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Cautereels C, Smets J, Bircham P, De Ruysscher D, Zimmermann A, De Rijk P, Steensels J, Gorkovskiy A, Masschelein J, Verstrepen KJ. Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast. Nat Commun 2024; 15:1112. [PMID: 38326309 PMCID: PMC10850122 DOI: 10.1038/s41467-024-44997-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter Bircham
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Dries De Ruysscher
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, 2610, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Joleen Masschelein
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium.
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2
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Cautereels C, Smets J, De Saeger J, Cool L, Zhu Y, Zimmermann A, Steensels J, Gorkovskiy A, Jacobs TB, Verstrepen KJ. Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts. Nat Commun 2024; 15:1113. [PMID: 38326330 PMCID: PMC10850332 DOI: 10.1038/s41467-024-44996-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Lloyd Cool
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Yanmei Zhu
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium.
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Zimmermann A, Prieto-Vivas JE, Cautereels C, Gorkovskiy A, Steensels J, Van de Peer Y, Verstrepen KJ. A Cas3-base editing tool for targetable in vivo mutagenesis. Nat Commun 2023; 14:3389. [PMID: 37296137 PMCID: PMC10256805 DOI: 10.1038/s41467-023-39087-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The generation of genetic diversity via mutagenesis is routinely used for protein engineering and pathway optimization. Current technologies for random mutagenesis often target either the whole genome or relatively narrow windows. To bridge this gap, we developed CoMuTER (Confined Mutagenesis using a Type I-E CRISPR-Cas system), a tool that allows inducible and targetable, in vivo mutagenesis of genomic loci of up to 55 kilobases. CoMuTER employs the targetable helicase Cas3, signature enzyme of the class 1 type I-E CRISPR-Cas system, fused to a cytidine deaminase to unwind and mutate large stretches of DNA at once, including complete metabolic pathways. The tool increases the number of mutations in the target region 350-fold compared to the rest of the genome, with an average of 0.3 mutations per kilobase. We demonstrate the suitability of CoMuTER for pathway optimization by doubling the production of lycopene in Saccharomyces cerevisiae after a single round of mutagenesis.
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Affiliation(s)
- Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Julian E Prieto-Vivas
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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4
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Wauters R, Herrera-Malaver B, Schreurs M, Bircham P, Cautereels C, Cortebeeck J, Duffin PM, Steensels J, Verstrepen KJ. Novel Saccharomyces cerevisiae variants slow down the accumulation of staling aldehydes and improve beer shelf-life. Food Chem 2022; 398:133863. [DOI: 10.1016/j.foodchem.2022.133863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 10/16/2022]
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5
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Chen S, Perez-Samper G, Herrera-Malaver B, Zhu L, Liu Y, Steensels J, Yang Q, Verstrepen KJ. Breeding of New Saccharomyces cerevisiae Hybrids with Reduced Higher Alcohol Production for Light-Aroma-Type- Xiaoqu Baijiu Production. Journal of the American Society of Brewing Chemists 2022. [DOI: 10.1080/03610470.2022.2033608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shenxi Chen
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Gemma Perez-Samper
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| | - Liping Zhu
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Yuancai Liu
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Jan Steensels
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
| | - Qiang Yang
- Hubei Provincial Key Lab for Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd, Daye, Hubei, People’s Republic of China
| | - Kevin J. Verstrepen
- Department M2S, CMPG Laborary for Genetics and Genomics, Leuven, Belgium
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Bio-Incubator, Leuven, Belgium
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6
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Ho PW, Piampongsant S, Gallone B, Del Cortona A, Peeters PJ, Reijbroek F, Verbaet J, Herrera B, Cortebeeck J, Nolmans R, Saels V, Steensels J, Jarosz DF, Verstrepen KJ. Massive QTL analysis identifies pleiotropic genetic determinants for stress resistance, aroma formation, and ethanol, glycerol and isobutanol production in Saccharomyces cerevisiae. Biotechnol Biofuels 2021; 14:211. [PMID: 34727964 PMCID: PMC8564995 DOI: 10.1186/s13068-021-02059-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The brewer's yeast Saccharomyces cerevisiae is exploited in several industrial processes, ranging from food and beverage fermentation to the production of biofuels, pharmaceuticals and complex chemicals. The large genetic and phenotypic diversity within this species offers a formidable natural resource to obtain superior strains, hybrids, and variants. However, most industrially relevant traits in S. cerevisiae strains are controlled by multiple genetic loci. Over the past years, several studies have identified some of these QTLs. However, because these studies only focus on a limited set of traits and often use different techniques and starting strains, a global view of industrially relevant QTLs is still missing. RESULTS Here, we combined the power of 1125 fully sequenced inbred segregants with high-throughput phenotyping methods to identify as many as 678 QTLs across 18 different traits relevant to industrial fermentation processes, including production of ethanol, glycerol, isobutanol, acetic acid, sulfur dioxide, flavor-active esters, as well as resistance to ethanol, acetic acid, sulfite and high osmolarity. We identified and confirmed several variants that are associated with multiple different traits, indicating that many QTLs are pleiotropic. Moreover, we show that both rare and common variants, as well as variants located in coding and non-coding regions all contribute to the phenotypic variation. CONCLUSIONS Our findings represent an important step in our understanding of the genetic underpinnings of industrially relevant yeast traits and open new routes to study complex genetics and genetic interactions as well as to engineer novel, superior industrial yeasts. Moreover, the major role of rare variants suggests that there is a plethora of different combinations of mutations that can be explored in genome editing.
