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Møller-Hansen I, Sáez-Sáez J, van der Hoek SA, Dyekjær JD, Christensen HB, Wright Muelas M, O’Hagan S, Kell DB, Borodina I. Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds. Front Microbiol 2024; 15:1376653. [PMID: 38680917 PMCID: PMC11045925 DOI: 10.3389/fmicb.2024.1376653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).
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Affiliation(s)
- Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jane D. Dyekjær
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Hanne B. Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Steve O’Hagan
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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Utomo JC, Barrell HB, Kumar R, Smith J, Brant MS, De la Hoz Siegler H, Ro DK. Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux. Metab Eng 2024; 82:286-296. [PMID: 38387678 DOI: 10.1016/j.ymben.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.
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Affiliation(s)
- Joseph Christian Utomo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hailey Brynn Barrell
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Rahul Kumar
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Jessica Smith
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Maximilian Simon Brant
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hector De la Hoz Siegler
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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Meng L, Diao M, Wang Q, Peng L, Li J, Xie N. Efficient biosynthesis of resveratrol via combining phenylalanine and tyrosine pathways in Saccharomyces cerevisiae. Microb Cell Fact 2023; 22:46. [PMID: 36890537 PMCID: PMC9996981 DOI: 10.1186/s12934-023-02055-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/04/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Resveratrol is a commercially available stilbenoid widely used as dietary supplements, functional food ingredients, and cosmetic ingredients due to its diverse physiological activities. The production of resveratrol in microorganisms provides an ideal source that reduces the cost of resveratrol, but the titer in Saccharomyces cerevisiae was still much lower than that in other hosts. RESULTS To achieve enhanced production of resveratrol in S. cerevisiae, we constructed a biosynthetic pathway via combining phenylalanine and tyrosine pathways by introducing a bi-functional phenylalanine/tyrosine ammonia lyase from Rhodotorula toruloides. The combination of phenylalanine pathway with tyrosine pathway led to a 462% improvement of resveratrol production in yeast extract peptone dextrose (YPD) medium with 4% glucose, suggesting an alternative strategy for producing p-coumaric acid-derived compounds. Then the strains were further modified by integrating multi-copy biosynthetic pathway genes, improving metabolic flux to aromatic amino acids and malonyl-CoA, and deleting by-pathway genes, which resulted in 1155.0 mg/L resveratrol in shake flasks when cultured in YPD medium. Finally, a non-auxotrophic strain was tailored for resveratrol production in minimal medium without exogenous amino acid addition, and the highest resveratrol titer (4.1 g/L) ever reported was achieved in S. cerevisiae to our knowledge. CONCLUSIONS This study demonstrates the advantage of employing a bi-functional phenylalanine/tyrosine ammonia lyase in the biosynthetic pathway of resveratrol, suggesting an effective alternative in the production of p-coumaric acid-derived compounds. Moreover, the enhanced production of resveratrol in S. cerevisiae lays a foundation for constructing cell factories for various stilbenoids.
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Affiliation(s)
- Lijun Meng
- State Key Laboratory of NonFood Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.
| | - Mengxue Diao
- State Key Laboratory of NonFood Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Qingyan Wang
- State Key Laboratory of NonFood Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Longyun Peng
- State Key Laboratory of NonFood Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Jianxiu Li
- State Key Laboratory of NonFood Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Nengzhong Xie
- State Key Laboratory of NonFood Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-Refinery, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.
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Costa CE, Romaní A, Teixeira JA, Domingues L. Resveratrol production for the valorisation of lactose-rich wastes by engineered industrial Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2022; 359:127463. [PMID: 35710047 DOI: 10.1016/j.biortech.2022.127463] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Resveratrol is an antioxidant with applications in the food and cosmetic industries. Its biosynthesis can side the hindrances of its extraction from plants. The dairy industry generates tonnes of lactose-rich wastes, which can be a carbon source. Saccharomyces cerevisiae is an industrial workhorse for biotechnological processes, being unable to naturally metabolise lactose. Here, an S. cerevisiae strain was engineered for de novo production of resveratrol from lactose. A resveratrol titre of 210 mg/L from 100 g/L of lactose in synthetic media was achieved. Process optimization increased by 35% the production by a two-stage process, one favouring ethanol production and a subsequent one with stronger agitation favouring ethanol and lactose consumption with conversion into resveratrol. Resveratrol production from cheese whey was further attained. To the best knowledge of the authors, this is the first report on resveratrol production from lactose, relevant in dairy wastes, establishing grounds for future resveratrol-producing lactose-based processes.
