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Stovicek V, Dato L, Almqvist H, Schöpping M, Chekina K, Pedersen LE, Koza A, Figueira D, Tjosås F, Ferreira BS, Forster J, Lidén G, Borodina I. Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:22. [PMID: 35219341 PMCID: PMC8882276 DOI: 10.1186/s13068-022-02121-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/12/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnological process. The aim of the present work was to develop a robust yeast strain able to convert xylose in SSL to carboxylic acids. RESULTS The industrial strain Ethanol Red of the yeast Saccharomyces cerevisiae was engineered for efficient utilization of xylose in a Eucalyptus globulus lignosulfonate stream at low pH using CRISPR/Cas genome editing and adaptive laboratory evolution. The engineered strain grew in synthetic medium with xylose as sole carbon source with maximum specific growth rate (µmax) of 0.28 1/h. Selected evolved strains utilized all carbon sources in the SSL at pH 3.5 and grew with µmax between 0.05 and 0.1 1/h depending on a nitrogen source supplement. Putative genetic determinants of the increased tolerance to the SSL were revealed by whole genome sequencing of the evolved strains. In particular, four top-candidate genes (SNG1, FIT3, FZF1 and CBP3) were identified along with other gene candidates with predicted important roles, based on the type and distribution of the mutations across different strains and especially the best performing ones. The developed strains were further engineered for production of dicarboxylic acids (succinic and malic acid) via overexpression of the reductive branch of the tricarboxylic acid cycle (TCA). The production strain produced 0.2 mol and 0.12 mol of malic acid and succinic acid, respectively, per mol of xylose present in the SSL. CONCLUSIONS The combined metabolic engineering and adaptive evolution approach provided a robust SSL-tolerant industrial strain that converts fermentable carbon content of the SSL feedstock into malic and succinic acids at low pH.in production yields reaching 0.1 mol and 0.065 mol per mol of total consumed carbon sources.. Moreover, our work suggests potential genetic background of the tolerance to the SSL stream pointing out potential gene targets for improving the tolerance to inhibitory industrial feedstocks.
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Affiliation(s)
- Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Laura Dato
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,River Stone Biotech ApS, Fruebjergvej 3, 2100, Copenhagen, Denmark
| | - Henrik Almqvist
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Marie Schöpping
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark.,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Ksenia Chekina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark
| | - Diogo Figueira
- Biotrend S.A., Biocant Park Núcleo 04, Lote 2, 3060-197, Cantanhede, Portugal
| | - Freddy Tjosås
- Borregaard ApS, Hjalmar Wessels vei 6, 1721, Sarpsborg, Norway
| | | | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.
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2
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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: 1.8] [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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3
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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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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5
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Fletcher E, Baetz K. Multi-Faceted Systems Biology Approaches Present a Cellular Landscape of Phenolic Compound Inhibition in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:539902. [PMID: 33154962 PMCID: PMC7591714 DOI: 10.3389/fbioe.2020.539902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023] Open
Abstract
Synthetic biology has played a major role in engineering microbial cell factories to convert plant biomass (lignocellulose) to fuels and bioproducts by fermentation. However, the final product yield is limited by inhibition of microbial growth and fermentation by toxic phenolic compounds generated during lignocellulosic pre-treatment and hydrolysis. Advances in the development of systems biology technologies (genomics, transcriptomics, proteomics, metabolomics) have rapidly resulted in large datasets which are necessary to obtain a holistic understanding of complex biological processes underlying phenolic compound toxicity. Here, we review and compare different systems biology tools that have been utilized to identify molecular mechanisms that modulate phenolic compound toxicity in Saccharomyces cerevisiae. By focusing on and comparing functional genomics and transcriptomics approaches we identify common mechanisms potentially underlying phenolic toxicity. Additionally, we discuss possible ways by which integration of data obtained across multiple unbiased approaches can result in new avenues to develop yeast strains with a significant improvement in tolerance to phenolic fermentation inhibitors.
