1
|
Drężek K, Antunovics Z, Grabiec AK. Novel Saccharomyces uvarum x Saccharomyces kudriavzevii synthetic hybrid with enhanced 2-phenylethanol production. Microb Cell Fact 2024; 23:203. [PMID: 39030609 PMCID: PMC11265027 DOI: 10.1186/s12934-024-02473-3] [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: 02/29/2024] [Accepted: 07/07/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Over the last two decades, hybridization has been a powerful tool used to construct superior yeast for brewing and winemaking. Novel hybrids were primarily constructed using at least one Saccharomyces cerevisiae parent. However, little is known about hybrids used for other purposes, such as targeted flavor production, for example, 2-phenylethanol (2-PE). 2-PE, an aromatic compound widely utilised in the food, cosmetic, and pharmaceutical industries, presents challenges in biotechnological production due to its toxic nature. Consequently, to enhance productivity and tolerance to 2-PE, various strategies such as mutagenesis and genetic engineering are extensively explored to improved yeast strains. While biotechnological efforts have predominantly focused on S. cerevisiae for 2-PE production, other Saccharomyces species and their hybrids remain insufficiently described. RESULTS To address this gap, in this study, we analysed a new interspecies yeast hybrid, II/6, derived from S. uvarum and S. kudriavzevii parents, in terms of 2-PE bioconversion and resistance to its high concentration, comparing it with the parental strains. Two known media for 2-PE biotransformation and three different temperatures were used during this study to determine optimal conditions. In 72 h batch cultures, the II/6 hybrid achieved a maximum of 2.36 ± 0.03 g/L 2-PE, which was 2-20 times higher than the productivity of the parental strains. Our interest lay not only in determining whether the hybrid improved in productivity but also in assessing whether its susceptibility to high 2-PE titers was also mitigated. The results showed that the hybrid exhibited significantly greater resistance to the toxic product than the original strains. CONCLUSIONS The conducted experiments have confirmed that hybridization is a promising method for modifying yeast strains. As a result, both 2-PE production yield and tolerance to its inhibitory effects can be increased. Furthermore, this strategy allows for the acquisition of non-GMO strains, alleviating concerns related to additional legislative requirements or consumer acceptance issues for producers. The findings obtained have the potential to contribute to the development of practical solutions in the future.
Collapse
Affiliation(s)
- Karolina Drężek
- Department of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland.
| | - Zsuzsa Antunovics
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Agnieszka Karolina Grabiec
- Department of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| |
Collapse
|
2
|
Jacobus AP, Cavassana SD, de Oliveira II, Barreto JA, Rohwedder E, Frazzon J, Basso TP, Basso LC, Gross J. Optimal trade-off between boosted tolerance and growth fitness during adaptive evolution of yeast to ethanol shocks. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:63. [PMID: 38730312 PMCID: PMC11088041 DOI: 10.1186/s13068-024-02503-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND The selection of Saccharomyces cerevisiae strains with higher alcohol tolerance can potentially increase the industrial production of ethanol fuel. However, the design of selection protocols to obtain bioethanol yeasts with higher alcohol tolerance poses the challenge of improving industrial strains that are already robust to high ethanol levels. Furthermore, yeasts subjected to mutagenesis and selection, or laboratory evolution, often present adaptation trade-offs wherein higher stress tolerance is attained at the expense of growth and fermentation performance. Although these undesirable side effects are often associated with acute selection regimes, the utility of using harsh ethanol treatments to obtain robust ethanologenic yeasts still has not been fully investigated. RESULTS We conducted an adaptive laboratory evolution by challenging four populations (P1-P4) of the Brazilian bioethanol yeast, Saccharomyces cerevisiae PE-2_H4, through 68-82 cycles of 2-h ethanol shocks (19-30% v/v) and outgrowths. Colonies isolated from the final evolved populations (P1c-P4c) were subjected to whole-genome sequencing, revealing mutations in genes enriched for the cAMP/PKA and trehalose degradation pathways. Fitness analyses of the isolated clones P1c-P3c and reverse-engineered strains demonstrated that mutations were primarily selected for cell viability under ethanol stress, at the cost of decreased growth rates in cultures with or without ethanol. Under this selection regime for stress survival, the population P4 evolved a protective snowflake phenotype resulting from BUD3 disruption. Despite marked adaptation trade-offs, the combination of reverse-engineered mutations cyr1A1474T/usv1Δ conferred 5.46% higher fitness than the parental PE-2_H4 for propagation in 8% (v/v) ethanol, with only a 1.07% fitness cost in a culture medium without alcohol. The cyr1A1474T/usv1Δ strain and evolved P1c displayed robust fermentations of sugarcane molasses using cell recycling and sulfuric acid treatments, mimicking Brazilian bioethanol production. CONCLUSIONS Our study combined genomic, mutational, and fitness analyses to understand the genetic underpinnings of yeast evolution to ethanol shocks. Although fitness analyses revealed that most evolved mutations impose a cost for cell propagation, combination of key mutations cyr1A1474T/usv1Δ endowed yeasts with higher tolerance for growth in the presence of ethanol. Moreover, alleles selected for acute stress survival comprising the P1c genotype conferred stress tolerance and optimal performance under conditions simulating the Brazilian industrial ethanol production.
Collapse
Affiliation(s)
- Ana Paula Jacobus
- Bioenergy Research Institute, São Paulo State University, Rio Claro, Brazil
- SENAI Innovation Institute for Biotechnology, São Paulo, Brazil
| | | | | | | | - Ewerton Rohwedder
- Biological Science Department, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Jeverson Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Thalita Peixoto Basso
- Department of Agri-Food Industry, Food and Nutrition, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Luiz Carlos Basso
- Biological Science Department, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Jeferson Gross
- Bioenergy Research Institute, São Paulo State University, Rio Claro, Brazil.
| |
Collapse
|
3
|
Chen X, Song C, Zhao J, Xiong Z, Peng L, Zou L, Shen C, Li Q. Application of Strain Selection Technology in Alcoholic Beverages: A Review. Foods 2024; 13:1396. [PMID: 38731767 PMCID: PMC11083718 DOI: 10.3390/foods13091396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The diversity of alcohol beverage microorganisms is of great significance for improving the brewing process and the quality of alcohol beverage products. During the process of making alcoholic beverages, a group of microorganisms, represented by yeast and lactic acid bacteria, conducts fermentation. These microorganisms have complex synergistic or competitive relationships, and the participation of different microorganisms has a major impact on the fermentation process and the flavor and aroma of the product. Strain selection is one of the key steps. Utilizing scientific breeding technology, the relationship between strains can be managed, the composition of the alcoholic beverage microbial community can be improved, and the quality and flavor of the alcoholic beverage products can be increased. Currently, research on the microbial diversity of alcohol beverages has received extensive attention. However, the selection technology for dominant bacteria in alcohol beverages has not yet been systematically summarized. To breed better-quality alcohol beverage strains and improve the quality and characteristics of wine, this paper introduces the microbial diversity characteristics of the world's three major brewing alcohols: beer, wine, and yellow wine, as well as the breeding technologies of related strains. The application of culture selection technology in the study of microbial diversity of brewed wine was reviewed and analyzed. The strain selection technology and alcohol beverage process should be combined to explore the potential application of a diverse array of alcohol beverage strains, thereby boosting the quality and flavor of the alcohol beverage and driving the sustainable development of the alcoholic beverage industry.
