1
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Stovicek V, Lengeler KB, Wendt T, Rasmussen M, Katz M, Förster J. Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast. N Biotechnol 2024; 82:92-106. [PMID: 38788897 DOI: 10.1016/j.nbt.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.
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Affiliation(s)
- Vratislav Stovicek
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Klaus B Lengeler
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; Traitomic A/S, J.C. Jacobsens Gade 1, DK-1799 Copenhagen V, Denmark
| | - Magnus Rasmussen
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Jochen Förster
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; DTU Biosustain, The Novo Nordisk Foundation Center for Biosustainability, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
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2
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Keyport Kik S, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Lin KM, Squires AH, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. Nat Commun 2024; 15:3127. [PMID: 38605014 PMCID: PMC11009240 DOI: 10.1038/s41467-024-47355-9] [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: 07/30/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Caitlin Wong Hickernell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | | | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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3
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Cai E, Zeng R, Feng R, Zhang L, Li L, Jia H, Zheng W, Chen S, Yan M, Chang C. Discovery of N-Benzyl-4-(1-bromonaphthalen-2-yl)oxybutan-1-amine as a Potential Antifungal Agent against Sporidia Growth and Teliospore Germination of Sporisorium scitamineum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3325-3333. [PMID: 38329286 DOI: 10.1021/acs.jafc.3c04589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The cultivation of sugar cane using perennial roots is the primary planting method, which is one of the reasons for the serious occurrence of sugar cane smut disease caused by the basidiomycetous fungus Sporisorium scitamineum in the sugar cane perennial root planting area. Consequently, it is crucial to eliminate pathogens from perennial sugar cane buds. In this study, we found that MAP kinase Hog1 is necessary for heat stress resistance. Subsequent investigations revealed a significant reduction in the expression of the heat shock protein 104-encoding gene, SsHSP104, in the ss1hog1Δ mutant. Additionally, the overexpression of SsHSP104 partially restored colony growth in the ss1hog1Δ strain following heat stress treatment, demonstrating the crucial role of SsHsp104 in SsHog1-mediated heat stress tolerance. Hence, we constructed the ss1hsp104:eGFP fusion strain in the wild type of S. scitamineum to identify small-molecule compounds that could inhibit the heat stress response, leading to the discovery of N-benzyl-4-(1-bromonaphthalen-2-yl)oxybutan-1-amine as a potential compound that targets the SsHog1 mediation SsHsp104 pathway during heat treatment. Furthermore, the combination of N-benzyl-4-(1-bromonaphthalen-2-yl)oxybutan-1-amine and warm water treatment (45 °C for 15 min) inhibits the growth of S. scitamineum and teliospore germination, thereby reducing the occurrence of sugar cane smut diseases and indicating its potential for eliminating pathogens from perennial sugar cane buds. In conclusion, these findings suggest that N-benzyl-4-(1-bromonaphthalen-2-yl)oxybutan-1-amine is promising as a targeted compound for the SsHog1-mediated SsHsp104 pathway and may enable the reduction of hot water treatment duration and/or temperature, thereby limiting the occurrence of sugar cane smut diseases caused by S. scitamineum.
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Affiliation(s)
- Enping Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Rong Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ruqing Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Li Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Lei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Huan Jia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Wenqiang Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Shaofang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Meixin Yan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Changqing Chang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Signals and Disease Control, Integrate Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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4
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Fay JC, Alonso-del-Real J, Miller JH, Querol A. Divergence in the Saccharomyces Species' Heat Shock Response Is Indicative of Their Thermal Tolerance. Genome Biol Evol 2023; 15:evad207. [PMID: 37972247 PMCID: PMC10683043 DOI: 10.1093/gbe/evad207] [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: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
The Saccharomyces species have diverged in their thermal growth profile. Both Saccharomyces cerevisiae and Saccharomyces paradoxus grow at temperatures well above the maximum growth temperature of Saccharomyces kudriavzevii and Saccharomyces uvarum but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature, we measured changes in gene expression in response to a 12 °C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families, we sequenced, assembled, and annotated a complete S. uvarum genome. In response to heat, the cryophilic species showed a stronger stress response than the thermophilic species, and the hybrids showed a mixture of parental responses that depended on the time point. After an initial strong response indicative of high thermal stress, hybrids with a thermophilic parent resolved their heat shock response to become similar to their thermophilic parent. Within the hybrids, only a small number of temperature-responsive genes showed consistent differences between alleles from the thermophilic and cryophilic species. Our results show that divergence in the heat shock response is mainly a consequence of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat-induced changes are relevant to thermal divergence in the Saccharomyces species.
