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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.
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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
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Nwaefuna AE, Garcia-Aloy M, Loeto D, Ncube T, Gombert AK, Boekhout T, Alwasel S, Zhou N. Dung beetle-associated yeasts display multiple stress tolerance: a desirable trait of potential industrial strains. BMC Microbiol 2023; 23:309. [PMID: 37884896 PMCID: PMC10601127 DOI: 10.1186/s12866-023-03044-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Stress-tolerant yeasts are highly desirable for cost-effective bioprocessing. Several strategies have been documented to develop robust yeasts, such as genetic and metabolic engineering, artificial selection, and natural selection strategies, among others. However, the significant drawbacks of such techniques have motivated the exploration of naturally occurring stress-tolerant yeasts. We previously explored the biodiversity of non-conventional dung beetle-associated yeasts from extremophilic and pristine environments in Botswana (Nwaefuna AE et.al., Yeast, 2023). Here, we assessed their tolerance to industrially relevant stressors individually, such as elevated concentrations of osmolytes, organic acids, ethanol, and oxidizing agents, as well as elevated temperatures. RESULTS Our findings suggest that these dung beetle-associated yeasts tolerate various stresses comparable to those of the robust bioethanol yeast strain, Saccharomyces cerevisiae (Ethanol Red™). Fifty-six percent of the yeast isolates were tolerant of temperatures up to 42 °C, 12.4% of them could tolerate ethanol concentrations up to 9% (v/v), 43.2% of them were tolerant to formic acid concentrations up to 20 mM, 22.7% were tolerant to acetic acid concentrations up to 45 mM, 34.0% of them could tolerate hydrogen peroxide up to 7 mM, and 44.3% of the yeasts could tolerate osmotic stress up to 1.5 M. CONCLUSION The ability to tolerate multiple stresses is a desirable trait in the selection of novel production strains for diverse biotechnological applications, such as bioethanol production. Our study shows that the exploration of natural diversity in the search for stress-tolerant yeasts is an appealing approach for the development of robust yeasts.
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Affiliation(s)
- Anita Ejiro Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Mar Garcia-Aloy
- Metabolomics Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098, San Michele All'Adige, Italy
| | - Daniel Loeto
- Department of Biological Sciences, University of Botswana, Private Bag, 0022, Gaborone, Botswana
| | - Thembekile Ncube
- Department of Applied Biology and Biochemistry, National University of Science and Technology, P.O. Box AC 939, Ascot, Bulawayo, Zimbabwe
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [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: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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Kuil T, Yayo J, Pechan J, Küchler J, van Maris AJA. Ethanol tolerance of Clostridium thermocellum: the role of chaotropicity, temperature and pathway thermodynamics on growth and fermentative capacity. Microb Cell Fact 2022; 21:273. [PMID: 36567317 PMCID: PMC9790125 DOI: 10.1186/s12934-022-01999-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/17/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Clostridium thermocellum is a promising candidate for consolidated bioprocessing of lignocellulosic biomass to ethanol. The low ethanol tolerance of this microorganism is one of the remaining obstacles to industrial implementation. Ethanol inhibition can be caused by end-product inhibition and/or chaotropic-induced stress resulting in increased membrane fluidization and disruption of macromolecules. The highly reversible glycolysis of C. thermocellum might be especially sensitive to end-product inhibition. The chaotropic effect of ethanol is known to increase with temperature. This study explores the relative contributions of these two aspects to investigate and possibly mitigate ethanol-induced stress in growing and non-growing C. thermocellum cultures. RESULTS To separate chaotropic from thermodynamic effects of ethanol toxicity, a non-ethanol producing strain AVM062 (Pclo1313_2638::ldh* ∆adhE) was constructed by deleting the bifunctional acetaldehyde/alcohol dehydrogenase gene, adhE, in a lactate-overproducing strain. Exogenously added ethanol lowered the growth rate of both wild-type and the non-ethanol producing mutant. The mutant strain grew quicker than the wild-type at 50 and 55 °C for ethanol concentrations ≥ 10 g L-1 and was able to reach higher maximum OD600 at all ethanol concentrations and temperatures. For the wild-type, the maximum OD600 and relative growth rates were higher at 45 and 50 °C, compared to 55 °C, for ethanol concentrations ≥ 15 g L-1. For the mutant strain, no positive effect on growth was observed at lower temperatures. Growth-arrested cells of the wild-type demonstrated improved fermentative capacity over time in the presence of ethanol concentrations up to 40 g L-1 at 45 and 50 °C compared to 55 °C. CONCLUSION Positive effects of temperature on ethanol tolerance were limited to wild-type C. thermocellum and are likely related to mechanisms involved in the ethanol-formation pathway and redox cofactor balancing. Lowering the cultivation temperature provides an attractive strategy to improve growth and fermentative capacity at high ethanol titres in high-cellulose loading batch cultivations. Finally, non-ethanol producing strains are useful platform strains to study the effects of chaotropicity and thermodynamics related to ethanol toxicity and allow for deeper understanding of growth and/or fermentation cessation under industrially relevant conditions.