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Affiliation(s)
- Ping-Wei Ho
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Supinya Piampongsant
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Brigida Gallone
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Andrea Del Cortona
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Pieter-Jan Peeters
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Frank Reijbroek
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jules Verbaet
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Beatriz Herrera
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jeroen Cortebeeck
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Robbe Nolmans
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Veerle Saels
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jan Steensels
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Kevin J. Verstrepen
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
- Labo VIB-CMPG, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Heverlee Belgium
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7
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Đurović G, Van Neerbos FAC, Bossaert S, Herrera-Malaver B, Steensels J, Arnó J, Wäckers F, Sobhy IS, Verstrepen KJ, Jacquemyn H, Lievens B. The Pupal Parasitoid Trichopria drosophilae Is Attracted to the Same Yeast Volatiles as Its Adult Host. J Chem Ecol 2021; 47:788-798. [PMID: 34269959 DOI: 10.1007/s10886-021-01295-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 10/20/2022]
Abstract
There is increasing evidence that microorganisms, particularly fungi and bacteria, emit volatile compounds that mediate the foraging behaviour of insects and therefore have the potential to affect key ecological relationships. However, to what extent microbial volatiles affect the olfactory response of insects across different trophic levels remains unclear. Adult parasitoids use a variety of chemical stimuli to locate potential hosts, including those emitted by the host's habitat, the host itself, and microorganisms associated with the host. Given the great capacity of parasitoids to utilize and learn odours to increase foraging success, parasitoids of eggs, larvae, or pupae may respond to the same volatiles the adult stage of their hosts use when locating their resources, but compelling evidence is still scarce. In this study, using Saccharomyces cerevisiae we show that Trichopria drosophilae, a pupal parasitoid of Drosophila species, is attracted to the same yeast volatiles as their hosts in the adult stage, i.e. acetate esters. Parasitoids significantly preferred the odour of S. cerevisiae over the blank medium in a Y-tube olfactometer. Deletion of the yeast ATF1 gene, encoding a key acetate ester synthase, decreased attraction of T. drosophilae, while the addition of synthetic acetate esters to the fermentation medium restored parasitoid attraction. Bioassays with individual compounds revealed that the esters alone were not as attractive as the volatile blend of S. cerevisiae, suggesting that other volatile compounds also contribute to the attraction of T. drosophilae. Altogether, our results indicate that pupal parasitoids respond to the same volatiles as the adult stage of their hosts, which may aid them in locating oviposition sites.
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Affiliation(s)
- Gordana Đurović
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Leuven Plant Institute (LPI), KU Leuven, B-3001, Leuven, Belgium.,Research and Innovation Centre, Fondazione Edmund Mach, 38098, San Michele all'Adige, Italy.,Biobest, B-2260, Westerlo, Belgium
| | - Francine A C Van Neerbos
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Leuven Plant Institute (LPI), KU Leuven, B-3001, Leuven, Belgium
| | - Sofie Bossaert
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Leuven Plant Institute (LPI), KU Leuven, B-3001, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Flanders Institute for Biotechnology (VIB), KU Leuven Center for Microbiology, B-3001, Leuven, Belgium
| | - Jan Steensels
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Flanders Institute for Biotechnology (VIB), KU Leuven Center for Microbiology, B-3001, Leuven, Belgium
| | | | - Felix Wäckers
- Biobest, B-2260, Westerlo, Belgium.,Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Islam S Sobhy
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Leuven Plant Institute (LPI), KU Leuven, B-3001, Leuven, Belgium.,Department of Plant Protection, Faculty of Agriculture, Suez Canal University, Ismailia, Egypt
| | - Kevin J Verstrepen
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, B-3001, Leuven, Belgium.,Flanders Institute for Biotechnology (VIB), KU Leuven Center for Microbiology, B-3001, Leuven, Belgium
| | - Hans Jacquemyn
- Leuven Plant Institute (LPI), KU Leuven, B-3001, Leuven, Belgium.,Laboratory of Plant Conservation and Population Biology, Biology Department, KU Leuven, B-3001, Leuven, Belgium
| | - Bart Lievens
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, B-3001, Leuven, Belgium. .,Leuven Plant Institute (LPI), KU Leuven, B-3001, Leuven, Belgium.
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8
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Gallone B, Steensels J, Verstrepen KJ. Moulded by humans: The domestication of blue-veined cheese fungi. Mol Ecol 2020; 29:2517-2520. [PMID: 32585769 DOI: 10.1111/mec.15525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/26/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022]
Abstract
It is hard to imagine a world without food-associated microbes. The production of bread, wine, beer, salami, coffee, chocolate, cheese and many other foods and beverages all rely on specific microbes. In cheese, myriad microbial species collaborate to yield the complex organoleptic properties that are appreciated by millions of people worldwide. In the early days of cheese making, these complex communities emerged spontaneously from the natural flora associated with the raw materials, the equipment, the production environment or craftsmen involved in the production process. However, in some cases, the microbes shifted their natural habitat to the new cheese-associated environment. The most obvious cause of this is backslopping, where part of a fermented product is used to inoculate the next batch. In addition, some microbes may simply adhere to the tools used in the production process. These microbial communities gradually adapted to the novel man-made niches, a process referred to as "domestication." Domestication is associated with specific genomic and phenotypic changes and ultimately leads to lineages that are genetically and phenotypically distinct from their wild ancestors. In this issue of Molecular Ecology, Dumas et al. have investigated a prime example of cheese-associated microbes, the fungus Penicillium roqueforti. The authors identified several hallmarks of domestication in the genome and phenome of this species, allowing them to hypothesize about the origin of blue-veined cheese fungi domestication, and the specific evolutionary processes involved in adaptation to the cheese matrix.
