1
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Koo YS, Chen AX, Tay CYJ, Wang VYE, See JY, Lim YH, Tay DWP. Navigating Side Reactions for Robust Colorimetric Detection of Galactose Oxidase Activity. Anal Chem 2025; 97:5266-5273. [PMID: 40021128 PMCID: PMC11912124 DOI: 10.1021/acs.analchem.4c07034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2025]
Abstract
Colorimetric assays are a rapid, scalable technique well suited to enzyme activity screening. However, side reactions or chromogenic reagent instability can result in false positives or false negatives that compromise the accuracy of such assays. Here, we identify three classes of compounds incompatible with the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) colorimetric assay for galactose oxidase activity. Dark green ABTS·+ cationic radicals indicating enzyme activity can get quenched to yield colorless solutions or couple with substrates to form differently colored adducts, thus preventing accurate colorimetric measurements. These side reactions limit the utility of the ABTS assay and introduce uncertainty in the substrate scope to which it is applicable. We have investigated the underlying mechanisms behind these side reactions to conclude that free radical scavengers, phenols with electron-donating substituents, and β,γ-unsaturated aryl ketones are incompatible with the ABTS colorimetric assay. In search of a viable alternative, we developed an assay using 2,4-dinitrophenylhydrazine under neutral conditions with isopropyl alcohol as a solubilizing agent. The use of neutral conditions was found to be critical to avoid hydrolysis of hydrazone adducts, ensuring reproducible measurements. Our assay is compatible with free radical scavengers (R2 = 0.98), phenols with electron-donating substituents (R2 = 0.97), and β,γ-unsaturated aryl ketones (R2 = 0.88). This modified assay enables galactose oxidase activity screening across a broader substrate scope, thus facilitating enzyme use for more practical applications.
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Affiliation(s)
- Ying Sin Koo
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
| | - Adrielle Xianwen Chen
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
| | - Charlotte Y J Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
| | - Valerie Y E Wang
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
| | - Jie Yang See
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Republic of Singapore
| | - Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore 138665, Republic of Singapore
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2
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Tagliabue B, Heckmann CM, Villa R, Grisel S, Berrin JG, Lafond M, Ribeaucourt D, Paul CE. Enantioselective synthesis of ( R)-citronellal from geraniol with an immobilised copper alcohol oxidase and ene reductase. REACT CHEM ENG 2025:d5re00034c. [PMID: 40093767 PMCID: PMC11908116 DOI: 10.1039/d5re00034c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Accepted: 03/01/2025] [Indexed: 03/19/2025]
Abstract
(R)-Citronellal is one of the key chiral intermediates in the synthesis of the isomer (-)-menthol, one of the most commercialised terpenoid flavours worldwide. Enzymatic approaches could represent a less energy-demanding alternative for its synthesis, such as a previously reported bienzymatic cascade starting from inexpensive, commercially available geraniol. A copper radical oxidase (CgrAlcOx) followed by a flavin-dependent ene reductase (OYE2) were used to obtain (R)-citronellal. Here, we used a metal-affinity immobilisation strategy on the His-tagged enzymes for the cascade and studied enzyme recovery and reusability as well as increased solvent tolerance. After screening a panel of resins for enzyme immobilisation and water-immiscible co-solvents, we successfully obtained 95% conversion to (R)-citronellal with 96.9% enantiomeric excess (ee) in a concurrent cascade after 7 h of reaction time, starting from 10 mM of geraniol.