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Affiliation(s)
- Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Aloia Romaní
- Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), As Lagoas, 32004 Ourense, Spain
| | - José A Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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5
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De novo biosynthesis of diverse plant-derived styrylpyrones in Saccharomyces cerevisiae. Metab Eng Commun 2022; 14:e00195. [PMID: 35287355 PMCID: PMC8917298 DOI: 10.1016/j.mec.2022.e00195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
Plant styrylpyrones exerting well-established neuroprotective properties have attracted increasing attention in recent years. The ability to synthesize each individual styrylpyrone in engineered microorganisms is important to understanding the biological activity of medicinal plants and the complex mixtures they produce. Microbial biomanufacturing of diverse plant-derived styrylpyrones also provides a sustainable and efficient approach for the production of valuable plant styrylpyrones as daily supplements or potential drugs complementary to the prevalent agriculture-based approach. In this study, we firstly demonstrated the heterogenous biosynthesis of two 7,8-saturated styrylpyrones (7,8-dihydro-5,6-dehydrokavain (DDK) and 7,8-dihydroyangonin (DHY)) and two 7,8-unsaturated styrylpyrones (desmethoxyyangonin (DMY) and yangonin (Y)), in Saccharomyces cerevisiae. Although plant styrylpyrone biosynthetic pathways have not been fully elucidated, we functionally reconstructed the recently discovered kava styrylpyrone biosynthetic pathway that has high substrate promiscuity in yeast, and combined it with upstream hydroxycinnamic acid biosynthetic pathways to produce diverse plant-derived styrylpyrones without the native plant enzymes. We optimized the de novo pathways by engineering yeast endogenous aromatic amino acid metabolism and endogenous double bond reductases and by CRISPR-mediated δ-integration to overexpress the rate-limiting pathway genes. These combinatorial engineering efforts led to the first three yeast strains that can produce diverse plant-derived styrylpyrones de novo, with the titers of DDK, DMY and Y at 4.40 μM, 1.28 μM and 0.10 μM, respectively. This work has laid the foundation for larger-scale styrylpyrone biomanufacturing and the complete biosynthesis of more complicated plant styrylpyrones. Complete biosynthesis of plant styrylpyrones was firstly achieved in yeast. Yeast enzyme replaces unknown plant enzymes to produce 7,8-saturated styrylpyrones. CRISPR-based δ-integration led to stable styrylpyrone overproduction in rich medium.
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Zhang Q, Zeng W, Xu S, Zhou J. Metabolism and strategies for enhanced supply of acetyl-CoA in Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2021; 342:125978. [PMID: 34598073 DOI: 10.1016/j.biortech.2021.125978] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Acetyl-CoA is a kind of important cofactor that is involved in many metabolic pathways. It serves as the precursor for many interesting commercial products, such as terpenes, flavonoids and anthraquinones. However, the insufficient supply of acetyl-CoA limits biosynthesis of its derived compounds in the intracellular. In this review, we outlined metabolic pathways involved in the catabolism and anabolism of acetyl-CoA, as well as some important derived products. We examined several strategies for the enhanced supply of acetyl-CoA, and provided insight into pathways that generate acetyl-CoA to balance metabolism, which can be harnessed to improve the titer, yield and productivities of interesting products in Saccharomyces cerevisiae and other eukaryotic microorganisms. We believe that peroxisomal fatty acid β-oxidation could be an attractive strategy for enhancing the supply of acetyl-CoA.
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Affiliation(s)
- Qian Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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7
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Costa CE, Møller-Hansen I, Romaní A, Teixeira JA, Borodina I, Domingues L. Resveratrol Production from Hydrothermally Pretreated Eucalyptus Wood Using Recombinant Industrial Saccharomyces cerevisiae Strains. ACS Synth Biol 2021; 10:1895-1903. [PMID: 34304554 DOI: 10.1021/acssynbio.1c00120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Resveratrol is a phenolic compound with strong antioxidant activity, being promising for several applications in health, food, and cosmetics. It is generally extracted from plants or chemically synthesized, in both complex and not sustainable processes, but microbial biosynthesis of resveratrol can counter these drawbacks. In this work, resveratrol production by microbial biosynthesis from lignocellulosic materials was assessed. Three robust industrial Saccharomyces cerevisiae strains known for their thermotolerance and/or resistance to inhibitory compounds were identified as suitable hosts for de novo resveratrol production from glucose and ethanol. Through the CRISPR/Cas9 system, all industrial strains, and a laboratory one, were successfully engineered with the resveratrol biosynthetic pathway via the phenylalanine intermediate. All strains were further screened at 30 °C and 39 °C to evaluate thermotolerance, which is a key feature for Simultaneous Saccharification and Fermentation processes. Ethanol Red RBP showed the best performance at 39 °C, with more than 2.6-fold of resveratrol production in comparison with the other strains. This strain was then used to assess resveratrol production from glucose and ethanol. A maximum resveratrol titer of 187.07 ± 19.88 mg/L was attained from a medium with 2% glucose and 5% ethanol (w/v). Lastly, Ethanol Red RBP produced 151.65 ± 3.84 mg/L resveratrol from 2.95% of cellulose from hydrothermally pretreated Eucalyptus globulus wood, at 39 °C, in a Simultaneous Saccharification and Fermentation process. To the best of our knowledge, this is the first report of lignocellulosic resveratrol production, establishing grounds for the implementation of an integrated lignocellulose-to-resveratrol process in an industrial context.