Collapse
Affiliation(s)
- Xiaodie Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Chuan Song
- Luzhou Laojiao Co., Ltd., Luzhou 646000, China;
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, China
- Postdoctoral Research Station of Luzhou Laojiao Company, Luzhou 646000, China
| | - Jian Zhao
- School of Life Sciences, Sichuan University, Chengdu 610041, China;
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Caihong Shen
- Luzhou Laojiao Co., Ltd., Luzhou 646000, China;
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, China
- Postdoctoral Research Station of Luzhou Laojiao Company, Luzhou 646000, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
- Postdoctoral Research Station of Luzhou Laojiao Company, Luzhou 646000, China
| |
Collapse
|
4
|
Gao S, Liao Y, He H, Yang H, Yang X, Xu S, Wang X, Chen K, Ouyang P. Advance of tolerance engineering on microbes for industrial production. Synth Syst Biotechnol 2023; 8:697-707. [PMID: 38025766 PMCID: PMC10656194 DOI: 10.1016/j.synbio.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Industrial microbes have become the core of biological manufacturing, which utilized as the cell factory for production of plenty of chemicals, fuels and medicine. However, the challenge that the extreme stress conditions exist in production is unavoidable for cell factory. Consequently, to enhance robustness of the chassis cell lays the foundation for development of bio-manufacturing. Currently, the researches on cell tolerance covered various aspects, involving reshaping regulatory network, cell membrane modification and other stress response. In fact, the strategies employed to improve cell robustness could be summarized into two directions, irrational engineering and rational engineering. In this review, the metabolic engineering technologies on enhancement of microbe tolerance to industrial conditions are summarized. Meanwhile, the novel thoughts emerged with the development of biological instruments and synthetic biology are discussed.
Collapse
Affiliation(s)
- Siyuan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Yang Liao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Hao He
- Petrochemical Research Institute of PetroChina Co. Ltd., Beijing, 102206, China
| | - Huiling Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xuewei Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| |
Collapse
|
5
|
Gong C, Cao L, Fang D, Zhang J, Kumar Awasthi M, Xue D. Genetic manipulation strategies for ethanol production from bioconversion of lignocellulose waste. BIORESOURCE TECHNOLOGY 2022; 352:127105. [PMID: 35378286 DOI: 10.1016/j.biortech.2022.127105] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulose waste was served as promising raw material for bioethanol production. Bioethanol was considered to be a potential alternative energy to take the place of fossil fuels. Lignocellulosic biomass synthesized by plants is regenerative, sufficient and cheap source for bioethanol production. The biotransformation of lignocellulose could exhibit dual significance-reduction of pollution and obtaining of energy. Some strategies are being developing and increasing the utilization of lignocellulose waste to produce ethanol. New technology of bioethanol production from natural lignocellulosic biomass is required. In this paper, the progress in genetic manipulation strategies including gene editing and synthetic genomics for the transformation from lignocellulose to ethanol was reviewed. At last, the application prospect of bioethanol was introduced.
Collapse
Affiliation(s)
- Chunjie Gong
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Liping Cao
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Donglai Fang
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Jiaqi Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dongsheng Xue
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan 430068, PR China.
| |
Collapse
|
6
|
How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses. Curr Genet 2022; 68:319-342. [PMID: 35362784 DOI: 10.1007/s00294-022-01237-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/01/2022] [Accepted: 03/06/2022] [Indexed: 12/25/2022]
Abstract
The yeast Saccharomyces cerevisiae is an excellent candidate for establishing cell factories to convert lignocellulosic biomass into chemicals and fuels. To enable this technology, yeast robustness must be improved to withstand the fermentation inhibitors (e.g., weak organic acids, phenols, and furan aldehydes) resulting from biomass pretreatment and hydrolysis. Here, we discuss how evolution experiments performed in the lab, a method commonly known as adaptive laboratory evolution (ALE), may contribute to lifting yeast tolerance against the inhibitors of lignocellulosic hydrolysates (LCHs). The key is that, through the combination of whole-genome sequencing and reverse engineering, ALE provides a robust platform for discovering and testing adaptive alleles, allowing to explore the genetic underpinnings of yeast responses to LCHs. We review the insights gained from past evolution experiments with S. cerevisiae in LCH inhibitors and propose experimental designs to optimise the discovery of genetic variants adaptive to biomass toxicity. The knowledge gathered through ALE projects is envisaged as a roadmap to engineer superior yeast strains for biomass-based bioprocesses.
Collapse
|
7
|
Chen S, Perez-Samper G, Herrera-Malaver B, Zhu L, Liu Y, Steensels J, Yang Q, Verstrepen KJ. Breeding of New Saccharomyces cerevisiae Hybrids with Reduced Higher Alcohol Production for Light-Aroma-Type- Xiaoqu Baijiu Production. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2033608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shenxi Chen
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Gemma Perez-Samper
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| | - Liping Zhu
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Yuancai Liu
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Jan Steensels
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| | - Qiang Yang
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Kevin J. Verstrepen
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| |
Collapse
|
8
|
Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits. Proc Natl Acad Sci U S A 2021; 118:2101242118. [PMID: 34518218 PMCID: PMC8463882 DOI: 10.1073/pnas.2101242118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
Hybrids between species can harbor a combination of beneficial traits from each parent and may exhibit hybrid vigor, more readily adapting to new harsher environments. Interspecies hybrids are also sterile and therefore an evolutionary dead end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than via further breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces interspecies hybrids to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids and for nuclear-mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified quantitative trait loci (QTLs) for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, in which the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type-dependent and -independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.
Collapse
|
9
|
Su B, Li A, Deng MR, Zhu H. Identification of a novel metabolic engineering target for carotenoid production in Saccharomyces cerevisiae via ethanol-induced adaptive laboratory evolution. BIORESOUR BIOPROCESS 2021; 8:47. [PMID: 38650275 PMCID: PMC10992865 DOI: 10.1186/s40643-021-00402-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Carotenoids are a large family of health-beneficial compounds that have been widely used in the food and nutraceutical industries. There have been extensive studies to engineer Saccharomyces cerevisiae for the production of carotenoids, which already gained high level. However, it was difficult to discover new targets that were relevant to the accumulation of carotenoids. Herein, a new, ethanol-induced adaptive laboratory evolution was applied to boost carotenoid accumulation in a carotenoid producer BL03-D-4, subsequently, an evolved strain M3 was obtained with a 5.1-fold increase in carotenoid yield. Through whole-genome resequencing and reverse engineering, loss-of-function mutation of phosphofructokinase 1 (PFK1) was revealed as the major cause of increased carotenoid yield. Transcriptome analysis was conducted to reveal the potential mechanisms for improved yield, and strengthening of gluconeogenesis and downregulation of cell wall-related genes were observed in M3. This study provided a classic case where the appropriate selective pressure could be employed to improve carotenoid yield using adaptive evolution and elucidated the causal mutation of evolved strain.
Collapse
Affiliation(s)
- Buli Su
- Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Anzhang Li
- Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ming-Rong Deng
- Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
| | - Honghui Zhu
- Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
| |
Collapse
|
10
|
Wang L, Li B, Wang SP, Xia ZY, Gou M, Tang YQ. Improving multiple stress-tolerance of a flocculating industrial Saccharomyces cerevisiae strain by random mutagenesis and hybridization. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
11
|
Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
Collapse
Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| |
Collapse
|
12
|
Abstract
Bioethanol is the largest biotechnology product and the most dominant biofuel globally. Saccharomyces cerevisiae is the most favored microorganism employed for its industrial production. However, obtaining maximum yields from an ethanol fermentation remains a technical challenge, since cellular stresses detrimentally impact on the efficiency of yeast cell growth and metabolism. Ethanol fermentation stresses potentially include osmotic, chaotropic, oxidative, and heat stress, as well as shifts in pH. Well-developed stress responses and tolerance mechanisms make S. cerevisiae industrious, with bioprocessing techniques also being deployed at industrial scale for the optimization of fermentation parameters and the effective management of inhibition issues. Overlap exists between yeast responses to different forms of stress. This review outlines yeast fermentation stresses and known mechanisms conferring stress tolerance, with their further elucidation and improvement possessing the potential to improve fermentation efficiency.