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Affiliation(s)
- Teun Kuil
- grid.5037.10000000121581746Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Yayo
- grid.5037.10000000121581746Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johanna Pechan
- grid.5037.10000000121581746Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jan Küchler
- grid.5037.10000000121581746Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden ,grid.5807.a0000 0001 1018 4307Present Address: Max Plank Institute for Dynamics of Complex Technical Systems, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Antonius J. A. van Maris
- grid.5037.10000000121581746Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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Miah R, Siddiqa A, Chakraborty U, Tuli JF, Barman NK, Uddin A, Aziz T, Sharif N, Dey SK, Yamada M, Talukder AA. Development of high temperature simultaneous saccharification and fermentation by thermosensitive Saccharomyces cerevisiae and Bacillus amyloliquefaciens. Sci Rep 2022; 12:3630. [PMID: 35256663 PMCID: PMC8901927 DOI: 10.1038/s41598-022-07589-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/27/2022] [Indexed: 11/09/2022] Open
Abstract
Scarcity of energy and pollution are two major challenges that have become a threat to all living things worldwide. Bioethanol is a renewable, ecological-friendly clean energy that may be utilized to address these issues. This study aimed to develop simultaneous saccharification and fermentation (SSF) process through high temperature-substrate adaptation and co-cultivation of S. cerevisiae with other potential amylolytic strains. In this study, we adapted our previously screened thermosensitive Saccharomyces cerevisiae Dj-3 strain up-to 42 °C and also screened three potential thermotolerant amylolytic strains based on their starch utilization capability. We performed SSF fermentation at high temperature by adapted Dj-3 and amylolytic strains using 10.0% starch feedstock. Interestingly, we observed significant ethanol concentration [3.86% (v/v)] from high temperature simultaneous saccharification and fermentation (HSSF) of adapted Bacillus amyloliquefaciens (C-7) and Dj-3. We attribute the significant ethanol concentration from starch of this HSSF process to C-7’s high levels of glucoamylase activity (4.01 U/ml/min) after adaptation in starch (up-to 42 °C) as well as Dj-3's strong glucose fermentation capacity and also their ethanol stress tolerance capability. This study suggests the significant feasibility of our HSSF process.
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Affiliation(s)
- Roni Miah
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh.,Department of Biological Chemistry, Yamaguchi University, Yamaguchi, 755, Japan
| | - Ayesha Siddiqa
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh.,Department of Biological Chemistry, Yamaguchi University, Yamaguchi, 755, Japan
| | | | | | - Noyon Kumar Barman
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Aukhil Uddin
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Tareque Aziz
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Nadim Sharif
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Mamoru Yamada
- Department of Biological Chemistry, Yamaguchi University, Yamaguchi, 755, Japan
| | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh. .,Department of Biological Chemistry, Yamaguchi University, Yamaguchi, 755, Japan.
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Nieto-Sarabia VL, Ballinas-Cesatti CB, Melgar-Lalanne G, Cristiani-Urbina E, Morales-Barrera L. Isolation, identification, and kinetic and thermodynamic characterization of a Pichia kudriavzevii yeast strain capable of fermentation. FOOD AND BIOPRODUCTS PROCESSING 2022. [DOI: 10.1016/j.fbp.2021.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Hospet R, Thangadurai D, Cruz-Martins N, Sangeetha J, Anu Appaiah KA, Chowdhury ZZ, Bedi N, Soytong K, Al Tawahaj ARM, Jabeen S, Tallur MM. Genome shuffling for phenotypic improvement of industrial strains through recursive protoplast fusion technology. Crit Rev Food Sci Nutr 2021:1-10. [PMID: 34592865 DOI: 10.1080/10408398.2021.1983763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Strains' improvement technology plays an essential role in enhancing the quality of industrial strains. Several traditional methods and modern techniques have been used to further improve strain engineering programs. The advances stated in strain engineering and the increasing demand for microbial metabolites leads to the invention of the genome shuffling technique, which ensures a specific phenotype improvement through inducing mutation and recursive protoplast fusion. In such technique, the selection of multi-parental strains with distinct phenotypic traits is crucial. In addition, as this evolutionary strain improvement technique involves combinative approaches, it does not require any gene sequence data for genome alteration and, therefore, strains developed by this elite technique will not be considered as genetically modified organisms. In this review, the different stages involved in the genome shuffling technique and its wide applications in various phenotype improvements will be addressed. Taken together, data discussed here highlight that the use of genome shuffling for strain improvement will be a plus for solving complex phenotypic traits and in promoting the rapid development of other industrially important strains.