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Affiliation(s)
- Carlos E. Costa
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Aloia Romaní
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - José A. Teixeira
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Lucília Domingues
- Centre of Biological Engineering, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
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8
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Isogai S, Okahashi N, Asama R, Nakamura T, Hasunuma T, Matsuda F, Ishii J, Kondo A. Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases. Metab Eng Commun 2021; 12:e00169. [PMID: 33868922 PMCID: PMC8040282 DOI: 10.1016/j.mec.2021.e00169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/01/2021] [Indexed: 11/29/2022] Open
Abstract
Reconstitution of prenylflavonoids using the flavonoid biosynthetic pathway and prenyltransferases (PTs) in microbes can be a promising attractive alternative to plant-based production or chemical synthesis. Here, we demonstrate that promiscuous microbial PTs can be a substitute for regiospecific but mostly unidentified botanical PTs. To test the prenylations of naringenin, we constructed a yeast strain capable of producing naringenin from l-phenylalanine by genomic integration of six exogenous genes encoding components of the naringenin biosynthetic pathway. Using this platform strain, various microbial PTs were tested for prenylnaringenin production. In vitro screening demonstrated that the fungal AnaPT (a member of the tryptophan dimethylallyltransferase family) specifically catalyzed C-3′ prenylation of naringenin, whereas SfN8DT-1, a botanical PT, specifically catalyzed C-8 prenylation. In vivo, the naringenin-producing strain expressing the microbial AnaPT exhibited heterologous microbial production of 3′-prenylnaringenin (3′-PN), in contrast to the previously reported in vivo production of 8-prenylnaringenin (8-PN) using the botanical SfN8DT-1. These findings provide strategies towards expanding the production of a variety of prenylated compounds, including well-known prenylnaringenins and novel prenylflavonoids. These results also suggest the opportunity for substituting botanical PTs, both known and unidentified, that display relatively strict regiospecificity of the prenyl group transfer. Promiscuous microbial prenyltransferases replaced regiospecific botanical enzymes. A stable yeast strain that produced naringenin from l-phenylalanine was constructed. A fungal prenyltransferase (AnaPT) catalyzed C-3′ prenylation of naringenin. AnaPT catalyzed the first microbial production of 3′-prenylnaringenin. Microbial prenyltransferases permit the production of various prenylated compounds.
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Affiliation(s)
- Shota Isogai
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ririka Asama
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomomi Nakamura
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
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9
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Methanol Production by " Methylacidiphilum fumariolicum" SolV under Different Growth Conditions. Appl Environ Microbiol 2020; 86:AEM.01188-20. [PMID: 32631865 PMCID: PMC7480378 DOI: 10.1128/aem.01188-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
The production of methanol, an important chemical, is completely dependent on natural gas. The current multistep chemical process uses high temperature and pressure to convert methane in natural gas to methanol. In this study, we used the methanotroph “Methylacidiphilum fumariolicum” SolV to achieve continuous methanol production from methane as the substrate. The production rate was highly dependent on the growth rate of this microorganism, and high conversion efficiencies were obtained. Using microorganisms for the production of methanol might enable the use of more sustainable sources of methane, such as biogas, rather than natural gas. Industrial methanol production converts methane from natural gas into methanol through a multistep chemical process. Biological methane-to-methanol conversion under moderate conditions and using biogas would be more environmentally friendly. Methanotrophs, bacteria that use methane as an energy source, convert methane into methanol in a single step catalyzed by the enzyme methane monooxygenase, but inhibition of methanol dehydrogenase, which catalyzes the subsequent conversion of methanol into formaldehyde, is a major challenge. In this study, we used the thermoacidophilic methanotroph “Methylacidiphilum fumariolicum” SolV for biological methanol production. This bacterium possesses a XoxF-type methanol dehydrogenase that is dependent on rare earth elements for activity. By using a cultivation medium nearly devoid of lanthanides, we reduced methanol dehydrogenase activity and obtained a continuous methanol-producing microbial culture. The methanol production rate and conversion efficiency were growth-rate dependent. A maximal conversion efficiency of 63% mol methanol produced per mol methane consumed was obtained at a relatively high growth rate, with a methanol production rate of 0.88 mmol/g (dry weight)/h. This study demonstrates that methanotrophs can be used for continuous methanol production. Full-scale application will require additional increases in the titer, production rate, and efficiency, which can be achieved by further decreasing the lanthanide concentration through the use of increased biomass concentrations and novel reactor designs to supply sufficient gases, including methane, oxygen, and hydrogen. IMPORTANCE The production of methanol, an important chemical, is completely dependent on natural gas. The current multistep chemical process uses high temperature and pressure to convert methane in natural gas to methanol. In this study, we used the methanotroph “Methylacidiphilum fumariolicum” SolV to achieve continuous methanol production from methane as the substrate. The production rate was highly dependent on the growth rate of this microorganism, and high conversion efficiencies were obtained. Using microorganisms for the production of methanol might enable the use of more sustainable sources of methane, such as biogas, rather than natural gas.