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Affiliation(s)
- Eugene Fletcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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6
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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: 6] [Impact Index Per Article: 1.2] [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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7
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Wu L, Wang M, Zha G, Zhou J, Yu Y, Lu H. Improving the expression of a heterologous protein by genome shuffling in Kluyveromyces marxianus. J Biotechnol 2020; 320:11-16. [DOI: 10.1016/j.jbiotec.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 04/21/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
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8
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A robust flow cytometry-based biomass monitoring tool enables rapid at-line characterization of S. cerevisiae physiology during continuous bioprocessing of spent sulfite liquor. Anal Bioanal Chem 2020; 412:2137-2149. [PMID: 32034454 PMCID: PMC7072058 DOI: 10.1007/s00216-020-02423-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 01/20/2023]
Abstract
Assessment of viable biomass is challenging in bioprocesses involving complex media with distinct biomass and media particle populations. Biomass monitoring in these circumstances usually requires elaborate offline methods or sophisticated inline sensors. Reliable monitoring tools in an at-line capacity represent a promising alternative but are still scarce to date. In this study, a flow cytometry-based method for biomass monitoring in spent sulfite liquor medium as feedstock for second generation bioethanol production with yeast was developed. The method is capable of (i) yeast cell quantification against medium background, (ii) determination of yeast viability, and (iii) assessment of yeast physiology though morphological analysis of the budding division process. Thus, enhanced insight into physiology and morphology is provided which is not accessible through common online and offline biomass monitoring methods. To demonstrate the capabilities of this method, firstly, a continuous ethanol fermentation process of Saccharomyces cerevisiae with filtered and unfiltered spent sulfite liquor media was analyzed. Subsequently, at-line process monitoring of viability in a retentostat cultivation was conducted. The obtained information was used for a simple control based on addition of essential nutrients in relation to viability. Thereby, inter-dependencies between nutrient supply, physiology, and specific ethanol productivity that are essential for process design could be illuminated. Graphical abstract ![]()
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9
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Second Generation Bioethanol Production: On the Use of Pulp and Paper Industry Wastes as Feedstock. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation5010004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Due to the health and environment impacts of fossil fuels utilization, biofuels have been investigated as a potential alternative renewable source of energy. Bioethanol is currently the most produced biofuel, mainly of first generation, resulting in food-fuel competition. Second generation bioethanol is produced from lignocellulosic biomass, but a costly and difficult pretreatment is required. The pulp and paper industry has the biggest income of biomass for non-food-chain production, and, simultaneously generates a high amount of residues. According to the circular economy model, these residues, rich in monosaccharides, or even in polysaccharides besides lignin, can be utilized as a proper feedstock for second generation bioethanol production. Biorefineries can be integrated in the existing pulp and paper industrial plants by exploiting the high level of technology and also the infrastructures and logistics that are required to fractionate and handle woody biomass. This would contribute to the diversification of products and the increase of profitability of pulp and paper industry with additional environmental benefits. This work reviews the literature supporting the feasibility of producing ethanol from Kraft pulp, spent sulfite liquor, and pulp and paper sludge, presenting and discussing the practical attempt of biorefineries implementation in pulp and paper mills for bioethanol production.
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10
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Biot-Pelletier D, Pinel D, Larue K, Martin VJJ. Determinants of selection in yeast evolved by genome shuffling. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:282. [PMID: 30356826 PMCID: PMC6190656 DOI: 10.1186/s13068-018-1283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Genome shuffling (GS) is a widely adopted methodology for the evolutionary engineering of desirable traits in industrially relevant microorganisms. We have previously used genome shuffling to generate a strain of Saccharomyces cerevisiae that is tolerant to the growth inhibitors found in a lignocellulosic hydrolysate. In this study, we expand on previous work by performing a population-wide genomic survey of our genome shuffling experiment and dissecting the molecular determinants of the evolved phenotype. RESULTS Whole population whole-genome sequencing was used to survey mutations selected during the experiment and extract allele frequency time series. Using growth curve assays on single point mutants and backcrossed derivatives, we explored the genetic architecture of the selected phenotype and detected examples of epistasis. Our results reveal cohorts of strongly correlated mutations, suggesting prevalent genetic hitchhiking and the presence of pre-existing founder mutations. From the patterns of apparent selection and the results of direct phenotypic assays, our results identify key driver mutations and deleterious hitchhikers. CONCLUSIONS We use these data to propose a model of inhibitor tolerance in our GS mutants. Our results also suggest a role for compensatory evolution and epistasis in our genome shuffling experiment and illustrate the impact of historical contingency on the outcomes of evolutionary engineering.
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Affiliation(s)
- Damien Biot-Pelletier
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Lallemand Inc., Montréal, QC H4P 2R2 Canada
| | - Dominic Pinel
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Amyris Inc, Emeryville, CA 94608 USA
| | - Kane Larue
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
- Present Address: Charles River Laboratories, Senneville, QC H9X 3R3 Canada
| | - Vincent J. J. Martin
- Department of Biology, Centre for Structural and Functional Genomics, Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
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11
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Su YK, Willis LB, Rehmann L, Smith DR, Jeffries TW. Spathaspora passalidarum selected for resistance to AFEX hydrolysate shows decreased cell yield. FEMS Yeast Res 2018; 18:5042277. [DOI: 10.1093/femsyr/foy011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 06/20/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yi-Kai Su
- Department of Biological Systems Engineering, University of Wisconsin, Madison, WI 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53705, USA
- Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 3K, Canada
| | - Laura B Willis
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53705, USA
- Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
- Department of Bacteriology, University of Madison, WI, 53705, USA
| | - Lars Rehmann
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 3K, Canada
| | - David R Smith
- Department of Biology, University of Western Ontario, London, ON, N6A 3K7, Canada
| | - Thomas W Jeffries
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53705, USA
- Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
- Department of Bacteriology, University of Madison, WI, 53705, USA
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12
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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: 124] [Impact Index Per Article: 15.5] [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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13
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Maurer MJ, Sutardja L, Pinel D, Bauer S, Muehlbauer AL, Ames TD, Skerker JM, Arkin AP. Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait. ACS Synth Biol 2017; 6:566-581. [PMID: 27936603 DOI: 10.1021/acssynbio.6b00264] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Engineering complex phenotypes for industrial and synthetic biology applications is difficult and often confounds rational design. Bioethanol production from lignocellulosic feedstocks is a complex trait that requires multiple host systems to utilize, detoxify, and metabolize a mixture of sugars and inhibitors present in plant hydrolysates. Here, we demonstrate an integrated approach to discovering and optimizing host factors that impact fitness of Saccharomyces cerevisiae during fermentation of a Miscanthus x giganteus plant hydrolysate. We first used high-resolution Quantitative Trait Loci (QTL) mapping and systematic bulk Reciprocal Hemizygosity Analysis (bRHA) to discover 17 loci that differentiate hydrolysate tolerance between an industrially related (JAY291) and a laboratory (S288C) strain. We then used this data to identify a subset of favorable allelic loci that were most amenable for strain engineering. Guided by this "genetic blueprint", and using a dual-guide Cas9-based method to efficiently perform multikilobase locus replacements, we engineered an S288C-derived strain with superior hydrolysate tolerance than JAY291. Our methods should be generalizable to engineering any complex trait in S. cerevisiae, as well as other organisms.