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Affiliation(s)
| | | | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal.,Institute of Research and Advanced Training in Health Sciences and Technologies (CESPU), Gandra PRD, Portugal
| | - Jeyabalan Sangeetha
- Department of Environmental Science, Central University of Kerala, Kasaragod, Kerala, India
| | - Konerira Aiyappa Anu Appaiah
- Department of Microbiology and Fermentation Technology, Central Food Technological Research Institute (CSIR), Mysore, Karnataka, India
| | - Zaira Zaman Chowdhury
- Nanotechnology and Catalysis Research Center (NANOCAT), Institute of Advanced Studies (IAS), University of Malaya, Kuala Lumpur, Malaysia
| | - Namita Bedi
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Kasem Soytong
- Department of Plant Production Technology, King Mongkut's Institute of Technology Ladkrabang (KMITL), Ladkrabang, Bangkok, Thailand
| | | | - Shoukat Jabeen
- Department of Botany, Karnatak University, Dharwad, Karnataka, India
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Li S, Wang L, Wang N, Cong W. Combining Genome Shuffling with Streptomycin Resistance to Improve Poly-γ-L-diaminobutanoic Acid Production in Bacillus pumilus. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0320-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Stress modulation as a means to improve yeasts for lignocellulose bioconversion. Appl Microbiol Biotechnol 2021; 105:4899-4918. [PMID: 34097119 DOI: 10.1007/s00253-021-11383-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
The second-generation (2G) fermentation environment for lignocellulose conversion presents unique challenges to the fermentative organism that do not necessarily exist in other industrial fermentations. While extreme osmotic, heat, and nutrient starvation stresses are observed in sugar- and starch-based fermentation environments, additional pre-treatment-derived inhibitor stress, potentially exacerbated by stresses such as pH and product tolerance, exist in the 2G environment. Furthermore, in a consolidated bioprocessing (CBP) context, the organism is also challenged to secrete enzymes that may themselves lead to unfolded protein response and other stresses. This review will discuss responses of the yeast Saccharomyces cerevisiae to 2G-specific stresses and stress modulation strategies that can be followed to improve yeasts for this application. We also explore published -omics data and discuss relevant rational engineering, reverse engineering, and adaptation strategies, with the view of identifying genes or alleles that will make positive contributions to the overall robustness of 2G industrial strains. KEYPOINTS: • Stress tolerance is a key driver to successful application of yeast strains in biorefineries. • A wealth of data regarding stress responses has been gained through omics studies. • Integration of this knowledge could inform engineering of fit for purpose strains.
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Mattoon ER, Casadevall A, Cordero RJB. Beat the heat: correlates, compounds, and mechanisms involved in fungal thermotolerance. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Liu C, Hou H, Lu X, Chen X, Fang D, Hu Q, Zhao L. Production of an innovative mixed Qu (fermentation starter) for waxy maize brewing and comparison of the quality of different waxy maize wines. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:2328-2336. [PMID: 33006380 DOI: 10.1002/jsfa.10854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/26/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Waxy maize (Zea mays L. sinensis Kulesh) is a good material for brewing. Waxy maize wine, a kind of Chinese rice wine, is strongly affected by a fermentation starter named Qu. In this study, an innovative mixed Qu, consisting of two yeasts and three molds, was produced and the raw-starch brewing method was applied in winemaking. Three other waxy maize wines fermented by three kinds of commercial Qu were also analyzed for comparison. RESULTS Due to superb growth and fermentation characteristics, Saccharomyces cerevisiae CICC1009 and Pichia anomala CICC1851 were chosen to produce yeast Qu. The addition amount of yeast Qu was determined to be 30 g kg-1 . In terms of chemical properties, mixed Qu was more suitable for making maize wine by the raw-starch brewing method than the three kinds of commercial Qu with which it was compared. The most influential components for the overall aroma profile in maize wines fermented by mixed Qu and Mifeng Qu were ethyl butyrate and β-damascenone, respectively, while in maize wines fermented by Angel Qu and Like Qu the most influential component was ethyl octanoate. Obvious differences were found among four maize wines regarding bitterness, umami, richness, saltiness, and sourness by the electronic tongue. The olfactory characteristics of maize wine fermented by Mifeng Qu were quite different from the other three according to the electronic nose. CONCLUSION The innovative mixed Qu can be considered as an excellent starter for raw-starch brewing of waxy maize. The chemical indices and volatile flavor compounds of waxy maize wines were greatly affected by different kinds of Qu. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Chang Liu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Hui Hou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiaoshuo Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xin Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Donglu Fang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Qiuhui Hu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Liyan Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
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12
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Wawro A. Improvement of Acetic Acid Tolerance in Saccharomyces cerevisiae by Novel Genome Shuffling. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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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]
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14
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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.
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15
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Li S, Wang L, Wang N. Enhanced poly-γ-L-diaminobutanoic acid production in Bacillus pumilus by combining genome shuffling with multiple antibiotic-resistance. J Ind Microbiol Biotechnol 2020; 47:1141-1154. [PMID: 32990840 DOI: 10.1007/s10295-020-02315-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/21/2020] [Indexed: 11/26/2022]
Abstract
A breeding approach combining genome shuffling with multiple antibiotic-resistance including gentamicin, rifampin and lincomycin, was developed in this research to improve the poly-γ-L-diaminobutanoic acid (γ-PAB) production in Bacillus pumilus LS-1. By this unique strategy, recombinants from the third round of genome shuffling could tolerate higher concentration of compound antibiotics and exhibited higher γ-PAB production as 392.4 mg/L in shake-flask fermentation, tenfold over the parent. In batch fermentation, B. pumilus GS3-M7 could produce γ-PAB as high as 2316.4 mg/L in two days, 5.4-fold higher than the control, which was the highest productivity ever reported. In addition, the optimal pH in B. pumilus for γ-PAB synthesis was decreased after ARTP mutagenesis and protoplast fusion, because the lower pH environment is favorable for accumulation of intracellular ATP. Some key enzymes in GS3-M7 showed higher activities than those in the parent, suggesting a greater flux to TCA circle and DAP pathway, which was a reason for enhanced γ-PAB production.
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Affiliation(s)
- Shu Li
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
| | - Liang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nan Wang
- Testing Center, Weihai Food and Drug Administration, Weihai, 264210, China
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16
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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.