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Affiliation(s)
- Brigida Gallone
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Jan Steensels
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Kevin J Verstrepen
- VIB - KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
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9
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Mertens S, Gallone B, Steensels J, Herrera-Malaver B, Cortebeek J, Nolmans R, Saels V, Vyas VK, Verstrepen KJ. Correction: Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts. PLoS One 2019; 14:e0224525. [PMID: 31648239 PMCID: PMC6812760 DOI: 10.1371/journal.pone.0224525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0209124.].
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10
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Gallone B, Steensels J, Mertens S, Dzialo MC, Gordon JL, Wauters R, Theßeling FA, Bellinazzo F, Saels V, Herrera-Malaver B, Prahl T, White C, Hutzler M, Meußdoerffer F, Malcorps P, Souffriau B, Daenen L, Baele G, Maere S, Verstrepen KJ. Interspecific hybridization facilitates niche adaptation in beer yeast. Nat Ecol Evol 2019; 3:1562-1575. [PMID: 31636425 DOI: 10.1038/s41559-019-0997-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 09/02/2019] [Indexed: 11/09/2022]
Abstract
Hybridization between species often leads to non-viable or infertile offspring, yet examples of evolutionarily successful interspecific hybrids have been reported in all kingdoms of life. However, many questions on the ecological circumstances and evolutionary aftermath of interspecific hybridization remain unanswered. In this study, we sequenced and phenotyped a large set of interspecific yeast hybrids isolated from brewing environments to uncover the influence of interspecific hybridization in yeast adaptation and domestication. Our analyses demonstrate that several hybrids between Saccharomyces species originated and diversified in industrial environments by combining key traits of each parental species. Furthermore, posthybridization evolution within each hybrid lineage reflects subspecialization and adaptation to specific beer styles, a process that was accompanied by extensive chimerization between subgenomes. Our results reveal how interspecific hybridization provides an important evolutionary route that allows swift adaptation to novel environments.
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Affiliation(s)
- Brigida Gallone
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jan Steensels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Stijn Mertens
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Maria C Dzialo
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Jonathan L Gordon
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Ruben Wauters
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Florian A Theßeling
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Francesca Bellinazzo
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Veerle Saels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | | | | | - Mathias Hutzler
- Research Center Weihenstephan for Brewing and Food Quality, TU München, Freising, Germany
| | - Franz Meußdoerffer
- Research Center Weihenstephan for Brewing and Food Quality, TU München, Freising, Germany
| | | | | | | | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium. .,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium. .,Leuven Institute for Beer Research, Leuven, Belgium.
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11
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12
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Vermeersch L, Perez-Samper G, Cerulus B, Jariani A, Gallone B, Voordeckers K, Steensels J, Verstrepen KJ. On the duration of the microbial lag phase. Curr Genet 2019; 65:721-727. [PMID: 30666394 PMCID: PMC6510831 DOI: 10.1007/s00294-019-00938-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/19/2022]
Abstract
When faced with environmental changes, microbes enter a lag phase during which cell growth is arrested, allowing cells to adapt to the new situation. The discovery of the lag phase started the field of gene regulation and led to the unraveling of underlying mechanisms. However, the factors determining the exact duration and dynamics of the lag phase remain largely elusive. Naively, one would expect that cells adapt as quickly as possible, so they can resume growth and compete with other organisms. However, recent studies show that the lag phase can last from several hours up to several days. Moreover, some cells within the same population take much longer than others, despite being genetically identical. In addition, the lag phase duration is also influenced by the past, with recent exposure to a given environment leading to a quicker adaptation when that environment returns. Genome-wide screens in Saccharomyces cerevisiae on carbon source shifts now suggest that the length of the lag phase, the heterogeneity in lag times of individual cells, and the history-dependent behavior are not determined by the time it takes to induce a few specific genes related to uptake and metabolism of a new carbon source. Instead, a major shift in general metabolism, and in particular a switch between fermentation and respiration, is the major bottleneck that determines lag duration. This suggests that there may be a fitness trade-off between complete adaptation of a cell’s metabolism to a given environment, and a short lag phase when the environment changes.