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Affiliation(s)
- Matthew J. Maurer
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lawrence Sutardja
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Dominic Pinel
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stefan Bauer
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Amanda L. Muehlbauer
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tyler D. Ames
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jeffrey M. Skerker
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Adam P. Arkin
- Energy Biosciences Institute and ‡Department of
Bioengineering, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, and ∥Environmental
Genomics and Systems
Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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14
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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: 168] [Impact Index Per Article: 18.7] [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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15
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Optimization of genome shuffling for high-yield production of the antitumor deacetylmycoepoxydiene in an endophytic fungus of mangrove plants. Appl Microbiol Biotechnol 2016; 100:7491-8. [DOI: 10.1007/s00253-016-7457-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/05/2016] [Indexed: 11/26/2022]
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16
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Karas BJ, Suzuki Y, Weyman PD. Strategies for cloning and manipulating natural and synthetic chromosomes. Chromosome Res 2015; 23:57-68. [PMID: 25596826 DOI: 10.1007/s10577-014-9455-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Advances in synthetic biology methods to assemble and edit DNA are enabling genome engineering at a previously impracticable scale and scope. The synthesis of the Mycoplasma mycoides genome followed by its transplantation to convert a related cell into M. mycoides has transformed strain engineering. This approach exemplifies the combination of newly emerging chromosome-scale genome editing strategies that can be defined in three main steps: (1) chromosome acquisition into a microbial engineering platform, (2) alteration and improvement of the acquired chromosome, and (3) installation of the modified chromosome into the original or alternative organism. In this review, we outline recent progress in methods for acquiring chromosomes and chromosome-scale DNA molecules in the workhorse organisms Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. We present overviews of important genetic strategies and tools for each of the three organisms, point out their respective strengths and weaknesses, and highlight how the host systems can be used in combination to facilitate chromosome assembly or engineering. Finally, we highlight efforts for the installation of the cloned/altered chromosomes or fragments into the target organism and present remaining challenges in expanding this powerful experimental approach to a wider range of target organisms.
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Affiliation(s)
- Bogumil J Karas
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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17
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Caspeta L, Castillo T, Nielsen J. Modifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes. Front Bioeng Biotechnol 2015; 3:184. [PMID: 26618154 PMCID: PMC4641163 DOI: 10.3389/fbioe.2015.00184] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
Saccharomyces cerevisiae strains having a broad range of substrate utilization, rapid substrate consumption, and conversion to ethanol, as well as good tolerance to inhibitory conditions are ideal for cost-competitive ethanol production from lignocellulose. A major drawback to directly design S. cerevisiae tolerance to inhibitory conditions of lignocellulosic ethanol production processes is the lack of knowledge about basic aspects of its cellular signaling network in response to stress. Here, we highlight the inhibitory conditions found in ethanol production processes, the targeted cellular functions, the key contributions of integrated -omics analysis to reveal cellular stress responses according to these inhibitors, and current status on design-based engineering of tolerant and efficient S. cerevisiae strains for ethanol production from lignocellulose.
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Affiliation(s)
- Luis Caspeta
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos , Cuernavaca , Mexico
| | - Tania Castillo
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos , Cuernavaca , Mexico
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology , Gothenburg , Sweden ; Department of Biology and Biological Engineering, Chalmers University of Technology , Gothenburg , Sweden ; Novo Nordisk Foundation Center for Biosustainability , Hørsholm , Denmark
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18
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Determinants of tolerance to inhibitors in hardwood spent sulfite liquor in genome shuffled Pachysolen tannophilus strains. Antonie van Leeuwenhoek 2015; 108:811-34. [PMID: 26231071 DOI: 10.1007/s10482-015-0537-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Genome shuffling was used to obtain Pachysolen tannophilus mutants with improved tolerance to inhibitors in hardwood spent sulfite liquor (HW SSL). Genome shuffled strains (GHW301, GHW302 and GHW303) grew at higher concentrations of HW SSL (80 % v/v) compared to the HW SSL UV mutant (70 % v/v) and the wild-type (WT) strain (50 % v/v). In defined media containing acetic acid (0.70-0.90 % w/v), GHW301, GHW302 and GHW303 exhibited a shorter lag compared to the acetic acid UV mutant, while the WT did not grow. Genome shuffled strains produced more ethanol than the WT at higher concentrations of HW SSL and an aspen hydrolysate. To identify the genetic basis of inhibitor tolerance, whole genome sequencing was carried out on GHW301, GHW302 and GHW303 and compared to the WT strain. Sixty single nucleotide variations were identified that were common to all three genome shuffled strains. Of these, 40 were in gene sequences and 20 were within 5 bp-1 kb either up or downstream of protein encoding genes. Based on the mutated gene products, mutations were grouped into functional categories and affected a variety of cellular functions, demonstrating the complexity of inhibitor tolerance in yeast. Sequence analysis of UV mutants (UAA302 and UHW303) from which GHW301, GHW302 and GHW303 were derived, confirmed the success of our cross-mating based genome shuffling strategy. Whole-genome sequencing analysis allowed identification of potential gene targets for tolerance to inhibitors in lignocellulosic hydrolysates.