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Affiliation(s)
- Justin C Fay
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Javier Alonso-del-Real
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - James H Miller
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Amparo Querol
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
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5
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Kik SK, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551061. [PMID: 37546789 PMCID: PMC10402146 DOI: 10.1101/2023.07.28.551061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | | | - Jared A. M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | | | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL
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6
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Fay JC, Alonso-Del-Real J, Miller JH, Querol A. Divergence in the Saccharomyces species' heat shock response is indicative of their thermal tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547718. [PMID: 37461527 PMCID: PMC10349932 DOI: 10.1101/2023.07.04.547718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The Saccharomyces species have diverged in their thermal growth profile. Both S. cerevisiae and S. paradoxus grow at temperatures well above the maximum growth temperature of S. kudriavzevii and S. uvarum, but grow more poorly at lower temperatures. In response to thermal shifts, organisms activate a stress response that includes heat shock proteins involved in protein homeostasis and acquisition of thermal tolerance. To determine whether Saccharomyces species have diverged in their response to temperature we measured changes in gene expression in response to a 12°C increase or decrease in temperature for four Saccharomyces species and their six pairwise hybrids. To ensure coverage of subtelomeric gene families we sequenced, assembled and annotated a complete S. uvarum genome. All the strains exhibited a stronger response to heat than cold treatment. In response to heat, the cryophilic species showed a stronger response than the thermophilic species. The hybrids showed a mixture of parental stress responses depending on the time point. After the initial response, hybrids with a thermophilic parent were more similar to S. cerevisiae and S. paradoxus, and the S. cerevisiae × S. paradoxus hybrid showed the weakest heat shock response. Within the hybrids a small subset of temperature responsive genes showed species specific responses but most were also hybrid specific. Our results show that divergence in the heat shock response is indicative of a strain's thermal tolerance, suggesting that cellular factors that signal heat stress or resolve heat induced changes are relevant to thermal divergence in the Saccharomyces species.
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Affiliation(s)
- Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Javier Alonso-Del-Real
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Valencia, Spain
- Present position: Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - James H Miller
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Amparo Querol
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Valencia, Spain
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7
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Physiological comparisons among Spathaspora passalidarum, Spathaspora arborariae, and Scheffersomyces stipitis reveal the bottlenecks for their use in the production of second-generation ethanol. Braz J Microbiol 2022; 53:977-990. [PMID: 35174461 PMCID: PMC9151973 DOI: 10.1007/s42770-022-00693-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/21/2021] [Indexed: 02/01/2023] Open
Abstract
The microbial conversion of pentoses to ethanol is one of the major drawbacks that limits the complete use of lignocellulosic sugars. In this study, we compared the yeast species Spathaspora arborariae, Spathaspora passalidarum, and Sheffersomyces stipitis regarding their potential use for xylose fermentation. Herein, we evaluated the effects of xylose concentration, presence of glucose, and temperature on ethanol production. The inhibitory effects of furfural, hydroxymethylfurfural (HMF), acetic acid, and ethanol were also determined. The highest ethanol yield (0.44 g/g) and productivity (1.02 g/L.h) were obtained using Sp. passalidarum grown in 100 g/L xylose at 32 °C. The rate of xylose consumption was reduced in the presence of glucose for the species tested. Hydroxymethylfurfural did not inhibit the growth of yeasts, whereas furfural extended their lag phase. Acetic acid inhibited the growth and fermentation of all yeasts. Furthermore, we showed that these xylose-fermenting yeasts do not produce ethanol concentrations greater than 4% (v/v), probably due to the inhibitory effects of ethanol on yeast physiology. Our data confirm that among the studied yeasts, Sp. passalidarum is the most promising for xylose fermentation, and the low tolerance to ethanol is an important aspect to be improved to increase its performance for second-generation (2G) ethanol production. Our molecular data showed that this yeast failed to induce the expression of some classical genes involved in ethanol tolerance. These findings suggest that Sp. passalidarum may have not activated a proper response to the stress, impacting its ability to overcome the negative effects of ethanol on the cells.