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Affiliation(s)
- Lieselotte Vermeersch
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Gemma Perez-Samper
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Bram Cerulus
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Abbas Jariani
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Brigida Gallone
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Karin Voordeckers
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium. .,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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13
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Mertens S, Gallone B, Steensels J, Herrera-Malaver B, Cortebeek J, Nolmans R, Saels V, Vyas VK, Verstrepen KJ. Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts. PLoS One 2019; 14:e0209124. [PMID: 30625138 PMCID: PMC6326464 DOI: 10.1371/journal.pone.0209124] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/29/2018] [Indexed: 11/18/2022] Open
Abstract
Today’s beer market is challenged by a decreasing consumption of traditional beer styles and an increasing consumption of specialty beers. In particular, lager-type beers (pilsner), characterized by their refreshing and unique aroma and taste, yet very uniform, struggle with their sales. The development of novel variants of the common lager yeast, the interspecific hybrid Saccharomyces pastorianus, has been proposed as a possible solution to address the need of product diversification in lager beers. Previous efforts to generate new lager yeasts through hybridization of the ancestral parental species (S. cerevisiae and S. eubayanus) yielded strains with an aromatic profile distinct from the natural biodiversity. Unfortunately, next to the desired properties, these novel yeasts also inherited unwanted characteristics. Most notably is their phenolic off-flavor (POF) production, which hampers their direct application in the industrial production processes. Here, we describe a CRISPR-based gene editing strategy that allows the systematic and meticulous introduction of a natural occurring mutation in the FDC1 gene of genetically complex industrial S. cerevisiae strains, S. eubayanus yeasts and interspecific hybrids. The resulting cisgenic POF- variants show great potential for industrial application and diversifying the current lager beer portfolio.
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Affiliation(s)
- Stijn Mertens
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Brigida Gallone
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Jeroen Cortebeek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Robbe Nolmans
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Veerle Saels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
| | - Valmik K. Vyas
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Leuven, Belgium
- Leuven Institute for Beer Research, KU Leuven, Bio-Incubator, Leuven, Belgium
- * E-mail:
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14
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Kruis AJ, Gallone B, Jonker T, Mars AE, van Rijswijck IMH, Wolkers-Rooijackers JCM, Smid EJ, Steensels J, Verstrepen KJ, Kengen SWM, van der Oost J, Weusthuis RA. Contribution of Eat1 and Other Alcohol Acyltransferases to Ester Production in Saccharomyces cerevisiae. Front Microbiol 2018; 9:3202. [PMID: 30622529 PMCID: PMC6308380 DOI: 10.3389/fmicb.2018.03202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
Esters are essential for the flavor and aroma of fermented products, and are mainly produced by alcohol acyl transferases (AATs). A recently discovered AAT family named Eat (Ethanol acetyltransferase) contributes to ethyl acetate synthesis in yeast. However, its effect on the synthesis of other esters is unknown. In this study, the role of the Eat family in ester synthesis was compared to that of other Saccharomyces cerevisiae AATs (Atf1p, Atf2p, Eht1p, and Eeb1p) in silico and in vivo. A genomic study in a collection of industrial S. cerevisiae strains showed that variation of the primary sequence of the AATs did not correlate with ester production. Fifteen members of the EAT family from nine yeast species were overexpressed in S. cerevisiae CEN.PK2-1D and were able to increase the production of acetate and propanoate esters. The role of Eat1p was then studied in more detail in S. cerevisiae CEN.PK2-1D by deleting EAT1 in various combinations with other known S. cerevisiae AATs. Between 6 and 11 esters were produced under three cultivation conditions. Contrary to our expectations, a strain where all known AATs were disrupted could still produce, e.g., ethyl acetate and isoamyl acetate. This study has expanded our understanding of ester synthesis in yeast but also showed that some unknown ester-producing mechanisms still exist.
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Affiliation(s)
- Aleksander J Kruis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.,Bioprocess Engineering, Wageningen University and Research, Wageningen, Netherlands
| | - Brigida Gallone
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Timo Jonker
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Astrid E Mars
- Biobased Products, Wageningen University and Research, Wageningen, Netherlands
| | - Irma M H van Rijswijck
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan Steensels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Wageningen, Netherlands
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15
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Steensels J, Gorkovskiy A, Verstrepen KJ. SCRaMbLEing to understand and exploit structural variation in genomes. Nat Commun 2018; 9:1937. [PMID: 29789533 PMCID: PMC5964227 DOI: 10.1038/s41467-018-04308-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 04/19/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Jan Steensels
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium. .,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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16
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Mertens S, Steensels J, Gallone B, Souffriau B, Malcorps P, Verstrepen KJ. Rapid Screening Method for Phenolic Off-Flavor (POF) Production in Yeast. Journal of the American Society of Brewing Chemists 2018. [DOI: 10.1094/asbcj-2017-4142-01] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Stijn Mertens
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), KU Leuven, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), KU Leuven, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Brigida Gallone
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), KU Leuven, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Ben Souffriau
- AB-InBev SA/NV, Brouwerijplein 1, B-3000 Leuven, Belgium
| | | | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Centre for Microbiology, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), KU Leuven, Bio-Incubator, Gaston Geenslaan 1, B-3001 Leuven, Belgium
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17
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Gallone B, Mertens S, Gordon JL, Maere S, Verstrepen KJ, Steensels J. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts. Curr Opin Biotechnol 2018; 49:148-155. [DOI: 10.1016/j.copbio.2017.08.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/20/2017] [Accepted: 08/14/2017] [Indexed: 11/27/2022]
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18
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Meersman E, Struyf N, Kyomugasho C, Jamsazzadeh Kermani Z, Santiago JS, Baert E, Hemdane S, Vrancken G, Verstrepen KJ, Courtin CM, Hendrickx M, Steensels J. Characterization and Degradation of Pectic Polysaccharides in Cocoa Pulp. J Agric Food Chem 2017; 65:9726-9734. [PMID: 29032689 DOI: 10.1021/acs.jafc.7b03854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microbial fermentation of the viscous pulp surrounding cocoa beans is a crucial step in chocolate production. During this process, the pulp is degraded, after which the beans are dried and shipped to factories for further processing. Despite its central role in chocolate production, pulp degradation, which is assumed to be a result of pectin breakdown, has not been thoroughly investigated. Therefore, this study provides a comprehensive physicochemical analysis of cocoa pulp, focusing on pectic polysaccharides, and the factors influencing its degradation. Detailed analysis reveals that pectin in cocoa pulp largely consists of weakly bound substances, and that both temperature and enzyme activity play a role in its degradation. Furthermore, this study shows that pulp degradation by an indigenous yeast fully relies on the presence of a single gene (PGU1), encoding for an endopolygalacturonase. Apart from their basic scientific value, these new insights could propel the selection of microbial starter cultures for more efficient pulp degradation.