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Affiliation(s)
- Beatrice Tagliabue
- Biocatalysis Section, Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629HZ Delft The Netherlands
| | - Christian M Heckmann
- Biocatalysis Section, Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629HZ Delft The Netherlands
| | - Rocio Villa
- Biocatalysis Section, Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629HZ Delft The Netherlands
| | - Sacha Grisel
- INRAE, Aix Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques Marseille France
- INRAE, Aix Marseille Univ 3PE Platform Marseille France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques Marseille France
| | - Mickael Lafond
- INRAE, Aix Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques Marseille France
| | - David Ribeaucourt
- INRAE, Aix Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques Marseille France
| | - Caroline E Paul
- Biocatalysis Section, Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629HZ Delft The Netherlands
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3
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Wohlgemuth R. Enzyme Catalysis for Sustainable Value Creation Using Renewable Biobased Resources. Molecules 2024; 29:5772. [PMID: 39683928 DOI: 10.3390/molecules29235772] [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: 08/09/2024] [Revised: 11/09/2024] [Accepted: 11/11/2024] [Indexed: 12/18/2024] Open
Abstract
Enzyme catalysis was traditionally used by various human cultures to create value long before its basic concepts were uncovered. This was achieved by transforming the raw materials available from natural resources into useful products. Tremendous scientific and technological progress has been made globally in understanding what constitutes an enzyme; what reactions enzymes can catalyze; and how to search, develop, apply, and improve enzymes to make desired products. The useful properties of enzymes as nature's preferred catalysts, such as their high selectivity, diversity, and adaptability, enable their optimal function, whether in single or multiple reactions. Excellent opportunities for the resource-efficient manufacturing of compounds are provided by the actions of enzymes working in reaction cascades and pathways within the same reaction space, like molecular robots along a production line. Enzyme catalysis plays an increasingly prominent role in industrial innovation and responsible production in various areas, such as green and sustainable chemistry and industrial or white biotechnology. Sources of inspiration include current manufacturing or supply chain challenges, the treasure of natural enzymes, and opportunities to engineer tailor-made enzymes. Making the best use of the power of enzyme catalysis is essential for changing how current products are manufactured; how renewable biobased resources can replace fossil-based resources; and improving the safety, health, and environmental aspects of manufacturing processes to support cleaner and more sustainable production.
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Affiliation(s)
- Roland Wohlgemuth
- Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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4
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Cinca-Fernando P, Ascaso-Alegre C, Sevilla E, Martínez-Júlvez M, Mangas-Sánchez J, Ferreira P. Discovery, characterization, and synthetic potential of two novel bacterial aryl-alcohol oxidases. Appl Microbiol Biotechnol 2024; 108:498. [PMID: 39470785 PMCID: PMC11522167 DOI: 10.1007/s00253-024-13314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 09/11/2024] [Accepted: 09/17/2024] [Indexed: 11/01/2024]
Abstract
The search for novel synthetic tools to prepare industrial chemicals in a safer and greener manner is a continuing challenge in synthetic chemistry. In this manuscript, we report the discovery, characterization, and synthetic potential of two novel aryl-alcohol oxidases from bacteria which are able to oxidize a variety of aliphatic and aromatic alcohols with efficiencies up to 4970 min-1 mM-1. Both enzymes have shown a reasonable thermostability (thermal melting temperature values of 50.9 and 48.6 °C for ShAAO and SdAAO, respectively). Crystal structures revealed an unusual wide-open entrance to the active-site pockets compared to that previously described for traditional fungal aryl-alcohol oxidases, which could be associated with differences observed in substrate scope, catalytic efficiency, and other functional properties. Preparative-scale reactions and the ability to operate at high substrate loadings also demonstrate the potential of these enzymes in synthetic chemistry with total turnover numbers > 38000. Moreover, their availability as soluble and active recombinant proteins enabled their use as cell-free extracts which further highlights their potential for the large-scale production of carbonyl compounds. KEY POINTS: • Identification and characterization of two novel bacterial aryl-alcohol oxidases • Crystal structures reveal wide-open active-site pockets, impacting substrate scope • Total turnover numbers and cell-free extracts demonstrate the synthetic potential.
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Affiliation(s)
- Paula Cinca-Fernando
- Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems (BIFI, GBsC-CSIC Joint Unit), University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Christian Ascaso-Alegre
- Department of Organic Chemistry, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Emma Sevilla
- Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems (BIFI, GBsC-CSIC Joint Unit), University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems (BIFI, GBsC-CSIC Joint Unit), University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Juan Mangas-Sánchez
- Department of Organic and Inorganic Chemistry, IUQOEM, University of Oviedo, Julián Clavería 8, 33006, Oviedo, Spain.
| | - Patricia Ferreira
- Department of Biochemistry and Molecular and Cellular Biology and Institute of Biocomputation and Physics of Complex Systems (BIFI, GBsC-CSIC Joint Unit), University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain.