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8
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Xia H, Chen L, Fan Z, Peng M, Zhao J, Chen W, Li H, Shi Y, Ding S, Li H. Heat Stress Tolerance Gene FpHsp104 Affects Conidiation and Pathogenicity of Fusarium pseudograminearum. Front Microbiol 2021; 12:695535. [PMID: 34394037 PMCID: PMC8355993 DOI: 10.3389/fmicb.2021.695535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Heat shock protein Hsp104, a homolog of the bacterial chaperone ClpB and plant Hsp100, plays an essential part in the response to heat and various chemical agents in Saccharomyces cerevisiae. However, their functions remain largely unknown in plant fungal pathogens. Here, we report the identification and functional characterization of a plausible ortholog of yeast Hsp104 in Fusarium pseudograminearum, which we termed FpHsp104. Deletion mutant of FpHsp104 displayed severe defects in the resistance of heat shock during F. pseudograminearum mycelia and conidia when exposed to extreme heat. We also found that the protein showed dynamic localization to small particles under high temperature. However, no significant differences were detected in osmotic, oxidative, or cell wall stress responses between the wild-type and Δfphsp104 strains. Quantitative real-time PCR analysis showed that FpHsp104 was upregulated in the conidia, and disruption of FpHsp104 gene resulted in defects in conidia production, morphology, and germination. The transcript levels of conidiation-related genes of FpFluG, FpVosA, FpWetA, and FpAbaA were reduced in the Δfphsp104 mutant vs. the wild-type strain, but heat-shocked mRNA splicing repair was not affected in Δfphsp104. Moreover, Δfphsp104 mutant also showed attenuated virulence, but its DON synthesis was normal. These data from the first study of Hsp104 in F. pseudograminearum strongly suggest that FpHsp104 gene is an important element in the heat tolerance, development, and pathogenicity processes of F. pseudograminearum.
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Affiliation(s)
- Huiqing Xia
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Linlin Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.,National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Zhuo Fan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Mengya Peng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Jingya Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Wenbo Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Haiyang Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shengli Ding
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.,National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.,National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, China
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9
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Reprogramming of the Ethanol Stress Response in Saccharomyces cerevisiae by the Transcription Factor Znf1 and Its Effect on the Biosynthesis of Glycerol and Ethanol. Appl Environ Microbiol 2021; 87:e0058821. [PMID: 34105981 PMCID: PMC8315178 DOI: 10.1128/aem.00588-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
High ethanol levels can severely inhibit the growth of yeast cells and fermentation productivity. The ethanologenic yeast Saccharomyces cerevisiae activates several well-defined cellular mechanisms of ethanol stress response (ESR); however, the involved regulatory control remains to be characterized. Here, we report a new transcription factor of ethanol stress adaptation called Znf1. It plays a central role in ESR by activating genes for glycerol and fatty acid production (GUP1, GPP1, GPP2, GPD1, GAT1, and OLE1) to preserve plasma membrane integrity. Importantly, Znf1 also activates genes implicated in cell wall biosynthesis (FKS1, SED1, and SMI1) and in the unfolded protein response (HSP30, HSP104, KAR1, and LHS1) to protect cells from proteotoxic stress. The znf1Δ strain displays increased