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Affiliation(s)
- Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- Lab for Systems Biology, VIB Center for Microbiology, Bio-Incubator , Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Nore Struyf
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Clare Kyomugasho
- Laboratory of Food Technology, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Zahra Jamsazzadeh Kermani
- Laboratory of Food Technology, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Jihan Santanina Santiago
- Laboratory of Food Technology, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Eline Baert
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- Lab for Systems Biology, VIB Center for Microbiology, Bio-Incubator , Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Sami Hemdane
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Gino Vrancken
- Barry Callebaut AG , Westpark, Pfingstweidstrasse 60, 8005 Zurich, Switzerland
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- Lab for Systems Biology, VIB Center for Microbiology, Bio-Incubator , Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Christophe M Courtin
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Marc Hendrickx
- Laboratory of Food Technology, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven , Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- Lab for Systems Biology, VIB Center for Microbiology, Bio-Incubator , Gaston Geenslaan 1, 3001 Leuven, Belgium
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19
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Abstract
Many genes are not only transcribed in the sense direction but also yield antisense transcripts. In this issue of Cell Reports, Huber et al. (2016) report that some of these transcripts may serve to suppress sense transcription and noise.
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Affiliation(s)
- Jan Steensels
- VIB Laboratory for Systems Biology and KU Leuven Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology and KU Leuven Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium.
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20
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Gemayel R, Yang Y, Dzialo MC, Kominek J, Vowinckel J, Saels V, Van Huffel L, van der Zande E, Ralser M, Steensels J, Voordeckers K, Verstrepen KJ. Variable repeats in the eukaryotic polyubiquitin gene ubi4 modulate proteostasis and stress survival. Nat Commun 2017; 8:397. [PMID: 28855501 PMCID: PMC5577197 DOI: 10.1038/s41467-017-00533-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/05/2017] [Indexed: 01/23/2023] Open
Abstract
Ubiquitin conjugation signals for selective protein degradation by the proteasome. In eukaryotes, ubiquitin is encoded both as a monomeric ubiquitin unit fused to a ribosomal gene and as multiple ubiquitin units in tandem. The polyubiquitin gene is a unique, highly conserved open reading frame composed solely of tandem repeats, yet it is still unclear why cells utilize this unusual gene structure. Using the Saccharomyces cerevisiae UBI4 gene, we show that this multi-unit structure allows cells to rapidly produce large amounts of ubiquitin needed to respond to sudden stress. The number of ubiquitin units encoded by UBI4 influences cellular survival and the rate of ubiquitin-proteasome system (UPS)-mediated proteolysis following heat stress. Interestingly, the optimal number of repeats varies under different types of stress indicating that natural variation in repeat numbers may optimize the chance for survival. Our results demonstrate how a variable polycistronic transcript provides an evolutionary alternative for gene copy number variation. Eukaryotic cells rely on the ubiquitin-proteasome system for selective degradation of proteins, a process vital to organismal fitness. Here the authors show that the number of repeats in the polyubiquitin gene is evolutionarily unstable within and between yeast species, and that this variability may tune the cell’s capacity to respond to sudden environmental perturbations.
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Affiliation(s)
- Rita Gemayel
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Yudi Yang
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Maria C Dzialo
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Jacek Kominek
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Veerle Saels
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Leen Van Huffel
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Elisa van der Zande
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis Court Road, Cambridge, CB2 1GA, UK.,The Francis Crick Institute, 1 Midland Rd, London, NW11AT, UK
| | - Jan Steensels
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Karin Voordeckers
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium.,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium
| | - Kevin J Verstrepen
- Laboratory of Systems Biology, VIB Center for Microbiology, Leuven, B-3001, Belgium. .,Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics (CMPG), Department M2S, KU Leuven, Gaston Geenslaan 1, B-3001, Heverlee, Belgium.
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21
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Dzialo MC, Park R, Steensels J, Lievens B, Verstrepen KJ. Physiology, ecology and industrial applications of aroma formation in yeast. FEMS Microbiol Rev 2017; 41:S95-S128. [PMID: 28830094 PMCID: PMC5916228 DOI: 10.1093/femsre/fux031] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/06/2017] [Indexed: 01/05/2023] Open
Abstract
Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.