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5
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Tay DWP, Tan LL, Heng E, Zulkarnain N, Chin EJ, Tan ZYQ, Leong CY, Ng VWP, Yang LK, Seow DCS, Kanagasundaram Y, Ng SB, Lim YH, Wong FT. Tandem mass spectral metabolic profiling of 54 actinobacterial strains and their 459 mutants. Sci Data 2024; 11:977. [PMID: 39244610 PMCID: PMC11380661 DOI: 10.1038/s41597-024-03833-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Natural products encompass a diverse range of compounds with high impact applications in consumer care, agriculture and most notably, therapeutics. However, despite the expansive chemical repertoire indicated in genomic information of microbes, only a small subset can be obtained under laboratory conditions. To increase accessible chemical space and realize Nature's full chemical potential, a multi-pronged genetic- and cultivation-based strategy has been employed to activate and upregulate natural product biosyntheses in native and heterologous strains. This data descriptor documents a characterized collection of 2,138 liquid chromatography-tandem mass spectrometry (LC/MS-MS) spectra of fermentation extracts from 54 native actinobacterial strains collected from soil and marine environments in Singapore, and their 459 activated mutants in 3 to 5 media. A total of 743 unique metabolites have been identified, with the activated mutants demonstrating an approximately 2-fold expansion in accessible chemical space over wild type strains. Interrogating this expanded chemical diversity with cheminformatic tools can provide direction for the discovery of novel natural products with desirable functional activity.
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Affiliation(s)
- Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Singapore Integrative Biosystems and Engineering Research (SIBER), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
| | - Lee Ling Tan
- Singapore Integrative Biosystems and Engineering Research (SIBER), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Singapore Integrative Biosystems and Engineering Research (SIBER), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Nadiah Zulkarnain
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elaine Jinfeng Chin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Zann Yi Qi Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Veronica Wee Pin Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Deborah C S Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
- Singapore Integrative Biosystems and Engineering Research (SIBER), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Fong Tian Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Singapore Integrative Biosystems and Engineering Research (SIBER), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore.
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6
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Cancellieri MC, Nobbio C, Gatti FG, Brenna E, Parmeggiani F. Applications of biocatalytic CC bond reductions in the synthesis of flavours and fragrances. J Biotechnol 2024; 390:13-27. [PMID: 38761886 DOI: 10.1016/j.jbiotec.2024.05.006] [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: 02/29/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Industrial biotechnology and biocatalysis can provide very effective synthetic tools to increase the sustainability of the production of fine chemicals, especially flavour and fragrance (F&F) ingredients, the market demand of which has been constantly increasing in the last years. One of the most important transformations in F&F chemistry is the reduction of CC bonds, typically carried out with metal-catalysed hydrogenations or hydride-based reagents. Its biocatalytic counterpart is a competitive alternative, showcasing a range of advantages such as excellent chemo-, regio- and stereoselectivity, ease of implementation, mild reaction conditions and modest environmental impact. In the present review, the application of biocatalysed alkene reductions (from microbial fermentations with wild-type strains to engineered isolated ene-reductase enzymes) to synthetic processes useful for the F&F industry will be described, highlighting not only the exquisite stereoselectivity achieved, but also the overall improvement when chirality is not involved. Multi-enzymatic cascades involving CC bioreductions are also examined, which allow much greater chemical complexity to be built in one-pot biocatalytic systems.
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Affiliation(s)
- Maria C Cancellieri
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Celeste Nobbio
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Francesco G Gatti
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Elisabetta Brenna
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy.
| | - Fabio Parmeggiani
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy.
