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Mizutani T, Hara R, Takeuchi M, Hibi M, Ueda M, Ogawa J. One-Pot Synthesis of Useful S-Substituted-l-cysteine Sulfoxides Using Genetically Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5339-5347. [PMID: 38417143 DOI: 10.1021/acs.jafc.3c08824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
S-Substituted-l-cysteine sulfoxides are valuable compounds that are contained in plants. Particularly, (+)-alliin and its degraded products have gained significant attention because of their human health benefits. However, (+)-alliin production has been limited to extraction from plants and chemical synthesis; both methods have drawbacks in terms of stability and safety. Here, we proposed the enzymatic cascade reaction for synthesizing (+)-alliin from readily available substrates. To achieve a one-pot (+)-alliin production, we constructed Escherichia coli coexpressing the genes encoding tryptophan synthase from Aeromonas hydrophila ssp. hydrophila NBRC 3820 and l-isoleucine hydroxylase from Bacillus thuringiensis 2e2 for the biocatalyst. Deletion of tryptophanase gene in E. coli increased the yield about 2-fold. Under optimized conditions, (+)-alliin accumulation reached 110 mM, which is the highest productivity thus far. Moreover, natural and unnatural S-substituted-l-cysteine sulfoxides were synthesized by applying various thiols to the cascade reaction. These results indicate that the developed bioprocess would enable the supply of diverse S-substituted-l-cysteine sulfoxides.
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Affiliation(s)
- Taku Mizutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryotaro Hara
- Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Michiki Takeuchi
- Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Makoto Hibi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama 939-0398, Japan
| | - Makoto Ueda
- Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, 771 Nakakuki, Oyama, Tochigi 323-0806, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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Mrudulakumari Vasudevan U, Mai DHA, Krishna S, Lee EY. Methanotrophs as a reservoir for bioactive secondary metabolites: Pitfalls, insights and promises. Biotechnol Adv 2023; 63:108097. [PMID: 36634856 DOI: 10.1016/j.biotechadv.2023.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/10/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
Methanotrophs are potent natural producers of several bioactive secondary metabolites (SMs) including isoprenoids, polymers, peptides, and vitamins. Cryptic biosynthetic gene clusters identified from these microbes via genome mining hinted at the vast and hidden SM biosynthetic potential of these microbes. Central carbon metabolism in methanotrophs offers rare pathway intermediate pools that could be further diversified using advanced synthetic biology tools to produce valuable SMs; for example, plant polyketides, rare carotenoids, and fatty acid-derived SMs. Recent advances in pathway reconstruction and production of isoprenoids, squalene, ectoine, polyhydroxyalkanoate copolymer, cadaverine, indigo, and shinorine serve as proof-of-concept. This review provides theoretical guidance for developing methanotrophs as microbial chassis for high-value SMs. We summarize the distinct secondary metabolic potentials of type I and type II methanotrophs, with specific attention to products relevant to biomedical applications. This review also includes native and non-native SMs from methanotrophs, their therapeutic potential, strategies to induce silent biosynthetic gene clusters, and challenges.