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Affiliation(s)
- Maria C Dzialo
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Rahel Park
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A B-2860 Sint-Katelijne Waver, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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22
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Lenaerts M, Goelen T, Paulussen C, Herrera‐Malaver B, Steensels J, Van den Ende W, Verstrepen KJ, Wäckers F, Jacquemyn H, Lievens B. Nectar bacteria affect life history of a generalist aphid parasitoid by altering nectar chemistry. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12933] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marijke Lenaerts
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular SystemsKU Leuven Sint‐Katelijne Waver Belgium
| | - Tim Goelen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular SystemsKU Leuven Sint‐Katelijne Waver Belgium
| | - Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular SystemsKU Leuven Sint‐Katelijne Waver Belgium
| | - Beatriz Herrera‐Malaver
- Lab for Systems BiologyVIB Center for Microbiology & Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and GenomicsDepartment of Microbial and Molecular SystemsKU Leuven Leuven Belgium
| | - Jan Steensels
- Lab for Systems BiologyVIB Center for Microbiology & Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and GenomicsDepartment of Microbial and Molecular SystemsKU Leuven Leuven Belgium
| | - Wim Van den Ende
- Laboratory of Molecular Plant BiologyBiology DepartmentKU Leuven Leuven Belgium
| | - Kevin J. Verstrepen
- Lab for Systems BiologyVIB Center for Microbiology & Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and GenomicsDepartment of Microbial and Molecular SystemsKU Leuven Leuven Belgium
| | - Felix Wäckers
- Biobest Westerlo Belgium
- Lancaster Environment CentreLancaster University Lancaster UK
| | - Hans Jacquemyn
- Plant Conservation and Population BiologyBiology DepartmentKU Leuven Leuven Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular SystemsKU Leuven Sint‐Katelijne Waver Belgium
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23
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Sharp DC, Steensels J, Shellhammer TH. The effect of hopping regime, cultivar and β
-glucosidase activity on monoterpene alcohol concentrations in wort and beer. J Inst Brew 2017. [DOI: 10.1002/jib.418] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel C. Sharp
- Department of Food Science and Technology; Oregon State University; 100 Wiegand Hall Corvallis OR 97331-4501 USA
| | - Jan Steensels
- VIB Laboratory for Systems Biology Bio-Incubator; Katholieke Universiteit Leuven; Gaston Geenslaan 1 Leuven B-3001 Belgium
| | - Thomas H. Shellhammer
- Department of Food Science and Technology; Oregon State University; 100 Wiegand Hall Corvallis OR 97331-4501 USA
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24
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Vervoort Y, Linares AG, Roncoroni M, Liu C, Steensels J, Verstrepen KJ. High-throughput system-wide engineering and screening for microbial biotechnology. Curr Opin Biotechnol 2017; 46:120-125. [PMID: 28346890 DOI: 10.1016/j.copbio.2017.02.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 01/08/2023]
Abstract
Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes. More specifically, we will emphasize the use of multiplex automated genome evolution (MAGE) and CRISPR/Cas systems for high-throughput genome engineering and the application of (lab-on-chip) nanoreactors for high-throughput single-cell or population screening.
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Affiliation(s)
- Yannick Vervoort
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Imec Life Science Technologies, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Alicia Gutiérrez Linares
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Miguel Roncoroni
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Chengxun Liu
- Imec Life Science Technologies, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Systems Biology, VIB Center for Microbiology, Gaston Geenslaan 1, B-3001 Leuven, Belgium; Laboratory for Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium.
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25
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Crauwels S, Van Opstaele F, Jaskula-Goiris B, Steensels J, Verreth C, Bosmans L, Paulussen C, Herrera-Malaver B, de Jonge R, De Clippeleer J, Marchal K, De Samblanx G, Willems KA, Verstrepen KJ, Aerts G, Lievens B. Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains. FEMS Yeast Res 2016; 17:fow105. [PMID: 27956491 DOI: 10.1093/femsyr/fow105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/08/2016] [Indexed: 11/14/2022] Open
Abstract
Brettanomyces (Dekkera) bruxellensis is an ascomycetous yeast of major importance in the food, beverage and biofuel industry. It has been isolated from various man-made ecological niches that are typically characterized by harsh environmental conditions such as wine, beer, soft drink, etc. Recent comparative genomics studies revealed an immense intraspecific diversity, but it is still unclear whether this genetic diversity also leads to systematic differences in fermentation performance and (off-)flavor production, and to what extent strains have evolved to match their ecological niche. Here, we present an evaluation of the fermentation properties of eight genetically diverse B. bruxellensis strains originating from beer, wine and soft drinks. We show that sugar consumption and aroma production during fermentation are determined by both the yeast strain and composition of the medium. Furthermore, our results indicate a strong niche adaptation of B. bruxellensis, most clearly for wine strains. For example, only strains originally isolated from wine were able to thrive well and produce the typical Brettanomyces-related phenolic off-flavors 4-ethylguaiacol and 4-ethylphenol when inoculated in red wine. Sulfite tolerance was found as a key factor explaining the observed differences in fermentation performance and off-flavor production. Sequence analysis of genes related to phenolic off-flavor production, however, revealed only marginal differences between the isolates tested, especially at the amino acid level. Altogether, our study provides novel insights in the Brettanomyces metabolism of flavor production, and is highly relevant for both the wine and beer industry.