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7
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of Macrocyclic Peptides with C-Terminal β-Amino-α-keto Acid Groups by Three Different Metalloenzymes. ACS CENTRAL SCIENCE 2024; 10:1022-1032. [PMID: 38799663 PMCID: PMC11117315 DOI: 10.1021/acscentsci.4c00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-l-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C cross-link between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid, while the methyltransferase acted on the β-carbon of this α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configuration of the atropisomer formed upon biaryl cross-linking. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to isolate new macrocyclic RiPPs biosynthesized via previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Danielle L. Gray
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Toby J. Woods
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kristen M. Flatt
- Materials
Research Laboratory, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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8
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Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of macrocyclic peptides with C-terminal β-amino-α-keto acid groups by three different metalloenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564719. [PMID: 37965205 PMCID: PMC10635010 DOI: 10.1101/2023.10.30.564719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new class involving modifications installed by a cytochrome P450, a multi-nuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-L-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes encoded by the BGC were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization with 2D-NMR and Marfey's method on the resulting RiPP demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C crosslink between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid while the methyltransferase acted on the β-carbon of the α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configurations of the atropisomer that formed upon biaryl crosslinking. The conserved Cys residue in the precursor peptide was not modified as in all other characterized MNIO-containing BGCs; However, mutational analyses demonstrated that it was essential for the MNIO activity on the C-terminal Asp. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to discover new macrocyclic RiPPs and that RiPPs remain a significant source of previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Danielle L. Gray
- School of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Toby J. Woods
- School of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Chandrashekhar Padhi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Kristen M. Flatt
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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10
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Wahart AJC, Dolan JP, Anderson SD, Cheallaigh AN, Staniland J, Lima MA, Skidmore MA, Miller GJ, Cosgrove SC. Harnessing a Biocatalyst to Bioremediate the Purification of Alkylglycosides. Chembiochem 2024; 25:e202300625. [PMID: 37830893 DOI: 10.1002/cbic.202300625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/14/2023]
Abstract
As the world moves towards net-zero carbon emissions, the development of sustainable chemical manufacturing processes is essential. Within manufacturing, purification by distillation is often used, however this process is energy intensive and methods that could obviate or reduce its use are desirable. Developed herein is an alternative, oxidative biocatalytic approach that enables purification of alkyl monoglucosides (essential bio-based surfactant components). Implementing an immobilised engineered alcohol oxidase, a long-chain alcohol by-product derived from alkyl monoglucoside synthesis (normally removed by distillation) is selectively oxidised to an aldehyde, conjugated to an amine resin and then removed by simple filtration. This affords recovery of the purified alkyl monoglucoside. The approach lays a blueprint for further development of sustainable alkylglycoside purification using biocatalysis and, importantly, for refining other important chemical feedstocks that currently rely on distillation.
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Affiliation(s)
- Alice J C Wahart
- Lennard-Jones Laboratory, School of Chemical & Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Jonathan P Dolan
- Lennard-Jones Laboratory, School of Chemical & Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Simon D Anderson
- Lennard-Jones Laboratory, School of Chemical & Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Aisling Ní Cheallaigh
- Lennard-Jones Laboratory, School of Chemical & Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Jessica Staniland
- Croda Europe Ltd., Croda Europe Ltd., Cowick Hall, Snaith, Goole, DN14 9AA, UK
| | - Marcelo A Lima
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Mark A Skidmore
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Gavin J Miller
- Lennard-Jones Laboratory, School of Chemical & Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Sebastian C Cosgrove
- Lennard-Jones Laboratory, School of Chemical & Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
- Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK
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11
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Qin X, Jiang Y, Yao F, Chen J, Kong F, Zhao P, Jin L, Cong Z. Anchoring a Structurally Editable Proximal Cofactor-like Module to Construct an Artificial Dual-center Peroxygenase. Angew Chem Int Ed Engl 2023; 62:e202311259. [PMID: 37713467 DOI: 10.1002/anie.202311259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 09/17/2023]
Abstract
A recent novel strategy for constructing artificial metalloenzymes (ArMs) that target new-to-nature functions uses dual-functional small molecules (DFSMs) with catalytic and anchoring groups for converting P450BM3 monooxygenase into a peroxygenase. However, this process requires excess DFSMs (1000 equivalent of P450) owing to their low binding affinity for P450, thus severely limiting its practical application. Herein, structural optimization of the DFSM-anchoring group considerably enhanced their binding affinity by three orders of magnitude (Kd ≈10-8 M), thus approximating native cofactors, such as FMN or FAD in flavoenzymes. An artificial cofactor-driven peroxygenase was thus constructed. The co-crystal structure of P450BM3 bound to a DFSM clearly revealed a precatalytic state in which the DFSM participates in H2 O2 activation, thus facilitating peroxygenase activity. Moreover, the increased binding affinity substantially decreases the DFSM load to as low as 2 equivalents of P450, while maintaining increased activity. Furthermore, replacement of catalytic groups showed disparate selectivity and activity for various substrates. This study provides an unprecedented approach for assembling ArMs by binding editable organic cofactors as a co-catalytic center, thereby increasing the catalytic promiscuity of P450 enzymes.