Collapse
|
13
|
Di Paola M, Meriggi N, Cavalieri D. Applications of Wild Isolates of Saccharomyces Yeast for Industrial Fermentation: The Gut of Social Insects as Niche for Yeast Hybrids' Production. Front Microbiol 2020; 11:578425. [PMID: 33193200 PMCID: PMC7661385 DOI: 10.3389/fmicb.2020.578425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 11/22/2022] Open
Abstract
In the industry of fermented food and beverages, yeast cultures are often selected and standardized in order to ensure a better control of fermentation and a more stable product over time. Several studies have shown that the organoleptic characteristics of fermented products reflect geographic variations of the microbial community composition. Despite investigations of the worldwide distribution and genetic diversity of Saccharomyces cerevisiae, it is still unclear how and to what extent human intervention has shaped the brewer’s yeast population structure. The genotypic and phenotypic characterization of environmental yeast populations and their potential application in the fermentative processes can significantly enrich the industrial fermentation products. Social insects have proven to be closely associated to the yeasts ecology. The relationships between yeasts and insects represent a fundamental aspect for understanding the ecological and evolutionary forces shaping their adaptation to different niches. Studies on phylogenetic relationships of S. cerevisiae populations showed genetic differences among strains isolated from gut and non-gut environments (i.e., natural sources and fermentation). Recent evidences showed that insect’s gut is a reservoir and an evolutionary niche for Saccharomyces, contributing to its survival and evolution, favoring its dispersion, mating and improving the inter-specific hybrids production during hibernation. Here, we discuss the potential use of social insects for production of a wide range of hybrid yeasts from environmental Saccharomyces isolates suitable for industrial and biotechnological applications.
Collapse
Affiliation(s)
- Monica Di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
| | | |
Collapse
|
14
|
Crossbreeding of Yeasts Domesticated for Fermentation: Infertility Challenges. Int J Mol Sci 2020; 21:ijms21217985. [PMID: 33121129 PMCID: PMC7662550 DOI: 10.3390/ijms21217985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/07/2023] Open
Abstract
Sexual reproduction is almost a universal feature of eukaryotic organisms, which allows the reproduction of new organisms by combining the genetic information from two individuals of different sexes. Based on the mechanism of sexual reproduction, crossbreeding provides an attractive opportunity to improve the traits of animals, plants, and fungi. The budding yeast Saccharomyces cerevisiae has been widely utilized in fermentative production since ancient times. Currently it is still used for many essential biotechnological processes including the production of beer, wine, and biofuels. It is surprising that many yeast strains used in the industry exhibit low rates of sporulation resulting in limited crossbreeding efficiency. Here, I provide an overview of the recent findings about infertility challenges of yeasts domesticated for fermentation along with the progress in crossbreeding technologies. The aim of this review is to create an opportunity for future crossbreeding of yeasts used for fermentation.
Collapse
|
15
|
Applications and research advance of genome shuffling for industrial microbial strains improvement. World J Microbiol Biotechnol 2020; 36:158. [PMID: 32968940 DOI: 10.1007/s11274-020-02936-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022]
Abstract
Genome shuffling, an efficient and practical strain improvement technology via recursive protoplasts fusion, can break through the limits of species even genus to accelerate the directed evolution of microbial strains, without requiring the comprehensively cognized genetic background and operable genetic system. Hence this technology has been widely used for many important strains to obtain the desirable industrial phenotypes. In this review, we introduce the procedure of genome shuffling, discuss the new aid strategies of genome shuffling, summarize the applications of genome shuffling for increasing metabolite yield, improving strain tolerance, enhancing substrate utilization, and put forward the outlook to the future development of this technology.
Collapse
|
16
|
Wu L, Wang M, Zha G, Zhou J, Yu Y, Lu H. Improving the expression of a heterologous protein by genome shuffling in Kluyveromyces marxianus. J Biotechnol 2020; 320:11-16. [DOI: 10.1016/j.jbiotec.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 04/21/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
|
17
|
Geshnizjani N, Snoek BL, Willems LAJ, Rienstra JA, Nijveen H, Hilhorst HWM, Ligterink W. Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings. PLANT, CELL & ENVIRONMENT 2020; 43:1973-1988. [PMID: 32419153 PMCID: PMC7496158 DOI: 10.1111/pce.13788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/01/2020] [Accepted: 05/12/2020] [Indexed: 05/17/2023]
Abstract
Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (Gmax ), germination rate (t50 ) and uniformity (U8416 ) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high-performance seeds.
Collapse
Affiliation(s)
- Nafiseh Geshnizjani
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsUtrecht UniversityUtrechtThe Netherlands
- Laboratory of NematologyWageningen UniversityWageningenThe Netherlands
| | - Leo A. J. Willems
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Juriaan A. Rienstra
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Harm Nijveen
- Bioinformatics GroupWageningen UniversityWageningenThe Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| |
Collapse
|
18
|
Dahabieh MS, Thevelein JM, Gibson B. Multimodal Microorganism Development: Integrating Top-Down Biological Engineering with Bottom-Up Rational Design. Trends Biotechnol 2019; 38:241-253. [PMID: 31653446 DOI: 10.1016/j.tibtech.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
Biological engineering has unprecedented potential to solve society's most pressing challenges. Engineering approaches must consider complex technical, economic, and social factors. This requires methods that confer gene/pathway-level functionality and organism-level robustness in rapid and cost-effective ways. This article compares foundational engineering approaches - bottom-up, gene-targeted engineering, and top-down, whole-genome engineering - and identifies significant complementarity between them. Cases drawn from engineering Saccharomyces cerevisiae exemplify the synergy of a combined approach. Indeed, multimodal engineering streamlines strain development by leveraging the complementarity of whole-genome and gene-targeted engineering to overcome the gap in design knowledge that restricts rational design. As biological engineers target more complex systems, this dual-track approach is poised to become an increasingly important tool to realize the promise of synthetic biology.
Collapse
Affiliation(s)
- Matthew S Dahabieh
- Renaissance BioScience, 410-2389 Health Sciences Mall, Vancouver, BC V6T1Z3, Canada
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Katholieke Universiteit (KU) Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, VTT, PO Box 1000, FI-02044 Espoo, Finland.
| |
Collapse
|
19
|
Li H, Alper HS. Producing Biochemicals in
Yarrowia lipolytica
from Xylose through a Strain Mating Approach. Biotechnol J 2019; 15:e1900304. [DOI: 10.1002/biot.201900304] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/16/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Haibo Li
- Institute for Cellular and Molecular BiologyThe University of Texas at Austin Austin TX 78712 USA
| | - Hal S. Alper
- Institute for Cellular and Molecular BiologyThe University of Texas at Austin Austin TX 78712 USA
- McKetta Department of Chemical EngineeringThe University of Texas at Austin Austin TX 78712 USA
| |
Collapse
|
20
|
Korhola M, Naumova ES, Partti E, Aittamaa M, Turakainen H, Naumov GI. Exploiting heterozygosity in industrial yeasts to create new and improved baker's yeasts. Yeast 2019; 36:571-587. [PMID: 31243797 DOI: 10.1002/yea.3428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023] Open
Abstract
The main aim of the work was to utilize heterozygosity of industrial yeast strains to construct new baker's yeast strains. Commercial baker's yeast strain ALKO 743, its more ethanol tolerant descendant ALKO 554 selected initially for growth over 300 generations in increasing ethanol concentrations in a glucose medium, and ALKO 3460 from an old domestic sour dough starter were used as starting strains. Isolated meiotic segregants of the strains were characterized genetically for sporulation ability and mating type, and the ploidy was determined physically. Heterozygosity of the segregant strains was estimated by a variety of molecular characterizations and fermentation and growth assays. The results showed wide heterozygosity and that the segregants were clustered into subgroups. This clustering was used for choosing distantly or closely related partners for strain construction crosses. Intrastrain hybrids made with segregants of ALKO 743 showed 16-24% hybrid vigour or heterosis. Interstrain hybrids with segregants of ALKO 743 and ALKO 3460 showed a wide variety of characteristics but also clear heterosis of 27-31% effects as assayed by lean and sugar dough raising. Distiller's yeast ALKO 554 turned out to be a diploid genetic segregant and not just a more ethanol tolerant mutant of the tetraploid parent strain ALKO 743.