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Affiliation(s)
- Sam Crauwels
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Filip Van Opstaele
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Barbara Jaskula-Goiris
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Jan Steensels
- VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics Lab for Genetics and Genomics, MS, KU Leuven, B-3001 Heverlee, Belgium
| | - Christel Verreth
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Lien Bosmans
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Beatriz Herrera-Malaver
- VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics Lab for Genetics and Genomics, MS, KU Leuven, B-3001 Heverlee, Belgium
| | - Ronnie de Jonge
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Jessika De Clippeleer
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics and Department of Information Technology, IMinds, Ghent University, B-9000 Ghent, Belgium
| | - Gorik De Samblanx
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Kris A Willems
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Kevin J Verstrepen
- VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics Lab for Genetics and Genomics, MS, KU Leuven, B-3001 Heverlee, Belgium
| | - Guido Aerts
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
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26
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Gallone B, Steensels J, Prahl T, Soriaga L, Saels V, Herrera-Malaver B, Merlevede A, Roncoroni M, Voordeckers K, Miraglia L, Teiling C, Steffy B, Taylor M, Schwartz A, Richardson T, White C, Baele G, Maere S, Verstrepen KJ. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell 2016; 166:1397-1410.e16. [PMID: 27610566 PMCID: PMC5018251 DOI: 10.1016/j.cell.2016.08.020] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/08/2016] [Accepted: 08/08/2016] [Indexed: 12/04/2022]
Abstract
Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today’s industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains. PaperClip
We sequenced and phenotyped 157 S. cerevisiae yeasts Present-day industrial yeasts originate from only a few domesticated ancestors Beer yeasts show strong genetic and phenotypic hallmarks of domestication Domestication of industrial yeasts predates microbe discovery
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Affiliation(s)
- Brigida Gallone
- 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; Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, 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
| | - Troels Prahl
- White Labs, 9495 Candida Street, San Diego, CA 92126, USA
| | - Leah Soriaga
- Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - 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
| | - Beatriz Herrera-Malaver
- 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
| | - Adriaan Merlevede
- 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
| | - Miguel Roncoroni
- 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
| | - Karin Voordeckers
- 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
| | - Loren Miraglia
- Encinitas Brewing Science, 141 Rodney Avenue, Encinitas, CA 92024, USA
| | | | - Brian Steffy
- Illumina, 5200 Illumina Way, San Diego, CA 92122, USA
| | - Maryann Taylor
- Biological & Popular Culture (BioPop), 2205 Faraday Avenue, Suite E, Carlsbad, CA 92008, USA
| | - Ariel Schwartz
- Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Toby Richardson
- Synthetic Genomics, 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, 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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Aslankoohi E, Herrera-Malaver B, Rezaei MN, Steensels J, Courtin CM, Verstrepen KJ. Non-Conventional Yeast Strains Increase the Aroma Complexity of Bread. PLoS One 2016; 11:e0165126. [PMID: 27776154 PMCID: PMC5077118 DOI: 10.1371/journal.pone.0165126] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/06/2016] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is routinely used yeast in food fermentations because it combines several key traits, including fermentation efficiency and production of desirable flavors. However, the dominance of S. cerevisiae in industrial fermentations limits the diversity in the aroma profiles of the end products. Hence, there is a growing interest in non-conventional yeast strains that can help generate the diversity and complexity desired in today's diversified and consumer-driven markets. Here, we selected a set of non-conventional yeast strains to examine their potential for bread fermentation. Here, we tested ten non-conventional yeasts for bread fermentation, including two Saccharomyces species that are not currently used in bread making and 8 non-Saccharomyces strains. The results show that Torulaspora delbrueckii and Saccharomyces bayanus combine satisfactory dough fermentation with an interesting flavor profile. Sensory analysis and HS-SPME-GC-MS analysis confirmed that these strains produce aroma profiles that are very different from that produced by a commercial bakery strain. Moreover, bread produced with these yeasts was preferred by a majority of a trained sensory panel. These results demonstrate the potential of T. delbrueckii and S. bayanus as alternative yeasts for bread dough leavening, and provide a general experimental framework for the evaluation of more yeasts and bacteria.
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Affiliation(s)
- Elham Aslankoohi
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Mohammad Naser Rezaei
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
| | - Jan Steensels
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
- * E-mail: (KV); (CC)
| | - Kevin J. Verstrepen
- Systems Biology Laboratory, VIB Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
- * E-mail: (KV); (CC)
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Meersman E, Steensels J, Struyf N, Paulus T, Saels V, Mathawan M, Allegaert L, Vrancken G, Verstrepen KJ. Tuning Chocolate Flavor through Development of Thermotolerant Saccharomyces cerevisiae Starter Cultures with Increased Acetate Ester Production. Appl Environ Microbiol 2016; 82:732-46. [PMID: 26590272 PMCID: PMC4711123 DOI: 10.1128/aem.02556-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/09/2015] [Indexed: 11/20/2022] Open
Abstract
Microbial starter cultures have extensively been used to enhance the consistency and efficiency of industrial fermentations. Despite the advantages of such controlled fermentations, the fermentation involved in the production of chocolate is still a spontaneous process that relies on the natural microbiota at cocoa farms. However, recent studies indicate that certain thermotolerant Saccharomyces cerevisiae cultures can be used as starter cultures for cocoa pulp fermentation. In this study, we investigate the potential of specifically developed starter cultures to modulate chocolate aroma. Specifically, we developed several new S. cerevisiae hybrids that combine thermotolerance and efficient cocoa pulp fermentation with a high production of volatile flavor-active esters. In addition, we investigated the potential of two strains of two non-Saccharomyces species that produce very large amounts of fruity esters (Pichia kluyveri and Cyberlindnera fabianii) to modulate chocolate aroma. Gas chromatography-mass spectrometry (GC-MS) analysis of the cocoa liquor revealed an increased concentration of various flavor-active esters and a decrease in spoilage-related off-flavors in batches inoculated with S. cerevisiae starter cultures and, to a lesser extent, in batches inoculated with P. kluyveri and Cyb. fabianii. Additionally, GC-MS analysis of chocolate samples revealed that while most short-chain esters evaporated during conching, longer and more-fat-soluble ethyl and acetate esters, such as ethyl octanoate, phenylethyl acetate, ethyl phenylacetate, ethyl decanoate, and ethyl dodecanoate, remained almost unaffected. Sensory analysis by an expert panel confirmed significant differences in the aromas of chocolates produced with different starter cultures. Together, these results show that the selection of different yeast cultures opens novel avenues for modulating chocolate flavor.