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19
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Snoek T, Picca Nicolino M, Van den Bremt S, Mertens S, Saels V, Verplaetse A, Steensels J, Verstrepen KJ. Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:32. [PMID: 25759747 PMCID: PMC4354739 DOI: 10.1186/s13068-015-0216-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/29/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND During the final phases of bioethanol fermentation, yeast cells face high ethanol concentrations. This stress results in slower or arrested fermentations and limits ethanol production. Novel Saccharomyces cerevisiae strains with superior ethanol tolerance may therefore allow increased yield and efficiency. Genome shuffling has emerged as a powerful approach to rapidly enhance complex traits including ethanol tolerance, yet previous efforts have mostly relied on a mutagenized pool of a single strain, which can potentially limit the effectiveness. Here, we explore novel robot-assisted strategies that allow to shuffle the genomes of multiple parental yeasts on an unprecedented scale. RESULTS Screening of 318 different yeasts for ethanol accumulation, sporulation efficiency, and genetic relatedness yielded eight heterothallic strains that served as parents for genome shuffling. In a first approach, the parental strains were subjected to multiple consecutive rounds of random genome shuffling with different selection methods, yielding several hybrids that showed increased ethanol tolerance. Interestingly, on average, hybrids from the first generation (F1) showed higher ethanol production than hybrids from the third generation (F3). In a second approach, we applied several successive rounds of robot-assisted targeted genome shuffling, yielding more than 3,000 targeted crosses. Hybrids selected for ethanol tolerance showed increased ethanol tolerance and production as compared to unselected hybrids, and F1 hybrids were on average superior to F3 hybrids. In total, 135 individual F1 and F3 hybrids were tested in small-scale very high gravity fermentations. Eight hybrids demonstrated superior fermentation performance over the commercial biofuel strain Ethanol Red, showing a 2 to 7% increase in maximal ethanol accumulation. In an 8-l pilot-scale test, the best-performing hybrid fermented medium containing 32% (w/v) glucose to dryness, yielding 18.7% (v/v) ethanol with a productivity of 0.90 g ethanol/l/h and a yield of 0.45 g ethanol/g glucose. CONCLUSIONS We report the use of several different large-scale genome shuffling strategies to obtain novel hybrids with increased ethanol tolerance and fermentation capacity. Several of the novel hybrids show best-parent heterosis and outperform the commonly used bioethanol strain Ethanol Red, making them interesting candidate strains for industrial production.
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Affiliation(s)
- Tim Snoek
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Martina Picca Nicolino
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Stefanie Van den Bremt
- />Laboratory of Enzyme, Fermentation and Brewing Technology, KU Leuven technologiecampus Ghent, Gebroeders De Smetstraat 1, 9000 Ghent, Belgium
| | - Stijn Mertens
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Veerle Saels
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Alex Verplaetse
- />Laboratory of Enzyme, Fermentation and Brewing Technology, KU Leuven technologiecampus Ghent, Gebroeders De Smetstraat 1, 9000 Ghent, Belgium
| | - Jan Steensels
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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20
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Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, Richter RA, Vashee S, Chuang RY, Winzeler EA, Hutchison CA, Gibson DG, Smith HO, Glass JI, Venter JC. Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling. Genome Res 2015; 25:435-44. [PMID: 25654978 PMCID: PMC4352883 DOI: 10.1101/gr.182477.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these organisms by identifying individually deletable regions using transposon mutagenesis and progressively clustering deleted genomic segments using meiotic recombination between the bacterial genomes harbored in yeast. Mycoplasmal genomes subjected to this process and transplanted into recipient cells yielded two mycoplasma strains. The first simultaneously lacked eight singly deletable regions of the genome, representing a total of 91 genes and ∼10% of the original genome. The second strain lacked seven of the eight regions, representing 84 genes. Growth assay data revealed an absence of genetic interactions among the 91 genes under tested conditions. Despite predicted effects of the deletions on sugar metabolism and the proteome, growth rates were unaffected by the gene deletions in the seven-deletion strain. These results support the feasibility of using single-gene disruption data to design and construct viable genomes lacking multiple genes, paving the way toward genome minimization. The progressive clustering method is expected to be effective for the reorganization of any mega-sized DNA molecules cloned in yeast, facilitating the construction of designer genomes in microbes as well as genomic fragments for genetic engineering of higher eukaryotes.