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Baldwin EL, Karki B, Johnson TJ, Zahler JD, Gibbons J, Gibbons WR. Enhancing Cellulase Production in Aureobasidium pullulans by Genome Shuffling. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2018.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emily L. Baldwin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Bishnu Karki
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Tylor J. Johnson
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
| | - Jacob D. Zahler
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Jaimie Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - William R. Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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18
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Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis. Nat Chem Biol 2020; 16:113-121. [DOI: 10.1038/s41589-019-0452-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
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19
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Dakal TC, Dhabhai B. Current status of genetic & metabolic engineering and novel QTL mapping-based strategic approach in bioethanol production. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Marullo P, Durrens P, Peltier E, Bernard M, Mansour C, Dubourdieu D. Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study. BMC Genomics 2019; 20:680. [PMID: 31462217 PMCID: PMC6714461 DOI: 10.1186/s12864-019-5959-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. Among them, high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes. RESULTS In this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genes VHS1 and OYE2 characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (> 240 g/L of sugar) carried out at high temperatures (> 28 °C). Phenotypes impacted were mostly related to the late stage of alcoholic fermentation during the stationary growth phase of yeast. CONCLUSIONS Our findings illustrate the complex genetic determinism of stuck fermentation and open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.
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Affiliation(s)
- Philippe Marullo
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
- Biolaffort, 33100 Bordeaux, France
| | - Pascal Durrens
- CNRS UMR 5800, University of Bordeaux, 33405 Talence, France
- Inria Bordeaux Sud-Ouest, Joint team Pleiade Inria/INRA/CNRS, 33405 Talence, France
| | - Emilien Peltier
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
- Biolaffort, 33100 Bordeaux, France
| | - Margaux Bernard
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
- Biolaffort, 33100 Bordeaux, France
| | | | - Denis Dubourdieu
- University of Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, 33140 Bordeaux INP, Villenave d’Ornon France
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Lv Z, Zhou J, Zhang Y, Zhou X, Xu N, Xin F, Ma J, Jiang M, Dong W. Techniques for enhancing the tolerance of industrial microbes to abiotic stresses: A review. Biotechnol Appl Biochem 2019; 67:73-81. [PMID: 31206805 DOI: 10.1002/bab.1794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022]
Abstract
The diversity of stress responses and survival strategies evolved by microorganism enables them to survive and reproduce in a multitude of harsh environments, whereas the discovery of the underlying resistance genes or mechanisms laid the foundation for the directional enhancement of microbial tolerance to abiotic stresses encountered in industrial applications. Many biological techniques have been developed for improving the stress resistance of industrial microorganisms, which greatly benefited the bacteria on which industrial production is based. This review introduces the main techniques for enhancing the resistance of microorganisms to abiotic stresses, including evolutionary engineering, metabolic engineering, and process engineering, developed in recent years. In addition, we also discuss problems that are still present in this area and offer directions for future research.
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Affiliation(s)
- Ziyao Lv
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Yue Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Xinhai Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
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Mitsui R, Yamada R, Ogino H. Improved Stress Tolerance of Saccharomyces cerevisiae by CRISPR-Cas-Mediated Genome Evolution. Appl Biochem Biotechnol 2019; 189:810-821. [PMID: 31119529 DOI: 10.1007/s12010-019-03040-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/10/2019] [Indexed: 11/30/2022]
Abstract
In bioprocesses, a microorganism with high tolerance to various stresses would be advantageous for efficient bio-based chemical production. Yeast Saccharomyces cerevisiae has long been used in the food industry because of its safety and convenience, and genetically engineered S. cerevisiae strains have been constructed and used for the production of various bio-based chemicals. In this study, we developed a novel genome shuffling method for S. cerevisiae using CRISPR-Cas. By using this, the thermotolerant mutant strain T8-292, which can grow well at 39 °C, was successfully created. The strain also showed higher cell viability in low pH and high ethanol concentration. In addition, the differences in genome structure between mutant and parent strains were suggested by random amplified polymorphic DNA PCR method. Our genome shuffling method could be a promising strategy for improvement of various stress tolerance in S. cerevisiae.
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Affiliation(s)
- Ryosuke Mitsui
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryosuke Yamada
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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Lehnen M, Ebert BE, Blank LM. Elevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts. BMC Microbiol 2019; 19:100. [PMID: 31101012 PMCID: PMC6525440 DOI: 10.1186/s12866-019-1453-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses. RESULTS To elaborate on the metabolic network response to increased fermentation temperatures of up to 49 °C, comprehensive physiological datasets of several Kluyveromyces and Ogataea strains were generated and used for 13C-metabolic flux analyses. While the maximum growth temperature was very similar in all investigated strains, the metabolic network response to elevated temperatures was not conserved among the different species. In fact, metabolic flux distributions were remarkably irresponsive to increasing temperatures in O. polymorpha, while the K. marxianus strains exhibited extensive flux rerouting at elevated temperatures. CONCLUSIONS While a clear mechanism of thermotolerance is not deducible from the fluxome level alone, the generated data can be valued as a knowledge repository for using temperature to modulate the metabolic activity towards engineering goals.
