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Besleaga M, Zimmermann C, Ebner K, Mach RL, Mach-Aigner AR, Geier M, Glieder A, Spadiut O, Kopp J. Bi-directionalized promoter systems allow methanol-free production of hard-to-express peroxygenases with Komagataella Phaffii. Microb Cell Fact 2024; 23:177. [PMID: 38879507 PMCID: PMC11179361 DOI: 10.1186/s12934-024-02451-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Heme-incorporating peroxygenases are responsible for electron transport in a multitude of organisms. Yet their application in biocatalysis is hindered due to their challenging recombinant production. Previous studies suggest Komagataella phaffi to be a suitable production host for heme-containing enzymes. In addition, co-expression of helper proteins has been shown to aid protein folding in yeast. In order to facilitate recombinant protein expression for an unspecific peroxygenase (AnoUPO), we aimed to apply a bi-directionalized expression strategy with Komagataella phaffii. RESULTS In initial screenings, co-expression of protein disulfide isomerase was found to aid the correct folding of the expressed unspecific peroxygenase in K. phaffi. A multitude of different bi-directionalized promoter combinations was screened. The clone with the most promising promoter combination was scaled up to bioreactor cultivations and compared to a mono-directional construct (expressing only the peroxygenase). The strains were screened for the target enzyme productivity in a dynamic matter, investigating both derepression and mixed feeding (methanol-glycerol) for induction. Set-points from bioreactor screenings, resulting in the highest peroxygenase productivity, for derepressed and methanol-based induction were chosen to conduct dedicated peroxygenase production runs and were analyzed with RT-qPCR. Results demonstrated that methanol-free cultivation is superior over mixed feeding in regard to cell-specific enzyme productivity. RT-qPCR analysis confirmed that mixed feeding resulted in high stress for the host cells, impeding high productivity. Moreover, the bi-directionalized construct resulted in a much higher specific enzymatic activity over the mono-directional expression system. CONCLUSIONS In this study, we demonstrate a methanol-free bioreactor production strategy for an unspecific peroxygenase, yet not shown in literature. Hence, bi-directionalized assisted protein expression in K. phaffii, cultivated under derepressed conditions, is indicated to be an effective production strategy for heme-containing oxidoreductases. This very production strategy might be opening up further opportunities for biocatalysis.
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Affiliation(s)
- Mihail Besleaga
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Christian Zimmermann
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Katharina Ebner
- bisy GmbH, Wünschendorf 292, Hofstätten an der Raab, 8200, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Martina Geier
- bisy GmbH, Wünschendorf 292, Hofstätten an der Raab, 8200, Austria
| | - Anton Glieder
- bisy GmbH, Wünschendorf 292, Hofstätten an der Raab, 8200, Austria
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Julian Kopp
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria.
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Shen Q, Yan J, Han Y, Zhang Z, Li H, Kong D, Shi J, Cui C, Zhang W. Peroxygenase-Enabled Reductive Kinetic Resolution for the Enantioenrichment of Organoperoxides. Angew Chem Int Ed Engl 2024; 63:e202401590. [PMID: 38477082 DOI: 10.1002/anie.202401590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Enantiomerically pure organoperoxides serve as valuable precursors in organic transformations. Herein, we present the first examples of unspecific peroxygenase catalyzed kinetic resolution of racemic organoperoxides through asymmetric reduction. Through meticulous investigation of the reaction conditions, it is shown that the unspecific peroxygenase from Agrocybe aegerita (AaeUPO) exhibits robust catalytic activity in the kinetic resolution reactions of the model substrate with turnover numbers up to 60000 and turnover frequency of 5.6 s-1. Various aralkyl organoperoxides were successfully resolved by AaeUPO, achieving excellent enantioselectivities (e.g., up to 99 % ee for the (S)-organoperoxide products). Additionally, we screened commercial peroxygenase variants to obtain the organoperoxides with complementary chirality, with one mutant yielding the (R)-products. While unspecific peroxygenases have been extensively demonstrated as a powerful oxidative catalysts, this study highlights their usefulness in catalyzing the reduction of organoperoxides and providing versatile chiral synthons.
