sulfide concentrations in wild-type cells, and the gene has a pleiotropic role in sulfur assimilation. In a mathematical model, the low efficiency of sulfide assimilation in met17Δ can explain the observed density-dependent growth of met17Δ on sulfate. Thus, having uncovered and explained the paradoxical growth of a commonly used "auxotroph," our findings may impact the design of future studies in yeast genetics, metabolism, and volatile-mediated microbial interactions.
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Affiliation(s)
- Sonal
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alex E. Yuan
- University of Washington, Seattle, Washington, United States of America
| | - Xueqin Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Wenying Shou
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Yu JSL, Heineike BM, Hartl J, Aulakh SK, Correia-Melo C, Lehmann A, Lemke O, Agostini F, Lee CT, Demichev V, Messner CB, Mülleder M, Ralser M. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy. PLoS Biol 2022; 20:e3001912. [PMID: 36455053 PMCID: PMC9757880 DOI: 10.1371/journal.pbio.3001912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/16/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.
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Affiliation(s)
- Jason S. L. Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Benjamin M. Heineike
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Johannes Hartl
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Simran K. Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Clara Correia-Melo
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Lehmann
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Oliver Lemke
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Cory T. Lee
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B. Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Mülleder
- Core Facility—High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
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Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
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Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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Nielsen JC, Senne de Oliveira Lino F, Rasmussen TG, Thykær J, Workman CT, Basso TO. Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells. Appl Microbiol Biotechnol 2017; 101:8237-8248. [PMID: 28993899 PMCID: PMC5719808 DOI: 10.1007/s00253-017-8548-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/06/2017] [Accepted: 09/17/2017] [Indexed: 01/08/2023]
Abstract
The Brazilian sugarcane industry constitutes one of the biggest and most efficient ethanol production processes in the world. Brazilian ethanol production utilizes a unique process, which includes cell recycling, acid wash, and non-aseptic conditions. Process characteristics, such as extensive CO2 generation, poor quality of raw materials, and frequent contaminations, all lead to excessive foam formation during fermentations, which is treated with antifoam agents (AFA). In this study, we have investigated the impact of industrial AFA treatments on the physiology and transcriptome of the industrial ethanol strain Saccharomyces cerevisiae CAT-1. The investigated AFA included industrially used AFA acquired from Brazilian ethanol plants and commercially available AFA commonly used in the fermentation literature. In batch fermentations, it was shown that industrial AFA compromised growth rates and glucose uptake rates, while commercial AFA had no effect in concentrations relevant for defoaming purposes. Industrial AFA were further tested in laboratory scale simulations of the Brazilian ethanol production process and proved to decrease cell viability compared to the control, and the effects were intensified with increasing AFA concentrations and exposure time. Transcriptome analysis showed that AFA treatments induced additional stress responses in yeast cells compared to the control, shown by an up-regulation of stress-specific genes and a down-regulation of lipid biosynthesis, especially ergosterol. By documenting the detrimental effects associated with chemical AFA, we highlight the importance of developing innocuous systems for foam control in industrial fermentation processes.
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Affiliation(s)
- Jens Christian Nielsen
- Novozymes Latin America Ltda, 83707-660, Araucária, Brazil
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK2800, Kgs. Lyngby, Denmark
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96, Gothenburg, Sweden
| | | | | | - Jette Thykær
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK2800, Kgs. Lyngby, Denmark
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK2800, Kgs. Lyngby, Denmark.
| | - Thiago Olitta Basso
- Novozymes Latin America Ltda, 83707-660, Araucária, Brazil.
- Department of Chemical Engineering, Polytechnic School, University of São Paulo, 05508-010, São Paulo, Brazil.
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Burgard J, Valli M, Graf AB, Gasser B, Mattanovich D. Biomarkers allow detection of nutrient limitations and respective supplementation for elimination in Pichia pastoris fed-batch cultures. Microb Cell Fact 2017; 16:117. [PMID: 28693509 PMCID: PMC5504661 DOI: 10.1186/s12934-017-0730-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/28/2017] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Industrial processes for recombinant protein production challenge production hosts, such as the yeast Pichia pastoris, on multiple levels. During a common P. pastoris fed-batch process, cells experience strong adaptations to different metabolic states or suffer from environmental stresses due to high cell density cultivation. Additionally, recombinant protein production and nutrient limitations are challenging in these processes. RESULTS Pichia pastoris producing porcine carboxypeptidase B (CpB) was cultivated in glucose or methanol-limited fed-batch mode, and the cellular response was analyzed using microarrays. Thereby, strong transcriptional regulations in transport-, regulatory- and metabolic processes connected to sulfur, phosphorus and nitrogen metabolism became obvious. The induction of these genes was observed in both glucose- and methanol- limited fed batch cultivations, but were stronger in the latter condition. As the transcriptional pattern was indicative for nutrient limitations, we performed fed-batch cultivations where we added the respective nutrients and compared them to non-supplemented cultures regarding cell growth, productivity and expression levels of selected biomarker genes. In the non-supplemented reference cultures we observed a strong increase in transcript levels of up to 89-fold for phosphorus limitation marker genes in the late fed-batch phase. Transcript levels of sulfur limitation marker genes were up to 35-fold increased. By addition of (NH4)2SO4 or (NH4)2HPO4, respectively, we were able to suppress the transcriptional response of the marker genes to levels initially observed at the start of the fed batch. Additionally, supplementation had also a positive impact on biomass generation and recombinant protein production. Supplementation with (NH4)2SO4 led to 5% increase in biomass and 52% higher CpB activity in the supernatant, compared to the non-supplemented reference cultivations. In (NH4)2HPO4 supplemented cultures 9% higher biomass concentrations and 60% more CpB activity were reached. CONCLUSIONS Transcriptional analysis of P. pastoris fed-batch cultivations led to the identification of nutrient limitations in the later phases, and respective biomarker genes for indication of limitations. Supplementation of the cultivation media with those nutrients eliminated the limitations on the transcriptional level, and was also shown to enhance productivity of a recombinant protein. The biomarker genes are versatily applicable to media and process optimization approaches, where tailor-made solutions are envisioned.