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Affiliation(s)
- Mathias Lehnen
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Birgitta E. Ebert
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
| | - Lars M. Blank
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52074 Aachen, Germany
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Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD, Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nat Catal 2019. [DOI: 10.1038/s41929-018-0212-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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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]
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26
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Tian K, Li Y, Wang B, Wu H, Caiyin Q, Zhang Z, Qiao J. The genome and transcriptome of Lactococcus lactis ssp. lactis F44 and G423: Insights into adaptation to the acidic environment. J Dairy Sci 2018; 102:1044-1058. [PMID: 30594364 DOI: 10.3168/jds.2018-14882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022]
Abstract
Nisin, as a common green (environmentally friendly), nontoxic antibacterial peptide secreted by Lactococcus lactis, is widely used to prevent the decomposition of meat and dairy products and maintains relatively high stability at low pH. However, the growth of Lc. lactis is frequently inhibited by high lactic acid concentrations produced during fermentation. This phenomenon has become a great challenge in enhancing the nisin yield for this strain. Here, the shuffled strain G423 that could survive on a solid plate at pH 3.7 was generated through protoplast fusion-mediated genome shuffling. The nisin titer of G423 peaked at 4,543 IU/mL, which was 59.9% higher than that of the same batch of the initial strain Lc. lactis F44. The whole genome comparisons between G423 and F44 indicated that 6 large fragments (86,725 bp) were inserted in G423 compared with that of Lc. lactis F44. Transcriptome data revealed that 4 novel noncoding transcripts, and the significantly upregulated genes were involved in multiple processes in G423. In particular, the expression of genes involved in cell wall and membrane biosynthesis was obviously perturbed under acidic stress. Quantitative real-time PCR analysis showed that the transcription of noncoding small RNA NC-1 increased by 2.35-fold at pH 3.0 compared with that of the control (pH 7.0). Overexpression assays indicated that small RNA NC-1 could significantly enhance the acid tolerance and nisin production of G423 and F44. Our work provided new insights into the sophisticated genetic mechanisms involved in Lc. lactis in an acidic environment, which might elucidate its potential application in food and dairy industries.
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Affiliation(s)
- Kairen Tian
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P.R. China
| | - Yanni Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P.R. China
| | - Binbin Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P.R. China
| | - Hao Wu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P.R. China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P.R. China
| | - Zhijun Zhang
- Forestry and Fruit Research Institute of Tianjin Academy of Agricultural Sciences, Tianjin 300072, P.R. China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjian 300072, P.R. China; SynBio Research Platform Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P.R. China.
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Rationally designed perturbation factor drives evolution in Saccharomyces cerevisiae for industrial application. ACTA ACUST UNITED AC 2018; 45:869-880. [DOI: 10.1007/s10295-018-2057-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/14/2018] [Indexed: 10/28/2022]
Abstract
Abstract
Saccharomyces cerevisiae strains with favorable characteristics are preferred for application in industries. However, the current ability to reprogram a yeast cell on the genome scale is limited due to the complexity of yeast ploids. In this study, a method named genome replication engineering-assisted continuous evolution (GREACE) was proved efficient in engineering S. cerevisiae with different ploids. Through iterative cycles of culture coupled with selection, GREACE could continuously improve the target traits of yeast by accumulating beneficial genetic modification in genome. The application of GREACE greatly improved the tolerance of yeast against acetic acid compared with their parent strain. This method could also be employed to improve yeast aroma profile and the phenotype could be stably inherited to the offspring. Therefore, GREACE method was efficient in S. cerevisiae engineering and it could be further used to evolve yeast with other specific characteristics.
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28
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Saini P, Beniwal A, Kokkiligadda A, Vij S. Response and tolerance of yeast to changing environmental stress during ethanol fermentation. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.07.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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Genome shuffling and high-throughput screening of Brevibacterium flavum MDV1 for enhanced l-valine production. World J Microbiol Biotechnol 2018; 34:121. [DOI: 10.1007/s11274-018-2502-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 07/10/2018] [Indexed: 11/25/2022]
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30
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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.
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31
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Effect of inorganic salt stress on the thermotolerance and ethanol production at high temperature of Pichia kudriavzevii. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1339-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Evolutionary engineering of industrial microorganisms-strategies and applications. Appl Microbiol Biotechnol 2018; 102:4615-4627. [DOI: 10.1007/s00253-018-8937-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
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Kordowska-Wiater M, Lisiecka U, Kostro K. Improvement of Candida parapsilosis by genome shuffling for the efficient production of arabitol from l-arabinose. Food Sci Biotechnol 2018; 27:1395-1403. [PMID: 30319849 PMCID: PMC6170280 DOI: 10.1007/s10068-018-0369-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/16/2018] [Accepted: 03/27/2018] [Indexed: 01/07/2023] Open
Abstract
Arabitol is used in the food industry as a low-calorie sweetener. It is produced by yeasts during the biotransformation process of l-arabinose. Genome shuffling was performed in Candida parapsilosis DSM 70125, an efficient producer of arabitol, to obtain fusants with improved arabitol production ability. Four mutants from the parental library were used for the first round of genome shuffling. The best fusants, GSI-1 and GSI-10A, were subjected to a second round of genome shuffling. Finally, two fusants, GSII-3 and GSII-16, produced concentrations of arabitol that were 50% higher than that of the wild-type strain during selection culture. Under the optimal conditions established for C. parapsilosis, the two fusants produced 11.83 and 11.75 g/L of arabitol and were approximately 15-16% more efficient than the wild-type strain. Flow cytometry analysis showed that the ploidy of the new strains did not change.