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Sáez-Sáez J, Wang G, Marella ER, Sudarsan S, Cernuda Pastor M, Borodina I. Engineering the oleaginous yeast Yarrowia lipolytica for high-level resveratrol production. Metab Eng 2020; 62:51-61. [PMID: 32818629 PMCID: PMC7672257 DOI: 10.1016/j.ymben.2020.08.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/05/2023]
Abstract
Resveratrol is a plant secondary metabolite with multiple health-beneficial properties. Microbial production of resveratrol in model microorganisms requires extensive engineering to reach commercially viable levels. Here, we explored the potential of the non-conventional yeast Yarrowia lipolytica to produce resveratrol and several other shikimate pathway-derived metabolites (p-coumaric acid, cis,cis-muconic acid, and salicylic acid). The Y. lipolytica strain expressing a heterologous pathway produced 52.1 ± 1.2 mg/L resveratrol in a small-scale cultivation. The titer increased to 409.0 ± 1.2 mg/L when the strain was further engineered with feedback-insensitive alleles of the key genes in the shikimate pathway and with five additional copies of the heterologous biosynthetic genes. In controlled fed-batch bioreactor, the strain produced 12.4 ± 0.3 g/L resveratrol, the highest reported titer to date for de novo resveratrol production, with a yield on glucose of 54.4 ± 1.6 mg/g and a productivity of 0.14 ± 0.01 g/L/h. The study showed that Y. lipolytica is an attractive host organism for the production of resveratrol and possibly other shikimate-pathway derived metabolites. Oleaginous yeast Y. lipolytica was engineered for production of aromatic compounds. High resveratrol production required increased activities of Aro4p and Aro7p. Multiple integration of resveratrol biosynthetic genes improved production. Fed-batch fermentation enabled de novo production of 12.4 g/L resveratrol.
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Affiliation(s)
- Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Eko Roy Marella
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Suresh Sudarsan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Marc Cernuda Pastor
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
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11
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Nieto-Taype MA, Garcia-Ortega X, Albiol J, Montesinos-Seguí JL, Valero F. Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. Front Bioeng Biotechnol 2020; 8:632. [PMID: 32671036 PMCID: PMC7330098 DOI: 10.3389/fbioe.2020.00632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and 13C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
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12
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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13
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Lu Y, Ye C, Che J, Xu X, Shao D, Jiang C, Liu Y, Shi J. Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1. Microb Cell Fact 2019; 18:13. [PMID: 30678677 PMCID: PMC6345013 DOI: 10.1186/s12934-019-1063-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternaria sp. MG1, an endophytic fungus isolated from grape, is a native producer of resveratrol, which has important application potential. However, the metabolic characteristics and physiological behavior of MG1 still remains mostly unraveled. In addition, the resveratrol production of the strain is low. Thus, the whole-genome sequencing is highly required for elucidating the resveratrol biosynthesis pathway. Furthermore, the metabolic network model of MG1 was constructed to provide a computational guided approach for improving the yield of resveratrol. RESULTS Firstly, a draft genomic sequence of MG1 was generated with a size of 34.7 Mbp and a GC content of 50.96%. Genome annotation indicated that MG1 possessed complete biosynthesis pathways for stilbenoids, flavonoids, and lignins. Eight secondary metabolites involved in these pathways were detected by GC-MS analysis, confirming the metabolic diversity of MG1. Furthermore, the first genome-scale metabolic network of Alternaria sp. MG1 (named iYL1539) was reconstructed, accounting for 1539 genes, 2231 metabolites, and 2255 reactions. The model was validated qualitatively and quantitatively by comparing the in silico simulation with experimental data, and the results showed a high consistency. In iYL1539, 56 genes were identified as growth essential in rich medium. According to constraint-based analysis, the importance of cofactors for the resveratrol biosynthesis was successfully demonstrated. Ethanol addition was predicted in silico to be an effective method to improve resveratrol production by strengthening acetyl-CoA synthesis and pentose phosphate pathway, and was verified experimentally with a 26.31% increase of resveratrol. Finally, 6 genes were identified as potential targets for resveratrol over-production by the recently developed methodology. The target-genes were validated using salicylic acid as elicitor, leading to an increase of resveratrol yield by 33.32% and the expression of gene 4CL and CHS by 1.8- and 1.6-fold, respectively. CONCLUSIONS This study details the diverse capability and key genes of Alternaria sp. MG1 to produce multiple secondary metabolites. The first model of the species Alternaria was constructed, providing an overall understanding of the physiological behavior and metabolic characteristics of MG1. The model is a highly useful tool for enhancing productivity by rational design of the metabolic pathway for resveratrol and other secondary metabolites.