sensitivity to ethanol, the endoplasmic reticulum (ER) stressor β-mercaptoethanol, and the cell wall-perturbing agent calcofluor white. To compensate for a defective cell wall, the strain lacking ZNF1 or its target SMI1 displays increased glycerol levels of 19.6% and 27.7%, respectively. Znf1 collectively regulates an intricate network of target genes essential for growth, protein refolding, and production of key metabolites. Overexpression of ZNF1 not only confers tolerance to high ethanol levels but also increases ethanol production by 4.6% (8.43 g/liter) or 2.8% (75.78 g/liter) when 2% or 20% (wt/vol) glucose, respectively, is used as a substrate, compared to that of the wild-type strain. The mutually stress-responsive transcription factors Msn2/4, Hsf1, and Yap1 are associated with some promoters of Znf1’s target genes to promote ethanol stress tolerance. In conclusion, this work implicates the novel regulator Znf1 in coordinating expression of ESR genes and illuminates the unifying transcriptional reprogramming during alcoholic fermentation. IMPORTANCE The yeast S. cerevisiae is a major microbe that is widely used in food and nonfood industries. However, accumulation of ethanol has a negative effect on its growth and limits ethanol production. The Znf1 transcription factor has been implicated as a key regulator of glycolysis and gluconeogenesis in the utilization of different carbon sources, including glucose, the most abundant sugar on earth, and nonfermentable substrates. Here, the role of Znf1 in ethanol stress response is defined. Znf1 actively reprograms expression of genes linked to the unfolded protein response (UPR), heat shock response, glycerol and carbohydrate metabolism, and biosynthesis of cell membrane and cell wall components. A complex interplay among transcription factors of ESR indicates transcriptional fine-tuning as the main mechanism of stress adaptation, and Znf1 plays a major regulatory role in the coordination. Understanding the adaptive ethanol stress mechanism is crucial to engineering robust yeast strains for enhanced stress tolerance or increased ethanol production.
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10
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Nakazawa N, Fukuda M, Ashizaki M, Shibata Y, Takahashi K. Hsp104 contributes to freeze-thaw tolerance by maintaining proteasomal activity in a spore clone isolated from Shirakami kodama yeast. J GEN APPL MICROBIOL 2021; 67:170-178. [PMID: 34148914 DOI: 10.2323/jgam.2020.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The supply of oven-fresh bakery products to consumers has been improved by frozen dough technology; however, freeze-thaw stress decreases the activity of yeast cells. To breed better baker's yeasts for frozen dough, it is important to understand the factors affecting freeze-thaw stress tolerance in baker's yeast. We analyzed the stress response in IB1411, a spore clone from Saccharomyces cerevisiae Shirakami kodama yeast, with an exceptionally high tolerance to freeze-thaw stress. Genes encoding trehalose-6-phosphate synthase (TPS1), catalase (CTT1), and disaggregase (HSP104) were highly expressed in IB1411 cells even under conditions of non-stress. The expression of Hsp104 protein was also higher in IB1411 cells even under non-stress conditions. Deletion of HSP104 (hsp104Δ) in IB1411 cells reduced the activity of the ubiquitin-proteasome system (UPS). By monitoring the accumulation of aggregated proteins using the ΔssCPY*-GFP fusion protein under freeze-thaw stress or treatment with proteasomal inhibitor, we found that IB1411 cells resolved aggregated proteins faster than the hsp104Δ strain. Thus, Hsp104 seems to contribute to freeze-thaw tolerance by maintaining UPS activity via the disaggregation of aggregated proteins. Lastly, we found that the IB1411 cells maintained high leavening ability in frozen dough as compared with the parental strain, Shirakami kodama yeast, and thus will be useful for making bread.