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Affiliation(s)
- Xiangquan Qin
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Department of Chemistry, Yanbian University, Yanji, 133002, China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Fuquan Yao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Fanhui Kong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Panxia Zhao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Longyi Jin
- Department of Chemistry, Yanbian University, Yanji, 133002, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
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12
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Michailidou F. The Scent of Change: Sustainable Fragrances Through Industrial Biotechnology. Chembiochem 2023; 24:e202300309. [PMID: 37668275 DOI: 10.1002/cbic.202300309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/29/2023] [Indexed: 09/06/2023]
Abstract
Current environmental and safety considerations urge innovation to address the need for sustainable high-value chemicals that are embraced by consumers. This review discusses the concept of sustainable fragrances, as high-value, everyday and everywhere chemicals. Current and emerging technologies represent an opportunity to produce fragrances in an environmentally and socially responsible way. Biotechnology, including fermentation, biocatalysis, and genetic engineering, has the potential to reduce the environmental footprint of fragrance production while maintaining quality and consistency. Computational and in silico methods, including machine learning (ML), are also likely to augment the capabilities of sustainable fragrance production. Continued innovation and collaboration will be crucial to the future of sustainable fragrances, with a focus on developing novel sustainable ingredients, as well as ethical sourcing practices.
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Affiliation(s)
- Freideriki Michailidou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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13
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Ayikpoe R, Zhu L, Chen JY, Ting CP, van der Donk WA. Macrocyclization and Backbone Rearrangement During RiPP Biosynthesis by a SAM-Dependent Domain-of-Unknown-Function 692. ACS CENTRAL SCIENCE 2023; 9:1008-1018. [PMID: 37252350 PMCID: PMC10214503 DOI: 10.1021/acscentsci.3c00160] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 05/31/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of post-translational modification enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes, and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme complex catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethyl group. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent reaction catalyzed by a DUF692 enzyme complex, further expanding the repertoire of remarkable reactions catalyzed by these enzymes. Based on the three currently characterized DUF692 family members, we suggest the family be called multinuclear non-heme iron dependent oxidative enzymes (MNIOs).
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Affiliation(s)
- Richard
S. Ayikpoe
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Jeff Y. Chen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Chi P. Ting
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
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14
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Nieto S, Bernal JM, Villa R, Garcia-Verdugo E, Donaire A, Lozano P. Sustainable Setups for the Biocatalytic Production and Scale-Up of Panthenyl Monoacyl Esters under Solvent-Free Conditions. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:5737-5747. [PMID: 37064495 PMCID: PMC10091472 DOI: 10.1021/acssuschemeng.3c00266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/10/2023] [Indexed: 06/19/2023]
Abstract
A sustainable scaling-up process for the biocatalytic production of new bioactive provitamin-B5 monoacyl esters has been demonstrated. A solvent-free reaction protocol, based on the formation of eutectic mixtures between neat substrates, renders highly efficient direct esterification of free fatty acids (i.e., from C6 to C18 alkyl-chain length) with panthenol catalyzed by lipase. The scale-up from 0.5 to 500 g was evaluated by means of using several reaction systems (i.e., ultrasound assistance, orbital shaking, rotary evaporator, and mechanical stirring coupled to vacuum). For all reactor systems, the yield in panthenyl monoacyl esters was improved by increasing the length of the alkyl chain of the fatty acid (i.e., from 63% yield for panthenyl butyrate to 83% yield for panthenyl myristate). The best results (87-95% product yield, for all cases) were obtained upon a scale-up (50-500 g size) and when a vacuum system was coupled to the biocatalytic reaction unit. Under the optimized conditions, a 5-fold reduction of the amount of biocatalysts with respect to reactors without vacuum was achieved. The recovery and reuse of the immobilized enzyme for five operation cycles were also demonstrated. Finally, different metrics have been applied to assess the greenness of the solvent-free biocatalytic synthesis of panthenyl monoesters here reported.