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Affiliation(s)
- Yo Suzuki
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA;
| | - Nacyra Assad-Garcia
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Maxim Kostylev
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Vladimir N Noskov
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Kim S Wise
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, USA
| | - Bogumil J Karas
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Jason Stam
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Michael G Montague
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Timothy J Hanly
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Nico J Enriquez
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Adi Ramon
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Gregory M Goldgof
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; University of California, San Diego, School of Medicine, La Jolla, California 92093, USA
| | - R Alexander Richter
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Sanjay Vashee
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Ray-Yuan Chuang
- Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - Elizabeth A Winzeler
- University of California, San Diego, School of Medicine, La Jolla, California 92093, USA
| | - Clyde A Hutchison
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Daniel G Gibson
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Hamilton O Smith
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - John I Glass
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
| | - J Craig Venter
- Synthetic Biology Group, J. Craig Venter Institute, La Jolla, California 92037, USA; Synthetic Biology Group, J. Craig Venter Institute, Rockville, Maryland 20850, USA
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21
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Pinel D, Colatriano D, Jiang H, Lee H, Martin VJJ. Deconstructing the genetic basis of spent sulphite liquor tolerance using deep sequencing of genome-shuffled yeast. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:53. [PMID: 25866561 PMCID: PMC4393574 DOI: 10.1186/s13068-015-0241-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/17/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Identifying the genetic basis of complex microbial phenotypes is currently a major barrier to our understanding of multigenic traits and our ability to rationally design biocatalysts with highly specific attributes for the biotechnology industry. Here, we demonstrate that strain evolution by meiotic recombination-based genome shuffling coupled with deep sequencing can be used to deconstruct complex phenotypes and explore the nature of multigenic traits, while providing concrete targets for strain development. RESULTS We determined genomic variations found within Saccharomyces cerevisiae previously evolved in our laboratory by genome shuffling for tolerance to spent sulphite liquor. The representation of these variations was backtracked through parental mutant pools and cross-referenced with RNA-seq gene expression analysis to elucidate the importance of single mutations and key biological processes that play a role in our trait of interest. Our findings pinpoint novel genes and biological determinants of lignocellulosic hydrolysate inhibitor tolerance in yeast. These include the following: protein homeostasis constituents, including Ubp7p and Art5p, related to ubiquitin-mediated proteolysis; stress response transcriptional repressor, Nrg1p; and NADPH-dependent glutamate dehydrogenase, Gdh1p. Reverse engineering a prominent mutation in ubiquitin-specific protease gene UBP7 in a laboratory S. cerevisiae strain effectively increased spent sulphite liquor tolerance. CONCLUSIONS This study advances understanding of yeast tolerance mechanisms to inhibitory substrates and biocatalyst design for a biomass-to-biofuel/biochemical industry, while providing insights into the process of mutation accumulation that occurs during genome shuffling.
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Affiliation(s)
- Dominic Pinel
- />Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6 Canada
- />Current address: Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA 94704 USA
| | - David Colatriano
- />Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6 Canada
| | - Heng Jiang
- />Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6 Canada
- />Current address: Crabtree Nutrition Laboratories, McGill University Health Center, Montreal, Quebec H3A 1A1 Canada
| | - Hung Lee
- />School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G 2 W1 Canada
| | - Vincent JJ Martin
- />Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6 Canada
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22
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Ding S, Zhang Y, Zhang J, Zeng W, Yang Y, Guan J, Pan L, Li W. Enhanced deacidification activity in Schizosaccharomyces pombe by genome shuffling. Yeast 2014; 32:317-25. [PMID: 25377082 DOI: 10.1002/yea.3053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 11/07/2022] Open
Abstract
A problem frequently occurring in making some kinds of wines, particularly Vitis quinquangularis Rehd wine, is the presence of malic acid at high concentrations, which is detrimental to the quality of wines. Thus, there is a need of the ways for effectively reducing the malic acid levels in wine. This study aimed to generate shuffled fusants of Schizosaccharomyces pombe with enhanced deacidification activity for reducing the excessive malic acid content in wine. Sz. pombe CGMCC 2.1628 was used as the original strain. The starting mutant population was generated by UV treatment. The mutants with higher deacidification activity were selected and subjected to recursive protoplast fusion. The resulting fusants were screened by using the indicator of malic acid concentration of fermentation supernatants on 96-well microtitre plates, measured with bromocresol green. After three rounds of genome shuffling, the best-performing fusant, named GS3-1, was obtained. Its deacidification activity (consumed 4.78 g/l malic acid within 10 days) was increased by 225.2% as compared to that of original strain. In the Vitis quinquangularis Rehd wine fermentation test, GS3-1 consumed 4.0 g/l malic acid during the whole cycle of fermentation, providing up to 185.7% improvement in malic acid consumption compared with that of the original strain. This study shows that GS3-1 has great potential for improving the quality of Vitis quinquangularis Rehd wine.