Collapse
Affiliation(s)
- Matti Korhola
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Elena S Naumova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Edvard Partti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Marja Aittamaa
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Hilkka Turakainen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Alkomohr Biotech Ltd., Helsinki, Finland
| | - Gennadi I Naumov
- State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Centre "Kurchatov Institute", Moscow, Russia
| |
Collapse
|
21
|
Davison SA, den Haan R, van Zyl WH. Identification of superior cellulase secretion phenotypes in haploids derived from natural Saccharomyces cerevisiae isolates. FEMS Yeast Res 2019; 19:5154912. [PMID: 30388213 DOI: 10.1093/femsyr/foy117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is considered an important host for consolidated bioprocessing and the production of high titres of recombinant cellulases is required for efficient hydrolysis of lignocellulosic substrates to fermentable sugars. Since recombinant protein secretion profiles vary highly among different strain backgrounds, careful selection of robust strains with optimal secretion profiles is of crucial importance. Here, we construct and screen sets of haploid derivatives, derived from natural strain isolates YI13, FINI and YI59, for improved general cellulase secretion. This report details a novel approach that combines secretion profiles of strains and phenotypic responses to stresses known to influence the secretion pathway for the development of a phenotypic screen to isolate strains with improved secretory capacities. A clear distinction was observed between the YI13 haploid derivatives and industrial and laboratory counterparts, Ethanol Red and S288c, respectively. By using sub-lethal concentrations of the secretion stressor tunicamycin and cell wall stressor Congo Red, YI13 haploid derivative strains demonstrated tolerance profiles related to their heterologous secretion profiles. Our results demonstrated that a new screening technique combined with a targeted mating approach could produce a pool of novel strains capable of high cellulase secretion.
Collapse
Affiliation(s)
- Steffi A Davison
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
| | - Willem Heber van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| |
Collapse
|
22
|
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]
|
23
|
Chen Y, Cheng L, Zhang X, Cao J, Wu Z, Zheng X. Transcriptomic and proteomic effects of (-)-epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3”Me) treatment on ethanol-stressed Saccharomyces cerevisiae cells. Food Res Int 2019; 119:67-75. [DOI: 10.1016/j.foodres.2019.01.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/23/2022]
|
24
|
Abstract
The budding yeast Saccharomyces cerevisiae has been widely utilized in fermentative production since ancient times. Several approaches for modification of yeast traits have been developed, including mutagenesis, protoplast fusion, and genetic modification. Crossbreeding provides an attractive means to improve and combine strain traits based on sexual reproduction. Common crossbreeding strategies require the isolation of MATa and MATα haploids via sporulation, as most of parental yeasts are MATa/α diploids and unable to mate directly. Unfortunately, many yeast strains used in industry exhibit low sporulation rates resulting in limited crossbreeding efficiency and numerous technical challenges. Here, we review the construction of synthetic gene expression circuits as a means to provide alternative methods for sporulation for yeast crossbreeding. These methods enable researchers to convert the sequence of the MAT locus and subsequently acquire crossbreds via mating of isolated yeast strains. The purpose of this chapter is to provide a basic guide for researchers who are attempting to expand the variety of yeast resources using the sexual reproduction machinery of yeast.
Collapse
|
25
|
Lin Y, Cai Y, Guo Y, Li X, Qi X, Qi Q, Wang Q. Development and genomic elucidation of hybrid yeast with improved glucose-xylose co-fermentation at high temperature. FEMS Yeast Res 2019; 19:5333307. [DOI: 10.1093/femsyr/foz015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/17/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Enhanced capability of co-fermenting glucose and xylose at high temperature is highly desirable for yeast application in second-generation bioethanol production. Here, we obtained hybrid strains with improved glucose-xylose co-fermentation properties at high temperature by combining genome shuffling and adaptive evolution. Genome resequencing of these strains suggested predominantly inherited genetic information from one parental strain Spathaspora passalidarum SP rather than the other parental strain Saccharomyces cerevisiae ScY01, possibly due to that the CUG codon system of S. passalidarum might have systematically eliminated most of the functional proteins from S. cerevisiae through misfolding. Compared to SP, one-copy loss of a 146-kb fragment was found in the hybrid strain and regained after being evolved for a while, whereas one-copy loss of an 11-kb fragment was only found after being evolved for a longer time. Besides, the genes affected by nonsynonymous variants were also identified, especially the mutation S540F in the endoplasmic reticulum chaperon Kar2. Structural prediction indicated that S540F might change the substrate binding activity of Kar2, and thus play a role in preventing protein aggregation in yeast at high temperature. Our results illustrated genomic alterations during this process and revealed some genomic factors that might be involved to determine yeast thermotolerance.
Collapse
Affiliation(s)
- Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanqing Cai
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yufeng Guo
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xin Li
- Impossible Foods Inc., Redwood City, CA 94063, USA
| | - Xianni Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qi Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
26
|
Mertens S, Gallone B, Steensels J, Herrera-Malaver B, Cortebeek J, Nolmans R, Saels V, Vyas VK, Verstrepen KJ. Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts. PLoS One 2019; 14:e0209124. [PMID: 30625138 PMCID: PMC6326464 DOI: 10.1371/journal.pone.0209124] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/29/2018] [Indexed: 11/18/2022] Open
Abstract
Today’s beer market is challenged by a decreasing consumption of traditional beer styles and an increasing consumption of specialty beers. In particular, lager-type beers (pilsner), characterized by their refreshing and unique aroma and taste, yet very uniform, struggle with their sales. The development of novel variants of the common lager yeast, the interspecific hybrid Saccharomyces pastorianus, has been proposed as a possible solution to address the need of product diversification in lager beers. Previous efforts to generate new lager yeasts through hybridization of the ancestral parental species (S. cerevisiae and S. eubayanus) yielded strains with an aromatic profile distinct from the natural biodiversity. Unfortunately, next to the desired properties, these novel yeasts also inherited unwanted characteristics. Most notably is their phenolic off-flavor (POF) production, which hampers their direct application in the industrial production processes. Here, we describe a CRISPR-based gene editing strategy that allows the systematic and meticulous introduction of a natural occurring mutation in the FDC1 gene of genetically complex industrial S. cerevisiae strains, S. eubayanus yeasts and interspecific hybrids. The resulting cisgenic POF- variants show great potential for industrial application and diversifying the current lager beer portfolio.