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Affiliation(s)
- Qianqian Shen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Juzhang Yan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Yuchen Han
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Zaoxiao Zhang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Huanhuan Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Dulin Kong
- School of Pharmacy, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Jianjun Shi
- College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Chengsen Cui
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Wuyuan Zhang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
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3
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Schmitz F, Röder A, Hoffrogge M, Urlacher VB, Koschorreck K. Agar plate-based activity assay for easy and fast screening of recombinant Pichia pastoris expressing unspecific peroxygenases. Biotechnol J 2024; 19:e2300421. [PMID: 38044796 DOI: 10.1002/biot.202300421] [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: 08/18/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 12/05/2023]
Abstract
Unspecific peroxygenases (UPOs) are promising biocatalysts that catalyze oxyfunctionalization reactions without the need for costly cofactors. Pichia pastoris (reclassified as Komagataella phaffii) is considered an attractive host for heterologous expression of UPOs. However, integration of UPO-expression cassettes into the genome via a single cross-over yields recombinant Pichia transformants with different UPO gene copy numbers resulting in different expression levels. Selection of the most productive Pichia transformants by a commonly used screening in liquid medium in 96-well plates is laborious and lasts up to 5 days. In this work, we developed a simple two-step agar plate-based assay to screen P. pastoris transformants for UPO activity with less effort, within shorter time, and without automated screening devices. After cell growth and protein expression on agar plates supplemented with methanol and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), an additional top agar layer supplemented with ABTS and peroxide is added. UPO activity is visualized within 15 min by formation of green zones around UPO-secreting P. pastoris transformants. The assay was validated with two UPOs, AbrUPO from Aspergillus brasiliensis and evolved PaDa-I from Agrocybe aegerita. The assay results were confirmed in a quantitative 96-deep well plate screening in liquid medium.
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Affiliation(s)
- Fabian Schmitz
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Annika Röder
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Maike Hoffrogge
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
| | - Katja Koschorreck
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf, Germany
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Discovery and Heterologous Expression of Unspecific Peroxygenases. Catalysts 2023. [DOI: 10.3390/catal13010206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Since 2004, unspecific peroxygenases, in short UPOs (EC. 1.11.2.1), have been explored. UPOs are closing a gap between P450 monooxygenases and chloroperoxidases. These enzymes are highly active biocatalysts for the selective oxyfunctionalisation of C–H, C=C and C-C bonds. UPOs are secreted fungal proteins and Komagataella phaffii (Pichia pastoris) is an ideal host for high throughput screening approaches and UPO production. Heterologous overexpression of 26 new UPOs by K. phaffii was performed in deep well plate cultivation and shake flask cultivation up to 50 mL volume. Enzymes were screened using colorimetric assays with 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,6-dimethoxyphenol (DMP), naphthalene and 5-nitro-1,3-benzodioxole (NBD) as reporter substrates. The PaDa-I (AaeUPO mutant) and HspUPO were used as benchmarks to find interesting new enzymes with complementary activity profiles as well as good producing strains. Herein we show that six UPOs from Psathyrella aberdarensis, Coprinopsis marcescibilis, Aspergillus novoparasiticus, Dendrothele bispora and Aspergillus brasiliensis are particularly active.
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Cochereau B, Meslet-Cladière L, Pouchus YF, Grovel O, Roullier C. Halogenation in Fungi: What Do We Know and What Remains to Be Discovered? Molecules 2022; 27:molecules27103157. [PMID: 35630634 PMCID: PMC9144378 DOI: 10.3390/molecules27103157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.
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Affiliation(s)
- Bastien Cochereau
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Laurence Meslet-Cladière
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Olivier Grovel
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
- Correspondence: ; Tel.: +33-251-125-686
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6
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Hofrichter M, Kellner H, Herzog R, Karich A, Kiebist J, Scheibner K, Ullrich R. Peroxide-Mediated Oxygenation of Organic Compounds by Fungal Peroxygenases. Antioxidants (Basel) 2022; 11:163. [PMID: 35052667 PMCID: PMC8772875 DOI: 10.3390/antiox11010163] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/03/2022] Open
Abstract
Unspecific peroxygenases (UPOs), whose sequences can be found in the genomes of thousands of filamentous fungi, many yeasts and certain fungus-like protists, are fascinating biocatalysts that transfer peroxide-borne oxygen (from H2O2 or R-OOH) with high efficiency to a wide range of organic substrates, including less or unactivated carbons and heteroatoms. A twice-proline-flanked cysteine (PCP motif) typically ligates the heme that forms the heart of the active site of UPOs and enables various types of relevant oxygenation reactions (hydroxylation, epoxidation, subsequent dealkylations, deacylation, or aromatization) together with less specific one-electron oxidations (e.g., phenoxy radical formation). In consequence, the substrate portfolio of a UPO enzyme always combines prototypical monooxygenase and peroxidase activities. Here, we briefly review nearly 20 years of peroxygenase research, considering basic mechanistic, molecular, phylogenetic, and biotechnological aspects.