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Affiliation(s)
- Yao Lu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jinxin Che
- Department of Biological and Food Engineering, College of Chemical Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
| | - Xiaoguang Xu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Dongyan Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Chunmei Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, 710072, Shaanxi, China.
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Faria C, Borges N, Rocha I, Santos H. Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization. Microb Cell Fact 2018; 17:178. [PMID: 30445960 PMCID: PMC6240254 DOI: 10.1186/s12934-018-1023-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/07/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Mannosylglycerate (MG) is one of the most widespread compatible solutes among marine microorganisms adapted to hot environments. This ionic solute holds excellent ability to protect proteins against thermal denaturation, hence a large number of biotechnological and clinical applications have been put forward. However, the current prohibitive production costs impose severe constraints towards large-scale applications. All known microbial producers synthesize MG from GDP-mannose and 3-phosphoglycerate via a two-step pathway in which mannosyl-3-phosphoglycerate is the intermediate metabolite. In an early work, this pathway was expressed in Saccharomyces cerevisiae with the goal to confirm gene function (Empadinhas et al. in J Bacteriol 186:4075-4084, 2004), but the level of MG accumulation was low. Therefore, in view of the potential biotechnological value of this compound, we decided to invest further effort to convert S. cerevisiae into an efficient cell factory for MG production. RESULTS To drive MG production, the pathway for the synthesis of GDP-mannose, one of the MG biosynthetic precursors, was overexpressed in S. cerevisiae along with the MG biosynthetic pathway. MG production was evaluated under different cultivation modes, i.e., flask bottle, batch, and continuous mode with different dilution rates. The genes encoding mannose-6-phosphate isomerase (PMI40) and GDP-mannose pyrophosphorylase (PSA1) were introduced into strain MG01, hosting a plasmid encoding the MG biosynthetic machinery. The resulting engineered strain (MG02) showed around a twofold increase in the activity of PMI40 and PSA1 in comparison to the wild-type. In batch mode, strain MG02 accumulated 15.86 mgMG g DCW -1 , representing a 2.2-fold increase relative to the reference strain (MG01). In continuous culture, at a dilution rate of 0.15 h-1, there was a 1.5-fold improvement in productivity. CONCLUSION In the present study, the yield and productivity of MG were increased by overexpression of the GDP-mannose pathway and optimization of the mode of cultivation. A maximum of 15.86 mgMG g DCW -1 was achieved in batch cultivation and maximal productivity of 1.79 mgMG g DCW -1 h-1 in continuous mode. Additionally, a positive correlation between MG productivity and growth rate/dilution rate was established, although this correlation is not observed for MG yield.
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Affiliation(s)
- Cristiana Faria
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal. .,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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Diderich JA, Weening SM, van den Broek M, Pronk JT, Daran JMG. Selection of Pof -Saccharomyces eubayanus Variants for the Construction of S. cerevisiae × S. eubayanus Hybrids With Reduced 4-Vinyl Guaiacol Formation. Front Microbiol 2018; 9:1640. [PMID: 30100898 PMCID: PMC6074607 DOI: 10.3389/fmicb.2018.01640] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/02/2018] [Indexed: 01/27/2023] Open
Abstract
Saccharomyces pastorianus is an interspecies hybrid between S. cerevisiae and S. eubayanus. The identification of the parental species of S. pastorianus enabled the de novo reconstruction of hybrids that could potentially combine a wide array of phenotypic traits. Lager yeasts are characterized by their inability to decarboxylate ferulic acid present in wort, a phenotype also known as Pof - (phenolic off-flavor). However, all known S. eubayanus strains characterized so far produce clove-like aroma specific of 4-vinyl guaiacol, a decarboxylated form of ferulic acid. This study explored a non-GMO approach to construct Pof -S. eubayanus variants derived from the parental strain S. eubayanus CBS 12357. To rapidly screen a population of UV-mutagenized cells two complementary assays were developed. The first assay was based on the difference of light absorption spectra of ferulic acid and 4-vinyl guaiacol, while the second was based on the difference of sensitivity of Pof - and Pof+ strains to cinnamic acid. The S. eubayanus variant HTSE042 was selected and was confirmed not to produce 4-vinyl guaiacol. Whole genome sequencing revealed that this variant lost the subtelomeric region of the CHRXIII right arm that carried the two clustered genes SePAD1- SeFDC1 whose deletion in a naïve S. eubayanus strain (CBS 12357/FM1318) resulted in an identical phenotype. Subsequently, the Pof - variant was crossed with a Pof-S. cerevisiae partner. The resulting hybrid was not able to convert ferulic acid demonstrating the undisputable value of the mutagenized variant HTSE042 to eventually construct S. cerevisiae × S. eubayanus hybrids with phenotypic characteristics of S. pastorianus.