Collapse
Affiliation(s)
- Stijn Mertens
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Brigida Gallone
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Jeroen Cortebeek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Robbe Nolmans
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Veerle Saels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Valmik K. Vyas
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
- * E-mail:
| |
Collapse
|
27
|
Liu CG, Li K, Wen Y, Geng BY, Liu Q, Lin YH. Bioethanol: New opportunities for an ancient product. ADVANCES IN BIOENERGY 2019. [DOI: 10.1016/bs.aibe.2018.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
28
|
Wang W, Wu B, Qin H, Liu P, Qin Y, Duan G, Hu G, He M. Genome shuffling enhances stress tolerance of Zymomonas mobilis to two inhibitors. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:288. [PMID: 31890016 PMCID: PMC6913010 DOI: 10.1186/s13068-019-1631-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 12/05/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Furfural and acetic acid are the two major inhibitors generated during lignocellulose pretreatment and hydrolysis, would severely inhibit the cell growth, metabolism, and ethanol fermentation efficiency of Zymomonas mobilis. Effective genome shuffling mediated by protoplast electrofusion was developed and then applied to Z. mobilis. RESULTS After two rounds of genome shuffling, 10 different mutants with improved cell growth and ethanol yield in the presence of 5.0 g/L acetic acid and 3.0 g/L furfural were obtained. The two most prominent genome-shuffled strains, 532 and 533, were further investigated along with parental strains in the presence of 7.0 g/L acetic acid and 3.0 g/L furfural. The results showed that mutants 532 and 533 were superior to the parental strain AQ8-1 in the presence of 7.0 g/L acetic acid, with a shorter fermentation time (30 h) and higher productivity than AQ8-1. Mutant 533 exhibited subtle differences from parental strain F34 in the presence of 3.0 g/L furfural. Mutations present in 10 genome-shuffled strains were identified via whole-genome resequencing, and the source of each mutation was identified as either de novo mutation or recombination of the parent genes. CONCLUSIONS These results indicate that genome shuffling is an efficient method for enhancing stress tolerance in Z. mobilis. The engineered strains generated in this study could be potential cellulosic ethanol producers in the future.
Collapse
Affiliation(s)
- Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Han Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Panting Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Yao Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610041 People’s Republic of China
| | - Guowei Duan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| |
Collapse
|
29
|
Mo W, Wang M, Zhan R, Yu Y, He Y, Lu H. Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:63. [PMID: 30949239 PMCID: PMC6429784 DOI: 10.1186/s13068-019-1393-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Kluyveromyces marxianus, the known fastest-growing eukaryote on the earth, has remarkable thermotolerance and capacity to utilize various agricultural residues to produce low-cost bioethanol, and hence is industrially important to resolve the imminent energy shortage crisis. Currently, the poor ethanol tolerance hinders its operable application in the industry, and it is necessary to improve K. marxianus' ethanol resistance and unravel the underlying systematical mechanisms. However, this has been seldom reported to date. RESULTS We carried out a wild-type haploid K. marxianus FIM1 in adaptive evolution in 6% (v/v) ethanol. After 100-day evolution, the KM-100d population was obtained; its ethanol tolerance increased up to 10% (v/v). Interestingly, DNA analysis and RNA-seq analysis showed that KM-100d yeasts' ethanol tolerance improvement was not due to ploidy change or meaningful mutations, but founded on transcriptional reprogramming in a genome-wide range. Even growth in an ethanol-free medium, many genes in KM-100d maintained their up-regulation. Especially, pathways of ethanol consumption, membrane lipid biosynthesis, anti-osmotic pressure, anti-oxidative stress, and protein folding were generally up-regulated in KM-100d to resist ethanol. Notably, enhancement of the secretory pathway may be the new strategy KM-100d developed to anti-osmotic pressure, instead of the traditional glycerol production way in S. cerevisiae. Inferred from the transcriptome data, besides ethanol tolerance, KM-100d may also develop the ability to resist osmotic, oxidative, and thermic stresses, and this was further confirmed by the cell viability test. Furthermore, under such environmental stresses, KM-100d greatly improved ethanol production than the original strain. In addition, we found that K. marxianus may adopt distinct routes to resist different ethanol concentrations. Trehalose biosynthesis was required for low ethanol, while sterol biosynthesis and the whole secretory pathway were activated for high ethanol. CONCLUSIONS This study reveals that ethanol-driven laboratory evolution could improve K. marxianus' ethanol tolerance via significant up-regulation of multiple pathways including anti-osmotic, anti-oxidative, and anti-thermic processes, and indeed consequently raised ethanol yield in industrial high-temperature and high-ethanol circumstance. Our findings give genetic clues for further rational optimization of K. marxianus' ethanol production, and also partly confirm the positively correlated relationship between yeast's ethanol tolerance and production.
Collapse
Affiliation(s)
- Wenjuan Mo
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Mengzhu Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Rongrong Zhan
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| |
Collapse
|
30
|
Shi J, Zhu X, Lu Y, Zhao H, Lu F, Lu Z. Improving Iturin A Production of Bacillus amyloliquefaciens by Genome Shuffling and Its Inhibition Against Saccharomyces cerevisiae in Orange Juice. Front Microbiol 2018; 9:2683. [PMID: 30467499 PMCID: PMC6236126 DOI: 10.3389/fmicb.2018.02683] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/19/2018] [Indexed: 11/13/2022] Open
Abstract
Genome shuffling is an effective method for the rapid improvement of the production of secondary metabolites. This study used the principle of gene shuffling to enhance the yield of iturin A produced by Bacillus amyloliquefaciens LZ-5. Improvements in lipopeptide yield were evident among four strains subjected to recursive protoplast fusion. The four strains were obtained through mutagenesis processes: nitrosoguanidine, ultraviolet irradiation, and atmospheric and room temperature plasma. A high yield strain with 179.22 mg/l of iturin A was obtained after two rounds of genome shuffling, which was a 2.03-fold increase compared with the wild strain. To evaluate the efficacy of iturin A for control of spoilage yeast in food, the anti-yeast efficacy of iturin A was evaluated in orange juice incubated with Saccharomyces cerevisiae. The juice treated with 0.76 mg/ml iturin A showed a significant (p < 0.05) control on yeast population during the storage, similar to that of the 0.30 mg/ml natamycin. In addition, iturin A showed a tiny effect on chemical-physical characteristics of orange juice. Our results provide a basis for the application of antimicrobial lipopeptide in juice products.
Collapse
Affiliation(s)
- Juran Shi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yingjian Lu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD, United States
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
31
|
Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
|
32
|
Yi S, Zhang X, Li HX, Du XX, Liang SW, Zhao XH. Screening and Mutation of Saccharomyces cerevisiae UV-20 with a High Yield of Second Generation Bioethanol and High Tolerance of Temperature, Glucose and Ethanol. Indian J Microbiol 2018; 58:440-447. [PMID: 30262954 DOI: 10.1007/s12088-018-0741-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/10/2018] [Indexed: 11/27/2022] Open
Abstract
A wild-type strain was isolated from slightly rotted pears after three rounds of enrichment culture, identified as Saccharomyces cerevisiae 3308, and evaluated for its fermentation capability of second generation bioethanol and tolerance of temperature, glucose and ethanol. S. cerevisiae 3308 was mutated by using the physical and chemical mutagenesis methods, ultraviolet (UV) and diethyl sulfate (DES), respectively. Positive mutated strains were mainly generated by the treatment of UV, but numerous negative mutations emerged under the treatment of DES. A positive mutated strain, UV-20, produced ethanol from 62.33 ± 1.34 to 122.22 ± 2.80 g/L at 30-45 °C, and had a maximum yield of ethanol at 37 °C. Furthermore, UV-20 produced 121.18 ± 2.51 g/L of second generation bioethanol at 37 °C. Simultaneously, UV-20 exhibited superior tolerance to 50% of glucose and 21% of ethanol. In a conclusion, all of these results indicated that UV-20 has a potential industrial application value.