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Affiliation(s)
- Jonas Burgard
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Minoska Valli
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B. Graf
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- School of Bioengineering, University of Applied Sciences FH Campus Vienna, Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Ito-Harashima S, Mizutani Y, Nishimura M, Kim HJ, Kim YJ, Kim HS, Bae JH, Koedrith P, Kawanishi M, Seo YR, Yagi T. A pilot study for construction of a new cadmium-sensing yeast strain carrying a reporter plasmid with the JLP1 promoter. J Toxicol Sci 2017; 42:103-109. [DOI: 10.2131/jts.42.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
| | - Yui Mizutani
- Department of Biology, Graduate School of Science, Osaka Prefecture University
| | - Motoshi Nishimura
- Department of Biology, Graduate School of Science, Osaka Prefecture University
| | - Hyo Jeong Kim
- Department of Life Science, Dongguk University, South Korea
| | - Yeo Jin Kim
- Department of Life Science, Dongguk University, South Korea
| | - Hyun Soo Kim
- Department of Life Science, Dongguk University, South Korea
| | - Ji Hye Bae
- Department of Life Science, Dongguk University, South Korea
| | - Preeyaporn Koedrith
- Department of Life Science, Dongguk University, South Korea
- Present address: Faculty of Environment and Resource Studies, Mahidol University, Thailand
| | - Masanobu Kawanishi
- Department of Biology, Graduate School of Science, Osaka Prefecture University
| | - Young Rok Seo
- Department of Life Science, Dongguk University, South Korea
| | - Takashi Yagi
- Department of Biology, Graduate School of Science, Osaka Prefecture University
- Department of Life Science, Dongguk University, South Korea
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New insights into sulfur metabolism in yeasts as revealed by studies of Yarrowia lipolytica. Appl Environ Microbiol 2012; 79:1200-11. [PMID: 23220962 DOI: 10.1128/aem.03259-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yarrowia lipolytica, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution.
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Hébert A, Forquin-Gomez MP, Roux A, Aubert J, Junot C, Loux V, Heilier JF, Bonnarme P, Beckerich JM, Landaud S. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Appl Microbiol Biotechnol 2011; 91:1409-23. [DOI: 10.1007/s00253-011-3481-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/29/2011] [Accepted: 07/13/2011] [Indexed: 10/17/2022]
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Lee TA, Jorgensen P, Bognar AL, Peyraud C, Thomas D, Tyers M. Dissection of combinatorial control by the Met4 transcriptional complex. Mol Biol Cell 2010; 21:456-69. [PMID: 19940020 PMCID: PMC2814790 DOI: 10.1091/mbc.e09-05-0420] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Met4 is the transcriptional activator of the sulfur metabolic network in Saccharomyces cerevisiae. Lacking DNA-binding ability, Met4 must interact with proteins called Met4 cofactors to target promoters for transcription. Two types of DNA-binding cofactors (Cbf1 and Met31/Met32) recruit Met4 to promoters and one cofactor (Met28) stabilizes the DNA-bound Met4 complexes. To dissect this combinatorial system, we systematically deleted each category of cofactor(s) and analyzed Met4-activated transcription on a genome-wide scale. We defined a core regulon for Met4, consisting of 45 target genes. Deletion of both Met31 and Met32 eliminated activation of the core regulon, whereas loss of Met28 or Cbf1 interfered with only a subset of targets that map to distinct sectors of the sulfur metabolic network. These transcriptional dependencies roughly correlated with the presence of Cbf1 promoter motifs. Quantitative analysis of in vivo promoter binding properties indicated varying levels of cooperativity and interdependency exists between members of this combinatorial system. Cbf1 was the only cofactor to remain fully bound to target promoters under all conditions, whereas other factors exhibited different degrees of regulated binding in a promoter-specific fashion. Taken together, Met4 cofactors use a variety of mechanisms to allow differential transcription of target genes in response to various cues.
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Affiliation(s)
- Traci A Lee
- Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, WI 53144, USA.
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Current Awareness. Yeast 2001. [DOI: 10.1002/yea.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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