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Affiliation(s)
- Ushasree Mrudulakumari Vasudevan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Dung Hoang Anh Mai
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Jungmann L, Hoffmann SL, Lang C, De Agazio R, Becker J, Kohlstedt M, Wittmann C. High-efficiency production of 5-hydroxyectoine using metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2022; 21:274. [PMID: 36578077 PMCID: PMC9798599 DOI: 10.1186/s12934-022-02003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Extremolytes enable microbes to withstand even the most extreme conditions in nature. Due to their unique protective properties, the small organic molecules, more and more, become high-value active ingredients for the cosmetics and the pharmaceutical industries. While ectoine, the industrial extremolyte flagship, has been successfully commercialized before, an economically viable route to its highly interesting derivative 5-hydroxyectoine (hydroxyectoine) is not existing. RESULTS Here, we demonstrate high-level hydroxyectoine production, using metabolically engineered strains of C. glutamicum that express a codon-optimized, heterologous ectD gene, encoding for ectoine hydroxylase, to convert supplemented ectoine in the presence of sucrose as growth substrate into the desired derivative. Fourteen out of sixteen codon-optimized ectD variants from phylogenetically diverse bacterial and archaeal donors enabled hydroxyectoine production, showing the strategy to work almost regardless of the origin of the gene. The genes from Pseudomonas stutzeri (PST) and Mycobacterium smegmatis (MSM) worked best and enabled hydroxyectoine production up to 97% yield. Metabolic analyses revealed high enrichment of the ectoines inside the cells, which, inter alia, reduced the synthesis of other compatible solutes, including proline and trehalose. After further optimization, C. glutamicum Ptuf ectDPST achieved a titre of 74 g L-1 hydroxyectoine at 70% selectivity within 12 h, using a simple batch process. In a two-step procedure, hydroxyectoine production from ectoine, previously synthesized fermentatively with C. glutamicum ectABCopt, was successfully achieved without intermediate purification. CONCLUSIONS C. glutamicum is a well-known and industrially proven host, allowing the synthesis of commercial products with granted GRAS status, a great benefit for a safe production of hydroxyectoine as active ingredient for cosmetic and pharmaceutical applications. Because ectoine is already available at commercial scale, its use as precursor appears straightforward. In the future, two-step processes might provide hydroxyectoine de novo from sugar.
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Affiliation(s)
- Lukas Jungmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sarah Lisa Hoffmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Caroline Lang
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Raphaela De Agazio
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
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From Cell-Free Protein Synthesis to Whole-Cell Biotransformation: Screening and Identification of Novel α-Ketoglutarate-Dependent Dioxygenases for Preparative-Scale Synthesis of Hydroxy-l-Lysine. Catalysts 2021. [DOI: 10.3390/catal11091038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The selective hydroxylation of non-activated C-H bonds is still a challenging reaction in chemistry. Non-heme Fe2+/α-ketoglutarate-dependent dioxygenases are remarkable biocatalysts for the activation of C-H-bonds, catalyzing mainly hydroxylations. The discovery of new Fe2+/α-ketoglutarate-dependent dioxygenases with suitable reactivity for biotechnological applications is therefore highly relevant to expand the limited range of enzymes described so far. In this study, we performed a protein BLAST to identify homologous enzymes to already described lysine dioxygenases (KDOs). Six novel and yet uncharacterized proteins were selected and synthesized by cell-free protein synthesis (CFPS). The subsequent in vitro screening of the selected homologs revealed activity towards the hydroxylation of l-lysine (Lys) into hydroxy-l-lysine (Hyl), which is a versatile chiral building block. With respect to biotechnological application, Escherichia coli whole-cell biocatalysts were developed and characterized in small-scale biotransformations. As the whole-cell biocatalyst expressing the gene coding for the KDO from Photorhabdus luminescens showed the highest specific activity of 8.6 ± 0.6 U gCDW−1, it was selected for the preparative synthesis of Hyl. Multi-gram scale product concentrations were achieved providing a good starting point for further bioprocess development for Hyl production. A systematic approach was established to screen and identify novel Fe2+/α-ketoglutarate-dependent dioxygenases, covering the entire pathway from gene to product, which contributes to accelerating the development of bioprocesses for the production of value-added chemicals.
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Hermann L, Mais CN, Czech L, Smits SHJ, Bange G, Bremer E. The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient. Biol Chem 2021; 401:1443-1468. [PMID: 32755967 DOI: 10.1515/hsz-2020-0223] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.