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Affiliation(s)
- Susana Nieto
- Departamento
de Bioquimica y Biologia Molecular B e Inmunologia. Facultad de Quimica,
Campus de Espinardo, Universidad de Murcia, E-30100 Murcia, Spain
| | - Juana M. Bernal
- Departamento
de Bioquimica y Biologia Molecular B e Inmunologia. Facultad de Quimica,
Campus de Espinardo, Universidad de Murcia, E-30100 Murcia, Spain
| | - Rocio Villa
- Departamento
de Bioquimica y Biologia Molecular B e Inmunologia. Facultad de Quimica,
Campus de Espinardo, Universidad de Murcia, E-30100 Murcia, Spain
- Department
of Biotechnology, Delft University of Technology, Building 58 Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Eduardo Garcia-Verdugo
- Departamento
de Quimica Organica e Inorganica, Universidad
Jaume I, E-12071 Castellon, Spain
| | - Antonio Donaire
- Departamento
de Quimica Inorganica. Facultad de Quimica, Campus de Espinardo, Universidad de Murcia, E-30100 Murcia, Spain
| | - Pedro Lozano
- Departamento
de Bioquimica y Biologia Molecular B e Inmunologia. Facultad de Quimica,
Campus de Espinardo, Universidad de Murcia, E-30100 Murcia, Spain
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15
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The Prospects of Algae-Derived Vitamins and Their Precursors for Sustainable Cosmeceuticals. Processes (Basel) 2023. [DOI: 10.3390/pr11020587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Aquatic algae are a rich source of a wide range of bioproducts intended to compete for a sizable global market share. Thanks to the gradual shift towards the use of natural products, microalgae-derived bioactive compounds offer an ecofriendly and vegan option to the cosmeceutical sector, whose products aim to improve skin health but currently consist of mostly synthetic chemicals. In particular, algae-derived vitamins and their precursors are being explored and widely used in the cosmeceuticals industry as compounds that contain biologically active ingredients with therapeutic benefits. The present review highlights the current strategies for industrial production of an array of vitamins from algae for cosmeceutical applications. When compared to traditional plant sources, algae have been found to accumulate vitamins, such as A, B1, B2, B6, B12, C and E, in high concentrations. The purpose of this review is to provide context for the development of a green and sustainable algae-derived bioeconomy by summarizing and comparing the current market for vitamins and precursors derived from algae, as well as presenting novel strategies and key findings from the most recent research in this area. Emphasis is placed on novel biotechnological interventions that encompass genetic modifications, genetic engineering, and media development to enhance vitamin biosynthesis.
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16
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Ayikpoe RS, Zhu L, Chen JY, Ting CP, van der Donk WA. A remarkable transformation catalyzed by a domain-of-unknown-function 692 during the biosynthesis of a new RiPP natural product. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527370. [PMID: 36798408 PMCID: PMC9934569 DOI: 10.1101/2023.02.06.527370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of posttranslational modification enzymes involved in the biosynthesis of ribosomally-synthesized and posttranslationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is ubiquitously encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethylation. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent DUF692 enzyme, further expanding the repertoire of remarkable reactions catalyzed by these enzymes.
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Affiliation(s)
- Richard S. Ayikpoe
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Jeff Y. Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Chi P. Ting
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Howard Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
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17
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Chemoenzymatic Synthesis of Optically Active Alcohols Possessing 1,2,3,4-Tetrahydroquinoline Moiety Employing Lipases or Variants of the Acyltransferase from Mycobacterium smegmatis. Catalysts 2022. [DOI: 10.3390/catal12121610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The enzymatic kinetic resolution (EKR) of racemic alcohols or esters is a broadly recognized methodology for the preparation of these compounds in optically active form. Although EKR approaches have been developed for the enantioselective transesterification of a vast number of secondary alcohols or hydrolysis of their respective esters, to date, there is no report of bio- or chemo-catalytic asymmetric synthesis of non-racemic alcohols possessing 1,2,3,4-tetrahydroquinoline moiety, which are valuable building blocks for the pharmaceutical industry. In this work, the kinetic resolution of a set of racemic 1,2,3,4-tetrahydroquinoline-propan-2-ols was successfully carried out in neat organic solvents (in the case of CAL-B and BCL) or in water (in the case of MsAcT single variants) using immobilized lipases from Candida antarctica type B (CAL-B) and Burkholderia cepacia (BCL) or engineered acyltransferase variants from Mycobacterium smegmatis (MsAcT) as the biocatalysts and vinyl acetate as irreversible acyl donor, yielding enantiomerically enriched (S)-alcohols and the corresponding (R)-acetates with E-values up to 328 and excellent optical purities (>99% ee). In general, higher ee-values were observed in the reactions catalyzed by lipases; however, the rates of the reactions were significantly better in the case of MsAcT-catalyzed enantioselective transesterifications. Interestingly, we have experimentally proved that enantiomerically enriched 1-(7-nitro-3,4-dihydroquinolin-1(2H)-yl)propan-2-ol undergoes spontaneous amplification of optical purity under achiral chromatographic conditions.