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Affiliation(s)
- Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Robert Herzog
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Alexander Karich
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
| | - Jan Kiebist
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany; (J.K.); (K.S.)
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Am Mühlenberg 13, 14476 Potsdam-Golm, Germany
| | - Katrin Scheibner
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany; (J.K.); (K.S.)
| | - René Ullrich
- Department of Bio- and Environmental Sciences, TU Dresden-International Institute Zittau, Markt 23, 02763 Zittau, Germany; (H.K.); (R.H.); (A.K.); (R.U.)
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7
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Hobisch M, Holtmann D, Gomez de Santos P, Alcalde M, Hollmann F, Kara S. Recent developments in the use of peroxygenases - Exploring their high potential in selective oxyfunctionalisations. Biotechnol Adv 2021; 51:107615. [PMID: 32827669 PMCID: PMC8444091 DOI: 10.1016/j.biotechadv.2020.107615] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022]
Abstract
Peroxygenases are an emerging new class of enzymes allowing selective oxyfunctionalisation reactions in a cofactor-independent way different from well-known P450 monooxygenases. Herein, we focused on recent developments from organic synthesis, molecular biotechnology and reaction engineering viewpoints that are devoted to bring these enzymes in industrial applications. This covers natural diversity from different sources, protein engineering strategies for expression, substrate scope, activity and selectivity, stabilisation of enzymes via immobilisation, and the use of peroxygenases in low water media. We believe that peroxygenases have much to offer for selective oxyfunctionalisations and we have much to study to explore the full potential of these versatile biocatalysts in organic synthesis.
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Affiliation(s)
- Markus Hobisch
- Department of Engineering, Biocatalysis and Bioprocessing Group, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstr. 14, Gießen 35390, Germany
| | | | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, C/Marie Curie 2, Madrid 28049, Spain; EvoEnzyme S.L, C/ Marie Curie 2, Madrid 28049, Spain
| | - Frank Hollmann
- Department of Biotechnology, Biocatalysis Group, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Selin Kara
- Department of Engineering, Biocatalysis and Bioprocessing Group, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark.
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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9
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Kinner A, Rosenthal K, Lütz S. Identification and Expression of New Unspecific Peroxygenases - Recent Advances, Challenges and Opportunities. Front Bioeng Biotechnol 2021; 9:705630. [PMID: 34307325 PMCID: PMC8293615 DOI: 10.3389/fbioe.2021.705630] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
In 2004, the fungal heme-thiolate enzyme subfamily of unspecific peroxygenases (UPOs) was first described in the basidiomycete Agrocybe aegerita. As UPOs naturally catalyze a broad range of oxidative transformations by using hydrogen peroxide as electron acceptor and thus possess a great application potential, they have been extensively studied in recent years. However, despite their versatility to catalyze challenging selective oxyfunctionalizations, the availability of UPOs for potential biotechnological applications is restricted. Particularly limiting are the identification of novel natural biocatalysts, their production, and the description of their properties. It is hence of great interest to further characterize the enzyme subfamily as well as to identify promising new candidates. Therefore, this review provides an overview of the state of the art in identification, expression, and screening approaches of fungal UPOs, challenges associated with current protein production and screening strategies, as well as potential solutions and opportunities.