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Affiliation(s)
- Nobushige Nakazawa
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Mami Fukuda
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Mizuki Ashizaki
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Yukari Shibata
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
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11
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Integrated transcriptomic and proteomic analysis of the ethanol stress response in Saccharomyces cerevisiae Sc131. J Proteomics 2019; 203:103377. [DOI: 10.1016/j.jprot.2019.103377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/12/2019] [Accepted: 05/12/2019] [Indexed: 12/29/2022]
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12
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Junker K, Chailyan A, Hesselbart A, Forster J, Wendland J. Multi-omics characterization of the necrotrophic mycoparasite Saccharomycopsis schoenii. PLoS Pathog 2019; 15:e1007692. [PMID: 31071195 PMCID: PMC6508603 DOI: 10.1371/journal.ppat.1007692] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/10/2019] [Indexed: 12/14/2022] Open
Abstract
Pathogenic yeasts and fungi are an increasing global healthcare burden, but discovery of novel antifungal agents is slow. The mycoparasitic yeast Saccharomycopsis schoenii was recently demonstrated to be able to kill the emerging multi-drug resistant yeast pathogen Candida auris. However, the molecular mechanisms involved in the predatory activity of S. schoenii have not been explored. To this end, we de novo sequenced, assembled and annotated a draft genome of S. schoenii. Using proteomics, we confirmed that Saccharomycopsis yeasts have reassigned the CTG codon and translate CTG into serine instead of leucine. Further, we confirmed an absence of all genes from the sulfate assimilation pathway in the genome of S. schoenii, and detected the expansion of several gene families, including aspartic proteases. Using Saccharomyces cerevisiae as a model prey cell, we honed in on the timing and nutritional conditions under which S. schoenii kills prey cells. We found that a general nutrition limitation, not a specific methionine deficiency, triggered predatory activity. Nevertheless, by means of genome-wide transcriptome analysis we observed dramatic responses to methionine deprivation, which were alleviated when S. cerevisiae was available as prey, and therefore postulate that S. schoenii acquired methionine from its prey cells. During predation, both proteomic and transcriptomic analyses revealed that S. schoenii highly upregulated and translated aspartic protease genes, probably used to break down prey cell walls. With these fundamental insights into the predatory behavior of S. schoenii, we open up for further exploitation of this yeast as a biocontrol yeast and/or source for novel antifungal agents.
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Affiliation(s)
- Klara Junker
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Anna Chailyan
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Ana Hesselbart
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Jochen Forster
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Jürgen Wendland
- Yeast & Fermentation, Carlsberg Research Laboratory, Copenhagen, Denmark
- Functional Yeast Genomics, Vrije Universiteit Brussel, Brussels, Belgium
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13
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Babele PK, Thakre PK, Kumawat R, Tomar RS. Zinc oxide nanoparticles induce toxicity by affecting cell wall integrity pathway, mitochondrial function and lipid homeostasis in Saccharomyces cerevisiae. CHEMOSPHERE 2018; 213:65-75. [PMID: 30212720 DOI: 10.1016/j.chemosphere.2018.09.028] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/29/2018] [Accepted: 09/04/2018] [Indexed: 05/27/2023]
Abstract
Growing numbers of nanotoxicity research demonstrating that mechanical damage and oxidative stress are potential modes of nanoparticles (NPs) induced toxicity. However, the underlying mechanisms by which NPs interact with the eukaryotic cell and affect their physiological and metabolic functions are not fully known. We investigated the toxic effects of zinc oxide nanoparticles (ZnO-NPs) on budding yeast, Saccharomyces cerevisiae and elucidated the underlying mechanism. We observed cell wall damage and accumulation of reactive oxygen species (ROS) leading to cell death upon ZnO-NPs exposure. We detected a significant change in the cellular distribution of lipid biosynthetic enzymes (Fas1 and Fas2). Furthermore, exposure of ZnO-NPs altered the architecture of endoplasmic reticulum (ER) and mitochondria as well as ER-mitochondria encounter structure (ERMES) complex causing cellular toxicity due to lipid disequilibrium and proteostasis. We also observed significant changes in heat shock and unfolded protein responses, monitored by Hsp104-GFP localization and cytosolic Hac1 splicing respectively. Moreover, we observed activation of MAP kinases of CWI (Mpk1) and HOG (Hog1) pathways upon exposure to ZnO-NPs. Transcript level analyses showed induction of chitin synthesis and redox homeostasis genes. Finally, we observed induction in lipid droplets (LDs) formation, distorted vacuolar morphology and induction of autophagy as monitored by localization of Atg8p. However, we did not observe any significant change in epigenetic marks, examined by western blotting. Altogether, we provide evidence that exposure of ZnO-NPs results in cell death by affecting cell wall integrity and ER homeostasis as well as accumulation of ROS and saturated free fatty acids.