Collapse
Affiliation(s)
- Shi Yi
- College of Life Science, Jiangxi Normal University, Nanchang, 330022 China
| | - Xiao Zhang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022 China
| | - Han-Xin Li
- College of Life Science, Jiangxi Normal University, Nanchang, 330022 China
| | - Xiao-Xia Du
- College of Life Science, Jiangxi Normal University, Nanchang, 330022 China
| | - Shao-Wei Liang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022 China
| | - Xi-Hua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang, 330022 China
| |
Collapse
|
33
|
Abstract
The yeast Kluyveromyces marxianus grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast Saccharomyces cerevisiae in industrial applications. Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using K. marxianus as a versatile synthetic biology platform organism for industrial applications. Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits—thermotolerance, lipid production, and facile transformation with exogenous DNA—into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.
Collapse
|
34
|
Krogerus K, Preiss R, Gibson B. A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction. Front Microbiol 2018; 9:2253. [PMID: 30319573 PMCID: PMC6165869 DOI: 10.3389/fmicb.2018.02253] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/04/2018] [Indexed: 12/04/2022] Open
Abstract
An unknown interspecies Saccharomyces hybrid, "Muri," was recently isolated from a "kveik" culture, a traditional Norwegian farmhouse brewing yeast culture (Preiss et al., 2018). Here we used whole genome sequencing to reveal the strain as an allodiploid Saccharomyces cerevisiae × Saccharomyces uvarum hybrid. Phylogenetic analysis of its sub-genomes revealed that the S. cerevisiae and S. uvarum parent strains of Muri appear to be most closely related to English ale and Central European cider and wine strains, respectively. We then performed phenotypic analysis on a number of brewing-relevant traits in a range of S. cerevisiae, S. uvarum and hybrid strains closely related to the Muri hybrid. The Muri strain possesses a range of industrially desirable phenotypic properties, including broad temperature tolerance, good ethanol tolerance, and efficient carbohydrate use, therefore making it an interesting candidate for not only brewing applications, but potentially various other industrial fermentations, such as biofuel production and distilling. We identified the two S. cerevisiae and S. uvarum strains that were genetically and phenotypically most similar to the Muri hybrid, and then attempted to reconstruct the Muri hybrid by generating de novo interspecific hybrids between these two strains. The de novo hybrids were compared with the original Muri hybrid, and many appeared phenotypically more similar to Muri than either of the parent strains. This study introduces a novel approach to studying hybrid strains and strain development by combining genomic and phenotypic analysis to identify closely related parent strains for construction of de novo hybrids.
Collapse
Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, Espoo, Finland
| | - Richard Preiss
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- Escarpment Laboratories, Guelph, ON, Canada
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| |
Collapse
|
35
|
Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES. Nat Commun 2018; 9:1930. [PMID: 29789541 PMCID: PMC5964233 DOI: 10.1038/s41467-017-00806-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/28/2017] [Indexed: 11/15/2022] Open
Abstract
SCRaMbLE is a novel system implemented in the synthetic yeast genome, enabling massive chromosome rearrangements to produce strains with a large genotypic diversity upon induction. Here we describe a reporter of SCRaMbLEd cells using efficient selection, termed ReSCuES, based on a loxP-mediated switch of two auxotrophic markers. We show that all randomly isolated clones contained rearrangements within the synthetic chromosome, demonstrating high efficiency of selection. Using ReSCuES, we illustrate the ability of SCRaMbLE to generate strains with increased tolerance to several stress factors, such as ethanol, heat and acetic acid. Furthermore, by analyzing the tolerant strains, we are able to identify ACE2, a transcription factor required for septum destruction after cytokinesis, as a negative regulator of ethanol tolerance. Collectively, this work not only establishes a generic platform to rapidly identify strains of interest by SCRaMbLE, but also provides methods to dissect the underlying mechanisms of resistance. The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.
Collapse
|
36
|
Sardi M, Gasch AP. Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering. FEMS Yeast Res 2018. [PMID: 28637316 DOI: 10.1093/femsyr/fox042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.
Collapse
Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
37
|
Sardi M, Paithane V, Place M, Robinson DE, Hose J, Wohlbach DJ, Gasch AP. Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. PLoS Genet 2018; 14:e1007217. [PMID: 29474395 PMCID: PMC5849340 DOI: 10.1371/journal.pgen.1007217] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/13/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cellulosic plant biomass is a promising sustainable resource for generating alternative biofuels and biochemicals with microbial factories. But a remaining bottleneck is engineering microbes that are tolerant of toxins generated during biomass processing, because mechanisms of toxin defense are only beginning to emerge. Here, we exploited natural diversity in 165 Saccharomyces cerevisiae strains isolated from diverse geographical and ecological niches, to identify mechanisms of hydrolysate-toxin tolerance. We performed genome-wide association (GWA) analysis to identify genetic variants underlying toxin tolerance, and gene knockouts and allele-swap experiments to validate the involvement of implicated genes. In the process of this work, we uncovered a surprising difference in genetic architecture depending on strain background: in all but one case, knockout of implicated genes had a significant effect on toxin tolerance in one strain, but no significant effect in another strain. In fact, whether or not the gene was involved in tolerance in each strain background had a bigger contribution to strain-specific variation than allelic differences. Our results suggest a major difference in the underlying network of causal genes in different strains, suggesting that mechanisms of hydrolysate tolerance are very dependent on the genetic background. These results could have significant implications for interpreting GWA results and raise important considerations for engineering strategies for industrial strain improvement. Understanding the genetic architecture of complex traits is important for elucidating the genotype-phenotype relationship. Many studies have sought genetic variants that underlie phenotypic variation across individuals, both to implicate causal variants and to inform on architecture. Here we used genome-wide association analysis to identify genes and processes involved in tolerance of toxins found in plant-biomass hydrolysate, an important substrate for sustainable biofuel production. We found substantial variation in whether or not individual genes were important for tolerance across genetic backgrounds. Whether or not a gene was important in a given strain background explained more variation than the alleleic differences in the gene. These results suggest substantial variation in gene contributions, and perhaps underlying mechanisms, of toxin tolerance.
Collapse
Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.,Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Vaishnavi Paithane
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - De Elegant Robinson
- Microbiology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dana J Wohlbach
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
38
|
Enhanced Wort Fermentation with De Novo Lager Hybrids Adapted to High-Ethanol Environments. Appl Environ Microbiol 2018; 84:AEM.02302-17. [PMID: 29196294 DOI: 10.1128/aem.02302-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
Interspecific hybridization is a valuable tool for developing and improving brewing yeast in a number of industry-relevant aspects. However, the genomes of newly formed hybrids can be unstable. Here, we exploited this trait by adapting four brewing yeast strains, three of which were de novo interspecific lager hybrids with different ploidy levels, to high ethanol concentrations in an attempt to generate variant strains with improved fermentation performance in high-gravity wort. Through a batch fermentation-based adaptation process and selection based on a two-step screening process, we obtained eight variant strains which we compared to the wild-type strains in 2-liter-scale wort fermentations replicating industrial conditions. The results revealed that the adapted variants outperformed the strains from which they were derived, and the majority also possessed several desirable brewing-relevant traits, such as increased ester formation and ethanol tolerance, as well as decreased diacetyl formation. The variants obtained from the polyploid hybrids appeared to show greater improvements in fermentation performance than those derived from diploid strains. Interestingly, it was not only the hybrid strains, but also the Saccharomyces cerevisiae parent strain, that appeared to adapt and showed considerable changes in genome size. Genome sequencing and ploidy analysis revealed that changes had occurred at both the chromosome and single nucleotide levels in all variants. Our study demonstrates the possibility of improving de novo lager yeast hybrids through adaptive evolution by generating stable and superior variants that possess traits relevant to industrial lager beer fermentation.IMPORTANCE Recent studies have shown that hybridization is a valuable tool for creating new and diverse strains of lager yeast. Adaptive evolution is another strain development tool that can be applied in order to improve upon desirable traits. Here, we apply adaptive evolution to newly created lager yeast hybrids by subjecting them to environments containing high ethanol levels. We isolated and characterized a number of adapted variants which possess improved fermentation properties and ethanol tolerance. Genome analysis revealed substantial changes in the variants compared to the original strains. These improved variant strains were produced without any genetic modification and are suitable for industrial lager beer fermentations.