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Affiliation(s)
- Jasper A Diderich
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Susan M Weening
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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16
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Levisson M, Patinios C, Hein S, de Groot PA, Daran JM, Hall RD, Martens S, Beekwilder J. Engineering de novo anthocyanin production in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:103. [PMID: 29970082 PMCID: PMC6029064 DOI: 10.1186/s12934-018-0951-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/27/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Anthocyanins are polyphenolic pigments which provide pink to blue colours in fruits and flowers. There is an increasing demand for anthocyanins, as food colorants and as health-promoting substances. Plant production of anthocyanins is often seasonal and cannot always meet demand due to low productivity and the complexity of the plant extracts. Therefore, a system of on-demand supply is useful. While a number of other (simpler) plant polyphenols have been successfully produced in the yeast Saccharomyces cerevisiae, production of anthocyanins has not yet been reported. RESULTS Saccharomyces cerevisiae was engineered to produce pelargonidin 3-O-glucoside starting from glucose. Specific anthocyanin biosynthetic genes from Arabidopsis thaliana and Gerbera hybrida were introduced in a S. cerevisiae strain producing naringenin, the flavonoid precursor of anthocyanins. Upon culturing, pelargonidin and its 3-O-glucoside were detected inside the yeast cells, albeit at low concentrations. A number of related intermediates and side-products were much more abundant and were secreted into the culture medium. To optimize titers of pelargonidin 3-O-glucoside further, biosynthetic genes were stably integrated into the yeast genome, and formation of a major side-product, phloretic acid, was prevented by engineering the yeast chassis. Further engineering, by removing two glucosidases which are known to degrade pelargonidin 3-O-glucoside, did not result in higher yields of glycosylated pelargonidin. In aerated, pH controlled batch reactors, intracellular pelargonidin accumulation reached 0.01 µmol/gCDW, while kaempferol and dihydrokaempferol were effectively exported to reach extracellular concentration of 20 µM [5 mg/L] and 150 µM [44 mg/L], respectively. CONCLUSION The results reported in this study demonstrate the proof-of-concept that S. cerevisiae is capable of de novo production of the anthocyanin pelargonidin 3-O-glucoside. Furthermore, while current conversion efficiencies are low, a number of clear bottlenecks have already been identified which, when overcome, have huge potential to enhance anthocyanin production efficiency. These results bode very well for the development of fermentation-based production systems for specific and individual anthocyanin molecules. Such systems have both great scientific value for identifying and characterising anthocyanin decorating enzymes as well as significant commercial potential for the production of, on-demand, pure bioactive compounds to be used in the food, health and even pharma industries.