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Affiliation(s)
- Su Ding
- Xingjian College of Science and Liberal Arts, Guangxi University, People's Republic of China; Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, People's Republic of China
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23
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Inoue H, Hashimoto S, Matsushika A, Watanabe S, Sawayama S. Breeding of a xylose-fermenting hybrid strain by mating genetically engineered haploid strains derived from industrial Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2014; 41:1773-81. [PMID: 25355632 DOI: 10.1007/s10295-014-1531-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 10/18/2014] [Indexed: 01/04/2023]
Abstract
The industrial Saccharomyces cerevisiae IR-2 is a promising host strain to genetically engineer xylose-utilizing yeasts for ethanol fermentation from lignocellulosic hydrolysates. Two IR-2-based haploid strains were selected based upon the rate of xylulose fermentation, and hybrids were obtained by mating recombinant haploid strains harboring heterogeneous xylose dehydrogenase (XDH) (wild-type NAD(+)-dependent XDH or engineered NADP(+)-dependent XDH, ARSdR), xylose reductase (XR) and xylulose kinase (XK) genes. ARSdR in the hybrids selected for growth rates on yeast extract-peptone-dextrose (YPD) agar and YP-xylose agar plates typically had a higher activity than NAD(+)-dependent XDH. Furthermore, the xylose-fermenting performance of the hybrid strain SE12 with the same level of heterogeneous XDH activity was similar to that of a recombinant strain of IR-2 harboring a single set of genes, XR/ARSdR/XK. These results suggest not only that the recombinant haploid strains retain the appropriate genetic background of IR-2 for ethanol production from xylose but also that ARSdR is preferable for xylose fermentation.
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Affiliation(s)
- Hiroyuki Inoue
- Biomass Refinery Research Center (BRRC), National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan,
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24
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Mukherjee V, Steensels J, Lievens B, Van de Voorde I, Verplaetse A, Aerts G, Willems KA, Thevelein JM, Verstrepen KJ, Ruyters S. Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production. Appl Microbiol Biotechnol 2014; 98:9483-98. [PMID: 25267160 DOI: 10.1007/s00253-014-6090-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 01/17/2023]
Abstract
Saccharomyces cerevisiae is the organism of choice for many food and beverage fermentations because it thrives in high-sugar and high-ethanol conditions. However, the conditions encountered in bioethanol fermentation pose specific challenges, including extremely high sugar and ethanol concentrations, high temperature, and the presence of specific toxic compounds. It is generally considered that exploring the natural biodiversity of Saccharomyces strains may be an interesting route to find superior bioethanol strains and may also improve our understanding of the challenges faced by yeast cells during bioethanol fermentation. In this study, we phenotypically evaluated a large collection of diverse Saccharomyces strains on six selective traits relevant for bioethanol production with increasing stress intensity. Our results demonstrate a remarkably large phenotypic diversity among different Saccharomyces species and among S. cerevisiae strains from different origins. Currently applied bioethanol strains showed a high tolerance to many of these relevant traits, but several other natural and industrial S. cerevisiae strains outcompeted the bioethanol strains for specific traits. These multitolerant strains performed well in fermentation experiments mimicking industrial bioethanol production. Together, our results illustrate the potential of phenotyping the natural biodiversity of yeasts to find superior industrial strains that may be used in bioethanol production or can be used as a basis for further strain improvement through genetic engineering, experimental evolution, or breeding. Additionally, our study provides a basis for new insights into the relationships between tolerance to different stressors.
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Affiliation(s)
- Vaskar Mukherjee
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), Campus De Nayer, KU Leuven, Fortsesteenweg 30A, B-2860, Sint-Katelijne-Waver, Belgium
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25
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Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
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Sandström AG, Almqvist H, Portugal-Nunes D, Neves D, Lidén G, Gorwa-Grauslund MF. Saccharomyces cerevisiae: a potential host for carboxylic acid production from lignocellulosic feedstock? Appl Microbiol Biotechnol 2014; 98:7299-318. [DOI: 10.1007/s00253-014-5866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
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Wang H, Ji B, Ren H, Meng C. The relationship between lysine 4 on histone H3 methylation levels of alcohol tolerance genes and changes of ethanol tolerance in Saccharomyces cerevisiae. Microb Biotechnol 2014; 7:307-14. [PMID: 24779776 PMCID: PMC4241724 DOI: 10.1111/1751-7915.12121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/31/2013] [Accepted: 01/22/2013] [Indexed: 01/09/2023] Open
Abstract
We evaluated whether epigenetic changes contributed to improve ethanol tolerance in mutant
populations of Saccharomyces cerevisiae (S. cerevisiae). Two
ethanol-tolerant variants of S. cerevisiae were used to evaluate the genetic
stability in the process of stress-free passage cultures. We found that acquired ethanol tolerance
was lost and transcription level of some genes (HSP104, PRO1,
TPS1, and SOD1) closely related to ethanol tolerance decreased
significantly after the 10th passage in ethanol-free medium. Tri-methylation of lysine 4 on histone
H3 (H3K4) enhanced at the promoter of HSP104, PRO1,
TPS1 and SOD1 in ethanol-tolerant variants of S.
cerevisiae was also diminished after tenth passage in stress-free cultures. The ethanol
tolerance was reacquired when exogenous SOD1 transferred in some tolerance-lost
strains. This showed that H3K4 methylation is involved in phenotypic variation with regard to
ethanol tolerance with respect to classic breeding methods used in yeast.