Collapse
|
39
|
Bar-Zvi D, Lupo O, Levy AA, Barkai N. Hybrid vigor: The best of both parents, or a genomic clash? ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Mating of natural Saccharomyces cerevisiae strains for improved glucose fermentation and lignocellulosic inhibitor tolerance. Folia Microbiol (Praha) 2017; 63:155-168. [PMID: 28887734 DOI: 10.1007/s12223-017-0546-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Natural Saccharomyces cerevisiae isolates from vineyards in the Western Cape, South Africa were evaluated for ethanol production in industrial conditions associated with the production of second-generation biofuels. The strains displayed high phenotypic diversity including the ability to grow at 45 °C and in the presence of 20% (v/v) ethanol, strain YI13. Strains HR4 and YI30 were inhibitor-tolerant under aerobic and oxygen-limited conditions, respectively. Spore-to-spore hybridization generated progeny that displayed heterosis, including increased ethanol productivity and improved growth in the presence of a synthetic inhibitor cocktail. Hybrid strains HR4/YI30#6 and V3/YI30#6 were able to grow at a high salt concentration (2 mol/L NaCl) with V3/YI30#6 also able to grow at a high temperature (45 °C). Strains HR4/YI30#1 and #3 were inhibitor-tolerant, with strain HR4/YI30#3 having similar productivity (0.36 ± 0.0036 g/L per h) as the superior parental strain, YI30 (0.35 ± 0.0058 g/L per h). This study indicates that natural S. cerevisiae strains display phenotypic variation and heterosis can be achieved through spore-to-spore hybridization. Several of the phenotypes (temperature-, osmo-, and inhibitor tolerance) displayed by both the natural strains and the generated progeny were at the maximum conditions reported for S. cerevisiae strains.
Collapse
|
42
|
van Rijswijck IMH, Wolkers-Rooijackers JCM, Abee T, Smid EJ. Performance of non-conventional yeasts in co-culture with brewers' yeast for steering ethanol and aroma production. Microb Biotechnol 2017; 10:1591-1602. [PMID: 28834151 PMCID: PMC5658577 DOI: 10.1111/1751-7915.12717] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/09/2017] [Accepted: 03/20/2017] [Indexed: 11/27/2022] Open
Abstract
Increasing interest in new beer types has stimulated the search for approaches to extend the metabolic variation of brewers’ yeast. Therefore, we tested two approaches using non‐conventional yeast to create a beer with lower ethanol content and a complex aroma bouquet. First, the mono‐culture performance was monitored of 49 wild yeast isolates of Saccharomyces cerevisiae (16 strains), Cyberlindnera fabianii (9 strains) and Pichia kudriavzevii (24 strains). Interestingly, both C. fabianii and P. kudriavzevii isolates produced relatively more esters compared with S. cerevisiae isolates, despite their limited fermentation capacity. Next, one representative strain of each species (Sc131, Cf65 and Pk129) was applied as co‐culture with brewers’ yeast (ratio 1:1). Co‐cultures with Cf65 and Pk129 resulted in a beer with lower alcohol content (3.5, 3.8 compared with 4.2% v/v) and relatively more esters. At higher inoculum ratios of Cf65 over brewers’ yeast, growth inhibition of brewers’ yeast was observed, most likely caused by competition for oxygen between brewers’ yeast and Cf65 resulting in a reduced level of ethanol and altered aroma profiles. With this study, we demonstrate the feasibility of using non‐conventional yeast species in co‐cultivation with traditional brewers’ yeast to tailor aroma profiles as well as the final ethanol content of beer.
Collapse
Affiliation(s)
- Irma M H van Rijswijck
- Laboratory of Food Microbiology, Wageningen University & Research, Wageningen Campus, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Judith C M Wolkers-Rooijackers
- Laboratory of Food Microbiology, Wageningen University & Research, Wageningen Campus, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University & Research, Wageningen Campus, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University & Research, Wageningen Campus, PO Box 17, 6700 AA, Wageningen, The Netherlands
| |
Collapse
|
43
|
Dzialo MC, Park R, Steensels J, Lievens B, Verstrepen KJ. Physiology, ecology and industrial applications of aroma formation in yeast. FEMS Microbiol Rev 2017; 41:S95-S128. [PMID: 28830094 PMCID: PMC5916228 DOI: 10.1093/femsre/fux031] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/06/2017] [Indexed: 01/05/2023] Open
Abstract
Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.
Collapse
Affiliation(s)
- Maria C Dzialo
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Rahel Park
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A B-2860 Sint-Katelijne Waver, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| |
Collapse
|
44
|
Jansen MLA, Bracher JM, Papapetridis I, Verhoeven MD, de Bruijn H, de Waal PP, van Maris AJA, Klaassen P, Pronk JT. Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation. FEMS Yeast Res 2017; 17:3868933. [PMID: 28899031 PMCID: PMC5812533 DOI: 10.1093/femsyr/fox044] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.
Collapse
Affiliation(s)
- Mickel L. A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jasmine M. Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Maarten D. Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Hans de Bruijn
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Paul P. de Waal
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
45
|
Gibson B, Geertman JMA, Hittinger CT, Krogerus K, Libkind D, Louis EJ, Magalhães F, Sampaio JP. New yeasts—new brews: modern approaches to brewing yeast design and development. FEMS Yeast Res 2017; 17:3861261. [DOI: 10.1093/femsyr/fox038] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/01/2017] [Indexed: 02/07/2023] Open
|
46
|
Genome shuffling of Colletotrichum lini for improving 3β,7α,15α-trihydroxy-5-androsten-17-one production from dehydroepiandrosterone. ACTA ACUST UNITED AC 2017; 44:937-947. [DOI: 10.1007/s10295-017-1918-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 02/05/2017] [Indexed: 10/20/2022]
Abstract
Abstract
3β,7α,15α-Trihydroxy-5-androsten-17-one (7α,15α-diOH-DHEA) is a key intermediate of the novel oral contraceptive Yasmin. It can be catalyzed from dehydroepiandrosterone (DHEA) through Colletotrichum lini. Improvement of 7α,15α-diOH-DHEA production was performed through recursive protoplast fusion of C. lini ST in a genome shuffling format. 7α,15α-diOH-DHEA yield of the best performing recombinant C. lini ST-F307 reached 6.08 g/L from 10 g/L DHEA, and this was 94.9% higher than that of the initial C. lini ST strain. Through optimized conditions, the 7α,15α-diOH-DHEA yield was increased to 9.32 g/L from 12 g/L DHEA, with 1.5% ethanol as cosolvent. This is the highest reported substrate concentration and 7α,15α-diOH-DHEA production with one-step substrate addition. Moreover, C. lini ST-F307 showed high P450 enzyme activity and gene transcript levels of several cytochrome P450s, and this might contribute to the enhancement of 7α,15α-diOH-DHEA production. Genome shuffling was an efficient approach to breed high-yield strains.