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Affiliation(s)
- Monika Kordowska-Wiater
- 1Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
| | - Urszula Lisiecka
- 2Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-950 Lublin, Poland
| | - Krzysztof Kostro
- 2Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-950 Lublin, Poland
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Xu K, Lv B, Huo YX, Li C. Toward the lowest energy consumption and emission in biofuel production: combination of ideal reactors and robust hosts. Curr Opin Biotechnol 2018; 50:19-24. [DOI: 10.1016/j.copbio.2017.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
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Yang Y, Xia Y, Lin X, Wang G, Zhang H, Xiong Z, Yu H, Yu J, Ai L. Improvement of flavor profiles in Chinese rice wine by creating fermenting yeast with superior ethanol tolerance and fermentation activity. Food Res Int 2018; 108:83-92. [PMID: 29735105 DOI: 10.1016/j.foodres.2018.03.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/09/2018] [Accepted: 03/11/2018] [Indexed: 01/18/2023]
Abstract
Producing alcoholic beverages with novel flavor are desirable for winemakers. We created fermenting yeast with superior ethanol tolerance and fermentation activity to improve the flavor profiles of Chinese rice wine. Strategies of ethanol domestication, ultraviolet mutagenesis (UV) and protoplast fusion were conducted to create yeast hybrids with excellent oenological characteristic. The obtained diploid hybrid F23 showed a cell viability of 6.2% under 25% ethanol, whereas its diploid parental strains could not survive under 20% ethanol. During Chinese rice wine-making, compared to diploid parents, F23 produced 7.07%-12.44% higher yield of ethanol. Flavor analysis indicated that the total content of flavor compounds in F23 wine was 19.99-26.55% higher than that of parent wines. Specifically, F23 exhibited higher capacity in producing 2-phenylethanol, short-chain and long-chain fatty-acid ethyl-ester than diploid parents. Compared to diploid parents, F23 introduced more flavor contributors with odor activity values (OAVs) above one to Chinese rice wine, and those contributors were found with higher OAVs. Based on principal component analysis (PCA), the flavor characteristic of F23 wine was similar to each of parent wine. Additionally, sensory evaluation showed that F23 wine was highly assessed for its intensive levels in fruit-aroma, alcohol-aroma and mouthfeel. Hybrid F23 not only displayed superior flavor production and oenological performance in making Chinese rice wine, but also could act as potential "mixed-like" starter to enrich wine style and differentiation.
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Affiliation(s)
- Yijin Yang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Yongjun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Xiangna Lin
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Guangqiang Wang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Hui Zhang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 200235, PR China
| | - Jianshen Yu
- Shanghai Jinfeng Wine Co., Ltd., Shanghai, 200120, PR China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, PR China.
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Xu N, Ye C, Liu L. Genome-scale biological models for industrial microbial systems. Appl Microbiol Biotechnol 2018; 102:3439-3451. [PMID: 29497793 DOI: 10.1007/s00253-018-8803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 01/08/2023]
Abstract
The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China. .,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China.
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37
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Huang S, Xue T, Wang Z, Ma Y, He X, Hong J, Zou S, Song H, Zhang M. Furfural-tolerant Zymomonas mobilis derived from error-prone PCR-based whole genome shuffling and their tolerant mechanism. Appl Microbiol Biotechnol 2018; 102:3337-3347. [PMID: 29464326 DOI: 10.1007/s00253-018-8817-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/22/2018] [Accepted: 01/27/2018] [Indexed: 11/29/2022]
Abstract
Furfural-tolerant strain is essential for the fermentative production of biofuels or chemicals from lignocellulosic biomass. In this study, Zymomonas mobilis CP4 was for the first time subjected to error-prone PCR-based whole genome shuffling, and the resulting mutants F211 and F27 that could tolerate 3 g/L furfural were obtained. The mutant F211 under various furfural stress conditions could rapidly grow when the furfural concentration reduced to 1 g/L. Meanwhile, the two mutants also showed higher tolerance to high concentration of glucose than the control strain CP4. Genome resequencing revealed that the F211 and F27 had 12 and 13 single-nucleotide polymorphisms. The activity assay demonstrated that the activity of NADH-dependent furfural reductase in mutant F211 and CP4 was all increased under furfural stress, and the activity peaked earlier in mutant than in control. Also, furfural level in the culture of F211 was also more rapidly decreased. These indicate that the increase in furfural tolerance of the mutants may be resulted from the enhanced NADH-dependent furfural reductase activity during early log phase, which could lead to an accelerated furfural detoxification process in mutants. In all, we obtained Z. mobilis mutants with enhanced furfural and high concentration of glucose tolerance, and provided valuable clues for the mechanism of furfural tolerance and strain development.
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Affiliation(s)
- Suzhen Huang
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Tingli Xue
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiquan Wang
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yuanyuan Ma
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China. .,Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, China.
| | - Xueting He
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jiefang Hong
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China
| | - Shaolan Zou
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China
| | - Hao Song
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
| | - Minhua Zhang
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, China
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38
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Xu K, Yu L, Bai W, Xiao B, Liu Y, Lv B, Li J, Li C. Construction of thermo-tolerant yeast based on an artificial protein quality control system (APQC) to improve the production of bio-ethanol. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2017.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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39
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Revin V, Atykyan N, Lyovina E, Dragunova Y, Ushkina V. Effect of ultraviolet radiation on physiological and biochemical properties of yeast Saccharomyces cerevisiae during fermentation of ultradispersed starch raw material. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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40
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Abstract
One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.