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Affiliation(s)
- Hang Wang
- Department of Bioengineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, Fujian, China
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Koppram R, Olsson L. Combined substrate, enzyme and yeast feed in simultaneous saccharification and fermentation allow bioethanol production from pretreated spruce biomass at high solids loadings. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:54. [PMID: 24713027 PMCID: PMC4234936 DOI: 10.1186/1754-6834-7-54] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/13/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Economically feasible cellulosic ethanol production requires that the process can be operated at high solid loadings, which currently imparts technical challenges including inefficient mixing leading to heat and mass transfer limitations and high concentrations of inhibitory compounds hindering microbial activity during simultaneous saccharification and fermentation (SSF) process. Consequently, there is a need to develop cost effective processes overcoming the challenges when working at high solid loadings. RESULTS In this study we have modified the yeast cultivation procedure and designed a SSF process to address some of the challenges at high water insoluble solids (WIS) content. The slurry of non-detoxified pretreated spruce when used in a batch SSF at 19% (w/w) WIS was found to be inhibitory to Saccharomyces cerevisiae Thermosacc that produced 2 g l-1 of ethanol. In order to reduce the inhibitory effect, the non-washed solid fraction containing reduced amount of inhibitors compared to the slurry was used in the SSF. Further, the cells were cultivated in the liquid fraction of pretreated spruce in a continuous culture wherein the outflow of cell suspension was used as cell feed to the SSF reactor in order to maintain the metabolic state of the cell. Enhanced cell viability was observed with cell, enzyme and substrate feed in a SSF producing 40 g l-1 ethanol after 96 h corresponding to 53% of theoretical yield based on available hexose sugars compared to 28 g l-1 ethanol in SSF with enzyme and substrate feed but no cell feed resulting in 37% of theoretical yield at a high solids loading of 20% (w/w) WIS content. The fed-batch SSF also significantly eased the mixing, which is usually challenging in batch SSF at high solids loading. CONCLUSIONS A simple modification of the cell cultivation procedure together with a combination of yeast, enzyme and substrate feed in a fed-batch SSF process, made it possible to operate at high solids loadings in a conventional bioreactor. The proposed process strategy significantly increased the yeast cell viability and overall ethanol yield. It was also possible to obtain 4% (w/v) ethanol concentration, which is a minimum requirement for an economical distillation process.
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Affiliation(s)
- Rakesh Koppram
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg SE-412 96, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg SE-412 96, Sweden
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Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 2014; 98:3877-87. [PMID: 24595425 DOI: 10.1007/s00253-014-5616-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/28/2023]
Abstract
An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.
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Zheng D, Zhang K, Gao K, Liu Z, Zhang X, Li O, Sun J, Zhang X, Du F, Sun P, Qu A, Wu X. Construction of novel Saccharomyces cerevisiae strains for bioethanol active dry yeast (ADY) production. PLoS One 2013; 8:e85022. [PMID: 24376860 PMCID: PMC3871550 DOI: 10.1371/journal.pone.0085022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/20/2013] [Indexed: 11/18/2022] Open
Abstract
The application of active dry yeast (ADY) in bioethanol production simplifies operation processes and reduces the risk of bacterial contamination. In the present study, we constructed a novel ADY strain with improved stress tolerance and ethanol fermentation performances under stressful conditions. The industrial Saccharomyces cerevisiae strain ZTW1 showed excellent properties and thus subjected to a modified whole-genome shuffling (WGS) process to improve its ethanol titer, proliferation capability, and multiple stress tolerance for ADY production. The best-performing mutant, Z3-86, was obtained after three rounds of WGS, producing 4.4% more ethanol and retaining 2.15-fold higher viability than ZTW1 after drying. Proteomics and physiological analyses indicated that the altered expression patterns of genes involved in protein metabolism, plasma membrane composition, trehalose metabolism, and oxidative responses contribute to the trait improvement of Z3-86. This work not only successfully developed a novel S. cerevisiae mutant for application in commercial bioethanol production, but also enriched the current understanding of how WGS improves the complex traits of microbes.
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Affiliation(s)
- Daoqiong Zheng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ke Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Kehui Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zewei Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xing Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Ou Li
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jianguo Sun
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xiaoyang Zhang
- State Key Laboratory of Motor Vehicle Biofuel Technology (Tianguan Group Co., Ltd.), Nanyang, Henan Province, China
| | - Fengguang Du
- State Key Laboratory of Motor Vehicle Biofuel Technology (Tianguan Group Co., Ltd.), Nanyang, Henan Province, China
| | - Peiyong Sun
- State Key Laboratory of Motor Vehicle Biofuel Technology (Tianguan Group Co., Ltd.), Nanyang, Henan Province, China
| | - Aimin Qu
- State Key Laboratory of Motor Vehicle Biofuel Technology (Tianguan Group Co., Ltd.), Nanyang, Henan Province, China
| | - Xuechang Wu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- * E-mail:
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Zheng DQ, Chen J, Zhang K, Gao KH, Li O, Wang PM, Zhang XY, Du FG, Sun PY, Qu AM, Wu S, Wu XC. Genomic structural variations contribute to trait improvement during whole-genome shuffling of yeast. Appl Microbiol Biotechnol 2013; 98:3059-70. [PMID: 24346281 DOI: 10.1007/s00253-013-5423-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 11/24/2022]
Abstract
Whole-genome shuffling (WGS) is a powerful technology of improving the complex traits of many microorganisms. However, the molecular mechanisms underlying the altered phenotypes in isolates were less clarified. Isolates with significantly enhanced stress tolerance and ethanol titer under very-high-gravity conditions were obtained after WGS of the bioethanol Saccharomyces cerevisiae strain ZTW1. Karyotype analysis and RT-qPCR showed that chromosomal rearrangement occurred frequently in genome shuffling. Thus, the phenotypic effects of genomic structural variations were determined in this study. RNA-Seq and physiological analyses revealed the diverse transcription pattern and physiological status of the isolate S3-110 and ZTW1. Our observations suggest that the improved stress tolerance of S3-110 can be largely attributed to the copy number variations in large DNA regions, which would adjust the ploidy of yeast cells and expression levels of certain genes involved in stress response. Overall, this work not only constructed shuffled S. cerevisiae strains that have potential industrial applications but also provided novel insights into the molecular mechanisms of WGS and enhanced our knowledge on this useful breeding strategy.