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18
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Chen X, Dou Z, Luo T, Sun Z, Ma H, Xu G, Ni Y. Directed reconstruction of a novel ancestral alcohol dehydrogenase featuring shifted pH-profile, enhanced thermostability and expanded substrate spectrum. BIORESOURCE TECHNOLOGY 2022; 363:127886. [PMID: 36067899 DOI: 10.1016/j.biortech.2022.127886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Ancestral enzymes are promising for industrial biotechnology due to high stability and catalytic promiscuity. An effective protocol was developed for the directed resurrection of ancestral enzymes. Employing genome mining with diaryl alcohol dehydrogenase KpADH as the probe, descendant enzymes D10 and D11 were firstly identified. Then through ancestral sequence reconstruction, A64 was resurrected with a specific activity of 4.3 U·mg-1. The optimum pH of A64 was 7.5, distinct from 5.5 of D10. The T15 50 and Tm values of A64 were 57.5 °C and 61.7 °C, significantly higher than those of the descendant counterpart. Substrate spectrum of A64 was quantitively characterized with a Shannon-Wiener index of 2.38, more expanded than D10, especially, towards bulky ketones in Group A and B. A64 also exhibited higher enantioselectivity. This study provides an effective protocol for constructing of ancestral enzymes and an efficient ancestral enzyme of industrial relevance for asymmetric synthesis of chiral alcohols.
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Affiliation(s)
- Xiaoyu Chen
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhe Dou
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Tianwei Luo
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zewen Sun
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Hongmin Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Guochao Xu
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Ye Ni
- Key laboratory of industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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19
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Lubberink M, Finnigan W, Schnepel C, Baldwin CR, Turner NJ, Flitsch SL. One-Step Biocatalytic Synthesis of Sustainable Surfactants by Selective Amide Bond Formation. Angew Chem Int Ed Engl 2022; 61:e202205054. [PMID: 35595679 PMCID: PMC9401052 DOI: 10.1002/anie.202205054] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 12/28/2022]
Abstract
N-alkanoyl-N-methylglucamides (MEGAs) are non-toxic surfactants widely used as commercial ingredients, but more sustainable syntheses towards these compounds are highly desirable. Here, we present a biocatalytic route towards MEGAs and analogues using a truncated carboxylic acid reductase construct tailored for amide bond formation (CARmm-A). CARmm-A is capable of selective amide bond formation without the competing esterification reaction observed in lipase catalysed reactions. A kinase was implemented to regenerate ATP from polyphosphate and by thorough reaction optimisation using design of experiments, the amine concentration needed for amidation was significantly reduced. The wide substrate scope of CARmm-A was exemplified by the synthesis of 24 commercially relevant amides, including selected examples on a preparative scale. This work establishes acyl-phosphate mediated chemistry as a highly selective strategy for biocatalytic amide bond formation in the presence of multiple competing alcohol functionalities.
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Affiliation(s)
- Max Lubberink
- Department of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK
| | - William Finnigan
- Department of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK
| | - Christian Schnepel
- Department of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK
| | - Christopher R. Baldwin
- Department of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK
| | - Nicholas J. Turner
- Department of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK
| | - Sabine L. Flitsch
- Department of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK
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20
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Lin Z, Huang B, Ouyang L, Zheng L. Synthesis of Cyclic Fragrances via Transformations of Alkenes, Alkynes and Enynes: Strategies and Recent Progress. Molecules 2022; 27:3576. [PMID: 35684511 PMCID: PMC9182196 DOI: 10.3390/molecules27113576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/04/2022] Open
Abstract
With increasing demand for customized commodities and the greater insight and understanding of olfaction, the synthesis of fragrances with diverse structures and odor characters has become a core task. Recent progress in organic synthesis and catalysis enables the rapid construction of carbocycles and heterocycles from readily available unsaturated molecular building blocks, with increased selectivity, atom economy, sustainability and product diversity. In this review, synthetic methods for creating cyclic fragrances, including both natural and synthetic ones, will be discussed, with a focus on the key transformations of alkenes, alkynes, dienes and enynes. Several strategies will be discussed, including cycloaddition, catalytic cyclization, ring-closing metathesis, intramolecular addition, and rearrangement reactions. Representative examples and the featured olfactory investigations will be highlighted, along with some perspectives on future developments in this area.
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Affiliation(s)
| | | | | | - Liyao Zheng
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China; (Z.L.); (B.H.); (L.O.)