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Affiliation(s)
- Piyoosh Kumar Babele
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Pilendra Kumar Thakre
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Ramesh Kumawat
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India.
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14
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Higgins R, Kabbaj MH, Hatcher A, Wang Y. The absence of specific yeast heat-shock proteins leads to abnormal aggregation and compromised autophagic clearance of mutant Huntingtin proteins. PLoS One 2018; 13:e0191490. [PMID: 29346421 PMCID: PMC5773196 DOI: 10.1371/journal.pone.0191490] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/05/2018] [Indexed: 11/25/2022] Open
Abstract
The functionality of a protein depends on its correct folding, but newly synthesized proteins are susceptible to aberrant folding and aggregation. Heat shock proteins (HSPs) function as molecular chaperones that aid in protein folding and the degradation of misfolded proteins. Trinucleotide (CAG) repeat expansion in the Huntingtin gene (HTT) results in the expression of misfolded Huntingtin protein (Htt), which contributes to the development of Huntington’s disease. We previously found that the degradation of mutated Htt with polyQ expansion (Htt103QP) depends on both ubiquitin proteasome system and autophagy. However, the role of heat shock proteins in the clearance of mutated Htt remains poorly understood. Here, we report that cytosolic Hsp70 (Ssa family), its nucleotide exchange factors (Sse1 and Fes1), and a Hsp40 co-chaperone (Ydj1) are required for inclusion body formation of Htt103QP proteins and their clearance via autophagy. Extended induction of Htt103QP-GFP leads to the formation of a single inclusion body in wild-type yeast cells, but mutant cells lacking these HSPs exhibit increased number of Htt103QP aggregates. Most notably, we detected more aggregated forms of Htt103QP in sse1Δ mutant cells using an agarose gel assay. Increased protein aggregates are also observed in these HSP mutants even in the absence Htt103QP overexpression. Importantly, these HSPs are required for autophagy-mediated Htt103QP clearance, but are less critical for proteasome-dependent degradation. These findings suggest a chaperone network that facilitates inclusion body formation of misfolded proteins and the subsequent autophagic clearance.
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Affiliation(s)
- Ryan Higgins
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Marie-Helene Kabbaj
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Alexa Hatcher
- College of Nursing, Florida State University, Tallahassee, Florida, United States of America
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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15
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Li R, Xiong G, Yuan S, Wu Z, Miao Y, Weng P. Investigating the underlying mechanism of Saccharomyces cerevisiae in response to ethanol stress employing RNA-seq analysis. World J Microbiol Biotechnol 2017; 33:206. [PMID: 29101531 DOI: 10.1007/s11274-017-2376-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/29/2017] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae has been widely used for wine fermentation and bio-fuels production. A S. cerevisiae strain Sc131 isolated from tropical fruit shows good fermentation properties and ethanol tolerance, exhibiting significant potential in Chinese bayberry wine fermentation. In this study, RNA-sequence and RT-qPCR was used to investigate the transcriptome profile of Sc131 in response to ethanol stress. Scanning Electron Microscopy were carried out to observe surface morphology of yeast cells. Totally, 937 genes were identified differential expressed, including 587 up-regulated and 350 down-regulated genes, after 4-h ethanol stress (10% v/v). Transcriptomic analysis revealed that, most genes involved in regulating filamentous growth or pseudohyphal growth were significantly up-regulated in response to ethanol stress. The complex protein quality control machineries, Hsp90/Hsp70 and Hsp104/Hsp70/Hsp40 based chaperone system combining with ubiquitin-proteasome proteolytic pathway were both activated to recognize and degrade misfolding proteins. Genes related to biosynthesis and metabolism of two well-known stress-responsive substances trehalose and ergosterol were generally up-regulated, while genes associated with amino acids biosynthesis and metabolism processes were differentially expressed. Moreover, thiamine was also important in response to ethanol stress. This research may promote the potential applications of Sc131 in the fermentation of Chinese bayberry wine.
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Affiliation(s)
- Ruoyun Li
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Guotong Xiong
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Shukun Yuan
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Zufang Wu
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
| | - Yingjie Miao
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Peifang Weng
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
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