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Affiliation(s)
- Dao-Qiong Zheng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
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Streptomycin resistance-aided genome shuffling to improve doramectin productivity of Streptomyces avermitilis NEAU1069. ACTA ACUST UNITED AC 2013; 40:877-89. [DOI: 10.1007/s10295-013-1280-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/25/2013] [Indexed: 11/30/2022]
Abstract
Abstract
Genome shuffling is an efficient approach for the rapid engineering of microbial strains with desirable industrial phenotypes. In this study, a strategy of incorporating streptomycin resistance screening into genome shuffling (GS-SR) was applied for rapid improvement of doramectin production by Streptomyces avermitilis NEAU1069. The starting mutant population was generated through treatment of the spores with N-methyl-N’-nitro-N-nitrosoguanidine and ultraviolet (UV) irradiation, respectively, and five mutants with higher productivity of doramectin were selected as starting strains for GS-SR. Finally, a genetically stable strain F4-137 was obtained and characterized to be able to yield 992 ± 4.4 mg/l doramectin in a shake flask, which was 7.3-fold and 11.2-fold higher than that of the starting strain UV-45 and initial strain NEAU1069, respectively. The doramectin yield by F4-137 in a 50-l fermentor reached 930.3 ± 3.8 mg/l. Furthermore, the factors associated with the improved doramectin yield were investigated and the results suggested that mutations in ribosomal protein S12 and the enhanced production of cyclohexanecarboxylic coenzyme A may contribute to the improved performance of the shuffled strains. The random amplified polymorphic DNA analysis showed a genetic diversity among the shuffled strains, which confirmed the occurrence of genome shuffling. In conclusion, our results demonstrated that GS-SR is a powerful method for enhancing the production of secondary metabolites in Streptomyces.
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Bajwa PK, Ho CY, Chan CK, Martin VJJ, Trevors JT, Lee H. Transcriptional profiling of Saccharomyces cerevisiae T2 cells upon exposure to hardwood spent sulphite liquor: comparison to acetic acid, furfural and hydroxymethylfurfural. Antonie van Leeuwenhoek 2013; 103:1281-95. [DOI: 10.1007/s10482-013-9909-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/20/2013] [Indexed: 10/27/2022]
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Kim SR, Lee KS, Kong II, Lesmana A, Lee WH, Seo JH, Kweon DH, Jin YS. Construction of an efficient xylose-fermenting diploid Saccharomyces cerevisiae strain through mating of two engineered haploid strains capable of xylose assimilation. J Biotechnol 2013; 164:105-11. [PMID: 23376240 DOI: 10.1016/j.jbiotec.2012.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/07/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Saccharomyces cerevisiae can be engineered for xylose fermentation through introduction of wild type or mutant genes (XYL1/XYL1 (R276H), XYL2, and XYL3) coding for xylose metabolic enzymes from Scheffersomyces stipitis. The resulting engineered strains, however, often yielded undesirable phenotypes such as slow xylose assimilation and xylitol accumulation. In this study, we performed the mating of two engineered strains that exhibit suboptimal xylose-fermenting phenotypes in order to develop an improved xylose-fermenting diploid strain. Specifically, we obtained two engineered haploid strains (YSX3 and SX3). The YSX3 strain consumed xylose rapidly and produced a lot of xylitol. On the contrary, the SX3 strain consumed xylose slowly with little xylitol production. After converting the mating type of SX3 from alpha to a, the resulting strain (SX3-2) was mated with YSX3 to construct a heterozygous diploid strain (KSM). The KSM strain assimilated xylose (0.25gxyloseh(-1)gcells(-1)) as fast as YSX3 and accumulated a small amount of xylitol (0.03ggxylose(-1)) as low as SX3, resulting in an improved ethanol yield (0.27ggxylose(-1)). We found that the improvement in xylose fermentation by the KSM strain was not because of heterozygosity or genome duplication but because of the complementation of the two xylose-metabolic pathways. This result suggested that mating of suboptimal haploid strains is a promising strategy to develop engineered yeast strains with improved xylose fermenting capability.
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Affiliation(s)
- Soo Rin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Kumar M, Pratap Singh M, Kumar Tuli D. Genome Shuffling of <i>Pseudomonas</i> Sp. Ioca11 for Improving Degradation of Polycyclic Aromatic Hydrocarbons. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/aim.2012.21004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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