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Affiliation(s)
- Mark Levisson
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Constantinos Patinios
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sascha Hein
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, Centro Ricerca e Innovazione, Via E. Mach, 1, 38010 San Michele all’Adige, TN Italy
| | - Philip A. de Groot
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Robert D. Hall
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Stefan Martens
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, Centro Ricerca e Innovazione, Via E. Mach, 1, 38010 San Michele all’Adige, TN Italy
| | - Jules Beekwilder
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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17
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Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicum. J Biotechnol 2018; 265:70-75. [DOI: 10.1016/j.jbiotec.2017.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/09/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022]
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18
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Glauche F, Glazyrina J, Cruz Bournazou MN, Kiesewetter G, Cuda F, Goelling D, Raab A, Lang C, Neubauer P. Detection of growth rate-dependent product formation in miniaturized parallel fed-batch cultivations. Eng Life Sci 2017; 17:1215-1220. [PMID: 32624749 PMCID: PMC6999230 DOI: 10.1002/elsc.201600029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 04/28/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
Saccharomyces cerevisiae is a popular expression system for recombinant proteins. In most cases, production processes are performed as carbon-limited fed-batch cultures to avoid aerobic ethanol formation. Especially for constitutive expression systems, the specific product formation rate depends on the specific growth rate. The development of optimal feeding strategies strongly depends on laboratory-scale cultivations, which are time and resource consuming, especially when continuous experiments are carried out. It is therefore beneficial for accelerated process development to look at alternatives. In this study, S. cerevisiae AH22 secreting a heterologous endo-polygalacturonase (EPG) was characterized in microwell plates with an enzyme-based fed-batch medium. Through variation of the glucose release rate, different growth profiles were established and the impact on EPG secretion was analyzed. Product formation rates of 200-400 U (gx h)-1 were determined. As a reference, bioreactor experiments using the change-stat cultivation technique were performed. The growth-dependent product formation was analyzed over dilution rates of D = 0.01-0.35 with smooth change of D at a rate of 0.003 h-2. EPG production was found to be comparable with a qp of 400 U (gx h)-1 at D = 0.27 h-1. The presented results indicate that parallel miniaturized fed-batch cultures can be applied to determine product formation profiles of putative production strains. With further automation and parallelization of the concept, strain characterization can be performed in shorter time.
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Affiliation(s)
- Florian Glauche
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | - Julia Glazyrina
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | - Fabian Cuda
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | | | - Peter Neubauer
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
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19
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Kadisch M, Willrodt C, Hillen M, Bühler B, Schmid A. Maximizing the stability of metabolic engineering-derived whole-cell biocatalysts. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Marvin Kadisch
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Christian Willrodt
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Michael Hillen
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Bruno Bühler
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Andreas Schmid
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
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20
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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21
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Salinas F, Rojas V, Delgado V, Agosin E, Larrondo LF. Optogenetic switches for light-controlled gene expression in yeast. Appl Microbiol Biotechnol 2017; 101:2629-2640. [DOI: 10.1007/s00253-017-8178-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 02/06/2023]
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22
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Lehka BJ, Eichenberger M, Bjørn-Yoshimoto WE, Vanegas KG, Buijs N, Jensen NB, Dyekjær JD, Jenssen H, Simon E, Naesby M. Improving heterologous production of phenylpropanoids in Saccharomyces cerevisiae by tackling an unwanted side reaction of Tsc13, an endogenous double-bond reductase. FEMS Yeast Res 2017; 17:fox004. [PMID: 28073929 PMCID: PMC5815076 DOI: 10.1093/femsyr/fox004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/07/2016] [Accepted: 01/08/2017] [Indexed: 11/22/2022] Open
Abstract
Phenylpropanoids, such as flavonoids and stilbenoids, are of great commercial interest, and their production in Saccharomyces cerevisiae is a very promising strategy. However, to achieve commercially viable production, each step of the process must be optimised. We looked at carbon loss, known to occur in the heterologous flavonoid pathway in yeast, and identified an endogenous enzyme, the enoyl reductase Tsc13, which turned out to be responsible for the accumulation of phloretic acid via reduction of p-coumaroyl-CoA. Tsc13 is an essential enzyme involved in fatty acid synthesis and cannot be deleted. Hence, two approaches were adopted in an attempt to reduce the side activity without disrupting the natural function: site saturation mutagenesis identified a number of amino acid changes which slightly increased flavonoid production but without reducing the formation of the side product. Conversely, the complementation of TSC13 by a plant gene homologue essentially eliminated the unwanted side reaction, while retaining the productivity of phenylpropanoids in a simulated fed batch fermentation.