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Affiliation(s)
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, CDMX, México
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41
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Inokuma K, Iwamoto R, Bamba T, Hasunuma T, Kondo A. Improvement of Xylose Fermentation Ability under Heat and Acid Co-Stress in Saccharomyces cerevisiae Using Genome Shuffling Technique. Front Bioeng Biotechnol 2017; 5:81. [PMID: 29326929 PMCID: PMC5742482 DOI: 10.3389/fbioe.2017.00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/08/2017] [Indexed: 12/26/2022] Open
Abstract
Xylose-assimilating yeasts with tolerance to both fermentation inhibitors (such as weak organic acids) and high temperature are required for cost-effective simultaneous saccharification and cofermentation (SSCF) of lignocellulosic materials. Here, we demonstrate the construction of a novel xylose-utilizing Saccharomyces cerevisiae strain with improved fermentation ability under heat and acid co-stress using the drug resistance marker-aided genome shuffling technique. The mutagenized genome pools derived from xylose-utilizing diploid yeasts with thermotolerance or acid tolerance were shuffled by sporulation and mating. The shuffled strains were then subjected to screening under co-stress conditions of heat and acids, and the hybrid strain Hyb-8 was isolated. The hybrid strain displayed enhanced xylose fermentation ability in comparison to both parental strains under co-stress conditions of heat and acids. Hyb-8 consumed 33.1 ± 0.6 g/L xylose and produced 11.1 ± 0.4 g/L ethanol after 72 h of fermentation at 38°C with 20 mM acetic acid and 15 mM formic acid. We also performed transcriptomic analysis of the hybrid strain and its parental strains to screen for key genes for multiple stress tolerances. We found that 13 genes, including 5 associated with cellular transition metal ion homeostasis, were significantly upregulated in Hyb-8 compared to levels in both parental strains under co-stress conditions. The hybrid strain Hyb-8 has strong potential for cost-effective SSCF of lignocellulosic materials. Moreover, the transcriptome data gathered in this study will be useful for understanding the mechanisms of multiple tolerance to high temperature and acids in yeast and facilitate the development of robust yeast strains for SSCF.
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Affiliation(s)
- Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Ryo Iwamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Takahiro Bamba
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Biomass Engineering Program, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Japan
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42
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Engineering of global regulators and cell surface properties toward enhancing stress tolerance in Saccharomyces cerevisiae. J Biosci Bioeng 2017; 124:599-605. [DOI: 10.1016/j.jbiosc.2017.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 01/22/2023]
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43
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Jiang Y, Xiao P, Shao Q, Qin H, Hu Z, Lei A, Wang J. Metabolic responses to ethanol and butanol in Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:239. [PMID: 29075323 PMCID: PMC5646117 DOI: 10.1186/s13068-017-0931-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microalgae have been demonstrated to be among the most promising phototrophic species for producing renewable biofuels and chemicals. Ethanol and butanol are clean energy sources with good chemical and physical properties as alternatives to gasoline. However, biosynthesis of these two biofuels has not been achieved due to low tolerance of algal cells to ethanol or butanol. RESULTS With an eye to circumventing these problems in the future and engineering the robust alcohol-producing microalgal hosts, we investigated the metabolic responses of the model green alga Chlamydomonas reinhardtii to ethanol and butanol. Using a quantitative proteomics approach with iTRAQ-LC-MS/MS technologies, we detected the levels of 3077 proteins; 827 and 730 of which were differentially regulated by ethanol and butanol, respectively, at three time points. In particular, 41 and 59 proteins were consistently regulated during at least two sampling times. Multiple metabolic processes were affected by ethanol or butanol, and various stress-related proteins, transporters, cytoskeletal proteins, and regulators were induced as the major protection mechanisms against toxicity of the organic solvents. The most highly upregulated butanol response protein was Cre.770 peroxidase. CONCLUSIONS The study is the first comprehensive view of the metabolic mechanisms employed by C. reinhardtii to defend against ethanol or butanol toxicity. Moreover, the proteomic analysis provides a resource for investigating potential gene targets for engineering microalgae to achieve efficient biofuel production.
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Affiliation(s)
- Yongguang Jiang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Peng Xiao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Qing Shao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Huan Qin
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Shenzhen, 518060 People’s Republic of China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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44
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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.
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45
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Deparis Q, Claes A, Foulquié-Moreno MR, Thevelein JM. Engineering tolerance to industrially relevant stress factors in yeast cell factories. FEMS Yeast Res 2017; 17:3861662. [PMID: 28586408 PMCID: PMC5812522 DOI: 10.1093/femsyr/fox036] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2017] [Indexed: 01/01/2023] Open
Abstract
The main focus in development of yeast cell factories has generally been on establishing optimal activity of heterologous pathways and further metabolic engineering of the host strain to maximize product yield and titer. Adequate stress tolerance of the host strain has turned out to be another major challenge for obtaining economically viable performance in industrial production. Although general robustness is a universal requirement for industrial microorganisms, production of novel compounds using artificial metabolic pathways presents additional challenges. Many of the bio-based compounds desirable for production by cell factories are highly toxic to the host cells in the titers required for economic viability. Artificial metabolic pathways also turn out to be much more sensitive to stress factors than endogenous pathways, likely because regulation of the latter has been optimized in evolution in myriads of environmental conditions. We discuss different environmental and metabolic stress factors with high relevance for industrial utilization of yeast cell factories and the experimental approaches used to engineer higher stress tolerance. Improving stress tolerance in a predictable manner in yeast cell factories should facilitate their widespread utilization in the bio-based economy and extend the range of products successfully produced in large scale in a sustainable and economically profitable way.