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Affiliation(s)
- Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Nore Struyf
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Tinneke Paulus
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | - Veerle Saels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
| | | | | | | | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium Laboratory for Systems Biology, VIB, Leuven, Belgium
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Steensels J, Daenen L, Malcorps P, Derdelinckx G, Verachtert H, Verstrepen KJ. Brettanomyces yeasts--From spoilage organisms to valuable contributors to industrial fermentations. Int J Food Microbiol 2015; 206:24-38. [PMID: 25916511 DOI: 10.1016/j.ijfoodmicro.2015.04.005] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/23/2015] [Accepted: 04/03/2015] [Indexed: 12/13/2022]
Abstract
Ever since the introduction of controlled fermentation processes, alcoholic fermentations and Saccharomyces cerevisiae starter cultures proved to be a match made in heaven. The ability of S. cerevisiae to produce and withstand high ethanol concentrations, its pleasant flavour profile and the absence of health-threatening toxin production are only a few of the features that make it the ideal alcoholic fermentation organism. However, in certain conditions or for certain specific fermentation processes, the physiological boundaries of this species limit its applicability. Therefore, there is currently a strong interest in non-Saccharomyces (or non-conventional) yeasts with peculiar features able to replace or accompany S. cerevisiae in specific industrial fermentations. Brettanomyces (teleomorph: Dekkera), with Brettanomyces bruxellensis as the most commonly encountered representative, is such a yeast. Whilst currently mainly considered a spoilage organism responsible for off-flavour production in wine, cider or dairy products, an increasing number of authors report that in some cases, these yeasts can add beneficial (or at least interesting) aromas that increase the flavour complexity of fermented beverages, such as specialty beers. Moreover, its intriguing physiology, with its exceptional stress tolerance and peculiar carbon- and nitrogen metabolism, holds great potential for the production of bioethanol in continuous fermentors. This review summarizes the most notable metabolic features of Brettanomyces, briefly highlights recent insights in its genetic and genomic characteristics and discusses its applications in industrial fermentation processes, such as the production of beer, wine and bioethanol.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Department of Microbial and Molecular Systems (M(2)S), 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
| | - Luk Daenen
- AB-InBev SA/NV, Brouwerijplein 1, B-3000 Leuven, Belgium
| | | | - Guy Derdelinckx
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems (M(2)S), LFoRCe, KU Leuven, Kasteelpark Arenberg 33, 3001 Leuven, Belgium
| | - Hubert Verachtert
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems (M(2)S), LFoRCe, KU Leuven, Kasteelpark Arenberg 33, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Department of Microbial and Molecular Systems (M(2)S), 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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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. Biotechnol Biofuels 2015; 8:32. [PMID: 25759747 PMCID: PMC4354739 DOI: 10.1186/s13068-015-0216-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium; ,
- Laboratory for Systems Biology, VIB, Bio-Incubator, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium; ,
- Laboratory for Systems Biology, VIB, Bio-Incubator, 3001 Leuven, Belgium
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Steensels J, Snoek T, Meersman E, Picca Nicolino M, 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: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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 Leuven, Leuven, Belgium; Laboratory for Systems Biology, VIB, Leuven, Belgium
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Meersman E, Steensels J, Mathawan M, Wittocx PJ, Saels V, Struyf N, Bernaert H, Vrancken G, Verstrepen KJ. Detailed analysis of the microbial population in Malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota. PLoS One 2013; 8:e81559. [PMID: 24358116 PMCID: PMC3864809 DOI: 10.1371/journal.pone.0081559] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/23/2013] [Indexed: 11/19/2022] Open
Abstract
The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a "core" and a "variable" part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations ("core" yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations ("variable" yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency.
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Affiliation(s)
- Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | | | - Pieter-Jan Wittocx
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Veerle Saels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Nore Struyf
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | | | | | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
- * E-mail: .
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Steensels J, Snoek T, Meersman E, Picca Nicolino M, Aslankoohi E, Christiaens JF, Gemayel R, Meert W, New AM, Pougach K, Saels V, van der Zande E, Voordeckers K, Verstrepen KJ. Selecting and generating superior yeasts for the brewing industry. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.cervis.2012.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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