Collapse
|
47
|
Benyamin MS, Jahnke JP, Mackie DM. Vapor-fed bio-hybrid fuel cell. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:68. [PMID: 28331544 PMCID: PMC5356349 DOI: 10.1186/s13068-017-0755-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/10/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Concentration and purification of ethanol and other biofuels from fermentations are energy-intensive processes, with amplified costs at smaller scales. To circumvent the need for these processes, and to potentially reduce transportation costs as well, we have previously investigated bio-hybrid fuel cells (FCs), in which a fermentation and FC are closely coupled. However, long-term operation requires strictly preventing the fermentation and FC from harming each other. We introduce here the concept of the vapor-fed bio-hybrid FC as a means of continuously extracting power from ongoing fermentations at ambient conditions. By bubbling a carrier gas (N2) through a yeast fermentation and then through a direct ethanol FC, we protect the FC anode from the catalyst poisons in the fermentation (which are non-volatile), and also protect the yeast from harmful FC products (notably acetic acid) and from build-up of ethanol. RESULTS Since vapor-fed direct ethanol FCs at ambient conditions have never been systematically characterized (in contrast to vapor-fed direct methanol FCs), we first assess the effects on output power and conversion efficiency of ethanol concentration, vapor flow rate, and FC voltage. The results fit a continuous stirred-tank reactor model. Over a wide range of ethanol partial pressures (2-8 mmHg), power densities are comparable to those for liquid-fed direct ethanol FCs at the same temperature, with power densities >2 mW/cm2 obtained. We then demonstrate the continuous operation of a vapor-fed bio-hybrid FC with fermentation for 5 months, with no indication of performance degradation due to poisoning (of either the FC or the fermentation). It is further shown that the system is stable, recovering quickly from disturbances or from interruptions in maintenance. CONCLUSIONS The vapor-fed bio-hybrid FC enables extraction of power from dilute bio-ethanol streams without costly concentration and purification steps. The concept should be scalable to both large and small operations and should be generalizable to other biofuels and waste-to-energy systems.
Collapse
Affiliation(s)
| | - Justin P. Jahnke
- Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20740 USA
| | - David M. Mackie
- Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20740 USA
| |
Collapse
|
48
|
Maurer MJ, Sutardja L, Pinel D, Bauer S, Muehlbauer AL, Ames TD, Skerker JM, Arkin AP. Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait. ACS Synth Biol 2017; 6:566-581. [PMID: 27936603 DOI: 10.1021/acssynbio.6b00264] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Engineering complex phenotypes for industrial and synthetic biology applications is difficult and often confounds rational design. Bioethanol production from lignocellulosic feedstocks is a complex trait that requires multiple host systems to utilize, detoxify, and metabolize a mixture of sugars and inhibitors present in plant hydrolysates. Here, we demonstrate an integrated approach to discovering and optimizing host factors that impact fitness of Saccharomyces cerevisiae during fermentation of a Miscanthus x giganteus plant hydrolysate. We first used high-resolution Quantitative Trait Loci (QTL) mapping and systematic bulk Reciprocal Hemizygosity Analysis (bRHA) to discover 17 loci that differentiate hydrolysate tolerance between an industrially related (JAY291) and a laboratory (S288C) strain. We then used this data to identify a subset of favorable allelic loci that were most amenable for strain engineering. Guided by this "genetic blueprint", and using a dual-guide Cas9-based method to efficiently perform multikilobase locus replacements, we engineered an S288C-derived strain with superior hydrolysate tolerance than JAY291. Our methods should be generalizable to engineering any complex trait in S. cerevisiae, as well as other organisms.
Collapse
Affiliation(s)
- Matthew J. Maurer
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lawrence Sutardja
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Dominic Pinel
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stefan Bauer
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Amanda L. Muehlbauer
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tyler D. Ames
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jeffrey M. Skerker
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Adam P. Arkin
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
49
|
Qi W, Guo HL, Wang CL, Hou LH, Cao XH, Liu JF, Lu FP. Comparative study on fermentation performance in the genome shuffled Candida versatilis and wild-type salt tolerant yeast strain. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:284-290. [PMID: 27012958 DOI: 10.1002/jsfa.7728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/31/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The fermentation performance of a genome-shuffled strain of Candida versatilis S3-5, isolated for improved tolerance to salt, and wild-type (WT) strain were analysed. The fermentation parameters, such as growth, reducing sugar, ethanol, organic acids and volatile compounds, were detected during soy sauce fermentation process. RESULTS The results showed that ethanol produced by the genome shuffled strain S3-5 was increasing at a faster rate and to a greater extent than WT. At the end of the fermentation, malic acid, citric acid and succinic acid formed in tricarboxylic acid cycle after S3-5 treatment elevated by 39.20%, 6.85% and 17.09% compared to WT, respectively. Moreover, flavour compounds such as phenethyl acetate, ethyl vanillate, ethyl acetate, isoamyl acetate, ethyl myristate, ethyl pentadecanoate, ethyl palmitate and phenylacetaldehyde produced by S3-5 were 2.26, 2.12, 2.87, 34.41, 6.32, 13.64, 2.23 and 78.85 times as compared to WT. CONCLUSIONS S3-5 exhibited enhanced metabolic ability as compared to the wild-type strain, improved conversion of sugars to ethanol, metabolism of organic acid and formation of volatile compounds, especially esters, Moreover, S3-5 might be an ester-flavour type salt-tolerant yeast. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Wei Qi
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
- National Engineering Laboratory for Industrial Enzymes (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
| | - Hong-Lian Guo
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Chun-Ling Wang
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Li-Hua Hou
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Xiao-Hong Cao
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Jin-Fu Liu
- Department of Food Science, Tianjin Agricultural University, Tianjin, 300384, P.R. China
| | - Fu-Ping Lu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
- National Engineering Laboratory for Industrial Enzymes (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
| |
Collapse
|
50
|
Liu G, Tao C, Zhu B, Bai W, Zhang L, Wang Z, Liang X. Identification of Zygosaccharomyces mellis strains in stored honey and their stress tolerance. Food Sci Biotechnol 2016; 25:1645-1650. [PMID: 30263457 DOI: 10.1007/s10068-016-0253-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 09/17/2016] [Accepted: 09/22/2016] [Indexed: 11/26/2022] Open
Abstract
To screen yeast with high sugar tolerance and evaluate their stress tolerance, six yeast strains were selected from 17 stored honey samples. The species were identified through 26S rRNA sequencing. Their stress tolerance was determined via the Durham fermentation method and ethanol production ability was determined via flask fermentation. The results demonstrated that all the six strains were Zygosaccharomyces mellis. Their sugar, ethanol, and acid tolerance ranges were 500-700 g/L, 10-12% (v/v), and pH 2.5-4.5, respectively. The SO2 tolerance was 250 mg/L. Among the six strains, 6-7431 had the best stress tolerance with sugar tolerance of 700 g/L, ethanol tolerance of 12% (v/v), and acid tolerance of pH 2.5. Furthermore, the strain of 6-7431 had the highest percentage of ethanol production at the same initial sugar content as the other strains. Therefore, the selected six yeast strains would be promising fermentation yeasts for wine-making, ethanol production, or other fermentation purposes.
Collapse
Affiliation(s)
- Gongliang Liu
- 1College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225 China
- Key Laboratory of Traditional Cantonese Food Processing and Safety Control, Guangzhou, Guangdong, 510225 China
| | - Changli Tao
- 3School of Life Science and Biopharmacology, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006 China
| | - Baosheng Zhu
- 1College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225 China
| | - Weidong Bai
- 1College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225 China
- Key Laboratory of Traditional Cantonese Food Processing and Safety Control, Guangzhou, Guangdong, 510225 China
| | - Liangliang Zhang
- 1College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225 China
| | - Zengpeng Wang
- 1College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225 China
| | - Xingting Liang
- 1College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225 China
| |
Collapse
|