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Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Arne Claes
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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46
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Improved antimicrobial activity of Pediococcus acidilactici against Salmonella Gallinarum by UV mutagenesis and genome shuffling. Appl Microbiol Biotechnol 2017; 101:5353-5363. [DOI: 10.1007/s00253-017-8293-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/02/2017] [Accepted: 04/06/2017] [Indexed: 11/25/2022]
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47
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Guan N, Li J, Shin HD, Du G, Chen J, Liu L. Microbial response to environmental stresses: from fundamental mechanisms to practical applications. Appl Microbiol Biotechnol 2017; 101:3991-4008. [PMID: 28409384 DOI: 10.1007/s00253-017-8264-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 10/19/2022]
Abstract
Environmental stresses are usually active during the process of microbial fermentation and have significant influence on microbial physiology. Microorganisms have developed a series of strategies to resist environmental stresses. For instance, they maintain the integrity and fluidity of cell membranes by modulating their structure and composition, and the permeability and activities of transporters are adjusted to control nutrient transport and ion exchange. Certain transcription factors are activated to enhance gene expression, and specific signal transduction pathways are induced to adapt to environmental changes. Besides, microbial cells also have well-established repair mechanisms that protect their macromolecules against damages inflicted by environmental stresses. Oxidative, hyperosmotic, thermal, acid, and organic solvent stresses are significant in microbial fermentation. In this review, we summarize the modus operandi by which these stresses act on cellular components, as well as the corresponding resistance mechanisms developed by microorganisms. Then, we discuss the applications of these stress resistance mechanisms on the production of industrially important chemicals. Finally, we prospect the application of systems biology and synthetic biology in the identification of resistant mechanisms and improvement of metabolic robustness of microorganisms in environmental stresses.
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Affiliation(s)
- Ningzi Guan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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48
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Overexpression of smORF YNR034W-A/EGO4 in Saccharomyces cerevisiae increases the fermentative efficiency of Agave tequilana Weber must. ACTA ACUST UNITED AC 2017; 44:63-74. [DOI: 10.1007/s10295-016-1871-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/09/2016] [Indexed: 10/20/2022]
Abstract
Abstract
Fermentative processes are widely used to produce food, beverages and biofuels. Saccharomyces cerevisiae is an efficient ethanol-producing microorganism. However, a concentration of high ethanol and other metabolites can affect yeast viability and decrease the ethanol yield. Many studies have focused on improving the fermentative efficiency, mostly through the genetic engineering of genes that have a direct impact on specific metabolic pathways. In the present study, we characterized a small open reading frame encoding a protein with an unknown function and biological role termed YNR034W-A. We analyzed the expression profile of the YNR034W-A gene during growth and glucose treatment, finding that it is expressed during the diauxic shift and stationary phase and is negatively regulated by glucose. We overexpressed the YNR034W-A gene in the BY4741 laboratory strain and a wild-type yeast strain (AR5) isolated during the Tequila fermentation process. Transformant derivatives of the AR5 strain showed an improved fermentative efficiency during fermentation of Agave tequilana Weber juice. We suggest that the improved fermentative efficiency is the result of a higher stress tolerance response in the YNR034W-A overexpressing transformant.
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49
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Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution. Appl Environ Microbiol 2016; 82:6736-6747. [PMID: 27613685 DOI: 10.1128/aem.01850-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/02/2016] [Indexed: 11/20/2022] Open
Abstract
Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. IMPORTANCE Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development.
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50
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Lv X, Wang F, Zhou P, Ye L, Xie W, Xu H, Yu H. Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae. Nat Commun 2016; 7:12851. [PMID: 27650330 PMCID: PMC5036000 DOI: 10.1038/ncomms12851] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
Microbial production of isoprene from renewable feedstock is a promising alternative to traditional petroleum-based processes. Currently, efforts to improve isoprenoid production in Saccharomyces cerevisiae mainly focus on cytoplasmic engineering, whereas comprehensive engineering of multiple subcellular compartments is rarely reported. Here, we propose dual metabolic engineering of cytoplasmic and mitochondrial acetyl-CoA utilization to boost isoprene synthesis in S. cerevisiae. This strategy increases isoprene production by 2.1-fold and 1.6-fold relative to the recombinant strains with solely mitochondrial or cytoplasmic engineering, respectively. By combining a modified reiterative recombination system for rapid pathway assembly, a two-phase culture process for dynamic metabolic regulation, and aerobic fed-batch fermentation for sufficient supply of acetyl-coA and carbon, we achieve 2527, mg l(-1) of isoprene, which is the highest ever reported in engineered eukaryotes. We propose this strategy as an efficient approach to enhancing isoprene production in yeast, which might open new possibilities for bioproduction of other value-added chemicals.
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Affiliation(s)
- Xiaomei Lv
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Fan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Wenping Xie
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Haoming Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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