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Affiliation(s)
- Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Karl-von Frisch Str. 10, D-35043 Marburg, Germany
| | - Christopher-Nils Mais
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Laura Czech
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von Frisch Str. 8, D-35043 Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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Hara R, Kino K. Enzymatic reactions and microorganisms producing the various isomers of hydroxyproline. Appl Microbiol Biotechnol 2020; 104:4771-4779. [PMID: 32291491 DOI: 10.1007/s00253-020-10603-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/24/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023]
Abstract
Hydroxyproline is an industrially important compound with applications in the pharmaceutical, nutrition, and cosmetic industries. trans-4-Hydroxy-L-proline is recognized as the most abundant of the eight possible isomers (hydroxy group at C-3 or C-4, cis- or trans-configuration, and L- or D-form). However, little attention has been paid to the rare isomers, probably due to their limited availability. This mini-review provides an overview of recent advances in microbial and enzymatic processes to develop practical production strategies for various hydroxyprolines. Here, we introduce three screening strategies, namely, activity-, sequence-, and metabolite-based approaches, allowing identification of diverse proline-hydroxylating enzymes with different product specificities. All naturally occurring hydroxyproline isomers can be produced by using suitable hydroxylases in a highly regio- and stereo-selective manner. Furthermore, crystal structures of relevant hydroxylases provide much insight into their functional roles. Since hydroxylases acting on free L-proline belong to the 2-oxoglutarate-dependent dioxygenase superfamily, cellular metabolism of Escherichia coli coupled with a hydroxylase is a valuable source of 2-oxoglutarate, which is indispensable as a co-substrate in L-proline hydroxylation. Further, microbial hydroxyproline 2-epimerase may serve as a highly adaptable tool to convert L-hydroxyproline into D-hydroxyproline. KEY POINTS: • Proline hydroxylases serve as powerful tools for selectivel-proline hydroxylation. • Engineered Escherichia coli are a robust platform for hydroxyproline production. • Hydroxyproline epimerase convertsl-hydroxyproline intod-hydroxyproline.
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Affiliation(s)
- Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kuniki Kino
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan. .,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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Czech L, Wilcken S, Czech O, Linne U, Brauner J, Smits SHJ, Galinski EA, Bremer E. Exploiting Substrate Promiscuity of Ectoine Hydroxylase for Regio- and Stereoselective Modification of Homoectoine. Front Microbiol 2019; 10:2745. [PMID: 31827466 PMCID: PMC6890836 DOI: 10.3389/fmicb.2019.02745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Extant enzymes are not only highly efficient biocatalysts for a single, or a group of chemically closely related substrates but often have retained, as a mark of their evolutionary history, a certain degree of substrate ambiguity. We have exploited the substrate ambiguity of the ectoine hydroxylase (EctD), a member of the non-heme Fe(II)-containing and 2-oxoglutarate-dependent dioxygenase superfamily, for such a task. Naturally, the EctD enzyme performs a precise regio- and stereoselective hydroxylation of the ubiquitous stress protectant and chemical chaperone ectoine (possessing a six-membered pyrimidine ring structure) to yield trans-5-hydroxyectoine. Using a synthetic ectoine derivative, homoectoine, which possesses an expanded seven-membered diazepine ring structure, we were able to selectively generate, both in vitro and in vivo, trans-5-hydroxyhomoectoine. For this transformation, we specifically used the EctD enzyme from Pseudomonas stutzeri in a whole cell biocatalyst approach, as this enzyme exhibits high catalytic efficiency not only for its natural substrate ectoine but also for homoectoine. Molecular docking approaches with the crystal structure of the Sphingopyxis alaskensis EctD protein predicted the formation of trans-5-hydroxyhomoectoine, a stereochemical configuration that we experimentally verified by nuclear-magnetic resonance spectroscopy. An Escherichia coli cell factory expressing the P. stutzeri ectD gene from a synthetic promoter imported homoectoine via the ProU and ProP compatible solute transporters, hydroxylated it, and secreted the formed trans-5-hydroxyhomoectoine, independent from all currently known mechanosensitive channels, into the growth medium from which it could be purified by high-pressure liquid chromatography.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Sarah Wilcken
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Oliver Czech
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jarryd Brauner
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-Universität Marburg, Marburg, Germany
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