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Affiliation(s)
- Beata Joanna Lehka
- Evolva Biotech A/S, Lersø Parkallé 42, DK-2100, Copenhagen Ø, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000, Roskilde, Denmark
| | - Michael Eichenberger
- Evolva SA, Duggingerstrasse 23, CH-4153, Reinach, Switzerland
- Department of Biology, Technical University Darmstadt, Schnittspahnstrasse 10, DE-64287, Darmstadt, Germany
| | - Walden Emil Bjørn-Yoshimoto
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100, Copenhagen Ø, Denmark
| | - Katherina Garcia Vanegas
- Evolva Biotech A/S, Lersø Parkallé 42, DK-2100, Copenhagen Ø, Denmark
- Department of systems Biology, Technical University of Denmark, Kemitorvet Building 208, DK-2800, Kgs. Lyngby, Denmark
| | - Nicolaas Buijs
- Evolva Biotech A/S, Lersø Parkallé 42, DK-2100, Copenhagen Ø, Denmark
| | | | | | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000, Roskilde, Denmark
| | - Ernesto Simon
- Evolva Biotech A/S, Lersø Parkallé 42, DK-2100, Copenhagen Ø, Denmark
- Evolva SA, Duggingerstrasse 23, CH-4153, Reinach, Switzerland
| | - Michael Naesby
- Evolva SA, Duggingerstrasse 23, CH-4153, Reinach, Switzerland
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23
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Li M, Schneider K, Kristensen M, Borodina I, Nielsen J. Engineering yeast for high-level production of stilbenoid antioxidants. Sci Rep 2016; 6:36827. [PMID: 27833117 PMCID: PMC5105057 DOI: 10.1038/srep36827] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/21/2016] [Indexed: 01/07/2023] Open
Abstract
Stilbenoids, including resveratrol and its methylated derivatives, are natural potent antioxidants, produced by some plants in trace amounts as defense compounds. Extraction of stilbenoids from natural sources is costly due to their low abundance and often limited availability of the plant. Here we engineered the yeast Saccharomyces cerevisiae for production of stilbenoids on a simple mineral medium typically used for industrial production. We applied a pull-push-block strain engineering strategy that included overexpression of the resveratrol biosynthesis pathway, optimization of the electron transfer to the cytochrome P450 monooxygenase, increase of the precursors supply, and decrease of the pathway intermediates degradation. Fed-batch fermentation of the final strain resulted in a final titer of 800 mg l−1 resveratrol, which is by far the highest titer reported to date for production of resveratrol from glucose. We further integrated heterologous methyltransferases into the resveratrol platform strain and hereby demonstrated for the first time de novo biosynthesis of pinostilbene and pterostilbene, which have better stability and uptake in the human body, from glucose.
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Affiliation(s)
- Mingji Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Konstantin Schneider
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Jens Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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24
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Vos T, Hakkaart XDV, de Hulster EAF, van Maris AJA, Pronk JT, Daran-Lapujade P. Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates. Microb Cell Fact 2016; 15:111. [PMID: 27317316 PMCID: PMC4912818 DOI: 10.1186/s12934-016-0501-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/31/2016] [Indexed: 11/24/2022] Open
Abstract
Background Saccharomyces cerevisiae is an established microbial platform for production of native and non-native compounds. When product pathways compete with growth for precursors and energy, uncoupling of growth and product formation could increase product yields and decrease formation of biomass as a by-product. Studying non-growing, metabolically active yeast cultures is a first step towards developing S. cerevisiae as a robust, non-growing cell factory. Microbial physiology at near-zero growth rates can be studied in retentostats, which are continuous-cultivation systems with full biomass retention. Hitherto, retentostat studies on S. cerevisiae have focused on anaerobic conditions, which bear limited relevance for aerobic industrial processes. The present study uses aerobic, glucose-limited retentostats to explore the physiology of non-dividing, respiring S. cerevisiae cultures, with a focus on industrially relevant features. Results Retentostat feeding regimes for smooth transition from exponential growth in glucose-limited chemostat cultures to near-zero growth rates were obtained by model-aided experimental design. During 20 days of retentostats cultivation, the specific growth rate gradually decreased from 0.025 h−1 to below 0.001 h−1, while culture viability remained above 80 %. The maintenance requirement for ATP (mATP) was estimated at 0.63 ± 0.04 mmol ATP (g biomass)−1 h−1, which is ca. 35 % lower than previously estimated for anaerobic retentostats. Concomitant with decreasing growth rate in aerobic retentostats, transcriptional down-regulation of genes involved in biosynthesis and up-regulation of stress-responsive genes resembled transcriptional regulation patterns observed for anaerobic retentostats. The heat-shock tolerance in aerobic retentostats far exceeded previously reported levels in stationary-phase batch cultures. While in situ metabolic fluxes in retentostats were intentionally low due to extreme caloric restriction, off-line measurements revealed that cultures retained a high metabolic capacity. Conclusions This study provides the most accurate estimation yet of the maintenance-energy coefficient in aerobic cultures of S. cerevisiae, which is a key parameter for modelling of industrial aerobic, glucose-limited fed-batch processes. The observed extreme heat-shock tolerance and high metabolic capacity at near-zero growth rates demonstrate the intrinsic potential of S. cerevisiae as a robust, non-dividing microbial cell factory for energy-intensive products. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0501-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tim Vos
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Xavier D V Hakkaart
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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25
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Liu X, Lin J, Hu H, Zhou B, Zhu B. De novobiosynthesis of resveratrol by site-specific integration of heterologous genes inEscherichia coli. FEMS Microbiol Lett 2016; 363:fnw061. [DOI: 10.1093/femsle/fnw061] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2016] [Indexed: 12/19/2022] Open
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