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21
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Lubberink M, Finnigan W, Schnepel C, Baldwin C, Turner N, Flitsch S. One‐Step Biocatalytic Synthesis of Sustainable Surfactants by Selective Amide Bond Formation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Max Lubberink
- The University of Manchester chemistry UNITED KINGDOM
| | | | | | | | - Nicholas Turner
- The University of Manchester chemistry Manchester Interdisciplinary Bio Centre131 Princess Street M1 7DN Manchester UNITED KINGDOM
| | - Sabine Flitsch
- The University of Manchester MIB School of Chemistry 131 Princess Street M1 7DN Manchester UNITED KINGDOM
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22
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Zha W, Zhang F, Shao J, Ma X, Zhu J, Sun P, Wu R, Zi J. Rationally engineering santalene synthase to readjust the component ratio of sandalwood oil. Nat Commun 2022; 13:2508. [PMID: 35523896 PMCID: PMC9076924 DOI: 10.1038/s41467-022-30294-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022] Open
Abstract
Plant essential oils (PEOs) are widely used in cosmetic and nutraceutical industries. The component ratios of PEOs determine their qualities. Controlling the component ratios is challenging in construction of PEO biotechnological platforms. Here, we explore the catalytic reaction pathways of both product-promiscuous and product-specific santalene synthases (i.e., SaSSy and SanSyn) by multiscale simulations. F441 of SanSyn is found as a key residue restricting the conformational dynamics of the intermediates, and thereby the direct deprotonation by the general base T298 dominantly produce α-santalene. The subsequent mutagenesis of this plastic residue leads to generation of a mutant enzyme SanSynF441V which can produce both α- and β-santalenes. Through metabolic engineering efforts, the santalene/santalol titer reaches 704.2 mg/L and the component ratio well matches the ISO 3518:2002 standard. This study represents a paradigm of constructing biotechnological platforms of PEOs with desirable component ratios by the combination of metabolic and enzymatic engineering. Controlling the component ratios of plant essential oils is challenging in their heterologous bioproduction. Here, the authors combine metabolic and enzymatic engineering strategies to achieve the production of sandalwood oil with a desirable component ratio in baker’s yeast.
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Affiliation(s)
- Wenlong Zha
- College of Pharmacy, Jinan University, 510632, Guangzhou, China
| | - Fan Zhang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, China
| | - Jiaqi Shao
- College of Pharmacy, Jinan University, 510632, Guangzhou, China
| | - Xingmei Ma
- College of Pharmacy, Jinan University, 510632, Guangzhou, China
| | - Jianxun Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050, Beijing, China
| | - Pinghua Sun
- College of Pharmacy, Jinan University, 510632, Guangzhou, China
| | - Ruibo Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, China.
| | - Jiachen Zi
- College of Pharmacy, Jinan University, 510632, Guangzhou, China. .,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050, Beijing, China. .,Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, 510632, Guangzhou, China.
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23
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Montiel MC, Asensi M, Gimeno-Martos S, Máximo F, Bastida J. Sustainable Biocatalytic Procedure for Obtaining New Branched Acid Esters. MATERIALS (BASEL, SWITZERLAND) 2021; 14:6847. [PMID: 34832249 PMCID: PMC8625366 DOI: 10.3390/ma14226847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022]
Abstract
Biocatalytic synthesis of 2-ethylhexyl 2-methylhexanoate is described in this work for the first time. This branched-chain ester is suitable for use at low temperatures in numerous applications. The immobilized lipase Novozym® 435 has demonstrated its ability to catalyze the ester synthesis from 2-ethylhexanol and 2-methylhexanoic acid in a solvent-free medium. The high reaction times that are required result in a loss of alcohol by evaporation, which must be compensated for with an excess of this substrate if high conversions are to be achieved. Therefore, two strategies are established: 70 °C with a 10% excess of alcohol, which requires a longer operating time and provides conversions of 97%, and 80 °C with a 20% excess of alcohol, which allows for the achievement of a 99% conversion in a shorter time. The optimal reaction conditions have been chosen based on reusability of the enzyme, process productivity, green metrics and preliminary economic study. When the synthesis is carried out under the best conditions (70 °C, 10% molar excess of alcohol and six uses of the immobilized enzyme) a productivity of 203.84 kg product × kg biocatalyst-1 is attained. The biocatalytic procedure matches many of the objectives of "green chemistry" and is suitable to be scaled up and used in industrial manufacturing.
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Affiliation(s)
| | | | | | | | - Josefa Bastida
- Chemical Engineering Department, Faculty of Chemistry, Campus Mare Nostrum, University of Murcia, 30100 Murcia, Spain; (M.C.M.); (M.A.); (S.G.-M.); (F.M.)
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