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Affiliation(s)
- Alina Kinner
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
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10
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Current state and future perspectives of engineered and artificial peroxygenases for the oxyfunctionalization of organic molecules. Nat Catal 2020. [DOI: 10.1038/s41929-020-00507-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Halogenating Enzymes for Active Agent Synthesis: First Steps Are Done and Many Have to Follow. Molecules 2019; 24:molecules24214008. [PMID: 31694313 PMCID: PMC6864650 DOI: 10.3390/molecules24214008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Halogens can be very important for active agents as vital parts of their binding mode, on the one hand, but are on the other hand instrumental in the synthesis of most active agents. However, the primary halogenating compound is molecular chlorine which has two major drawbacks, high energy consumption and hazardous handling. Nature bypassed molecular halogens and evolved at least six halogenating enzymes: Three kind of haloperoxidases, flavin-dependent halogenases as well as α-ketoglutarate and S-adenosylmethionine (SAM)-dependent halogenases. This review shows what is known today on these enzymes in terms of biocatalytic usage. The reader may understand this review as a plea for the usage of halogenating enzymes for fine chemical syntheses, but there are many steps to take until halogenating enzymes are reliable, flexible, and sustainable catalysts for halogenation.
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12
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Bormann S, Gomez Baraibar A, Ni Y, Holtmann D, Hollmann F. Specific oxyfunctionalisations catalysed by peroxygenases: opportunities, challenges and solutions. Catal Sci Technol 2015. [DOI: 10.1039/c4cy01477d] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Peroxygenases are promising oxyfunctionalisation catalysts for organic synthesis.
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Affiliation(s)
| | - Alvaro Gomez Baraibar
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
| | - Yan Ni
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
| | - Dirk Holtmann
- DECHEMA Research Institute
- 60486 Frankfurt am Main
- Germany
| | - Frank Hollmann
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
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14
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Directed evolution of unspecific peroxygenase from Agrocybe aegerita. Appl Environ Microbiol 2014; 80:3496-507. [PMID: 24682297 DOI: 10.1128/aem.00490-14] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unspecific peroxygenase (UPO) represents a new type of heme-thiolate enzyme with self-sufficient mono(per)oxygenase activity and many potential applications in organic synthesis. With a view to taking advantage of these properties, we subjected the Agrocybe aegerita UPO1-encoding gene to directed evolution in Saccharomyces cerevisiae. To promote functional expression, several different signal peptides were fused to the mature protein, and the resulting products were tested. Over 9,000 clones were screened using an ad hoc dual-colorimetric assay that assessed both peroxidative and oxygen transfer activities. After 5 generations of directed evolution combined with hybrid approaches, 9 mutations were introduced that resulted in a 3,250-fold total activity improvement with no alteration in protein stability. A breakdown between secretion and catalytic activity was performed by replacing the native signal peptide of the original parental type with that of the evolved mutant; the evolved leader increased functional expression 27-fold, whereas an 18-fold improvement in the kcat/Km value for oxygen transfer activity was obtained. The evolved UPO1 was active and highly stable in the presence of organic cosolvents. Mutations in the hydrophobic core of the signal peptide contributed to enhance functional expression up to 8 mg/liter, while catalytic efficiencies for peroxidative and oxygen transfer reactions were increased by several mutations in the vicinity of the heme access channel. Overall, the directed-evolution platform described is a valuable point of departure for the development of customized UPOs with improved features and for the study of structure-function relationships.
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Hüttmann S, Buchhaupt M, Schrader J. Identification of a Caldariomyces fumago mutant secreting an inactive form of chloroperoxidase lacking the heme group and N-glycans. PLoS One 2013; 8:e67857. [PMID: 23844113 PMCID: PMC3699481 DOI: 10.1371/journal.pone.0067857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 05/28/2013] [Indexed: 12/01/2022] Open
Abstract
By mutant colony screening of Caldariomyces fumago a mutant was isolated which was slightly greenish on fructose minimal medium and grew slower in comparison to the wild type. The supernatant samples lacked the Soret band typical for the heme group of the CPO and nearly no CPO activity was detected. SDS-PAGE analysis of mutant culture supernatant samples showed production of a 38–40 kDa protein while wild type samples contain the 42 kDa CPO protein. Protein identification using nanoLC-ESI-MS/MS was performed and based on three peptides the protein in the mutant culture was identified as CPO. No differences in the CPO gene sequences of wild type and mutant were found indicating a post-translational defect in protein maturation. Deglycosylation experiments using CPO from wild type and mutant were carried out. After removing N-linked oligosaccharides from wild type CPO a protein band at 38–40 kDa was detected. Our results reveal that the mutant protein lacks the heme group as well as the N-glycans.
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Affiliation(s)
| | | | - Jens Schrader
- DECHEMA Research Institute, Frankfurt am Main, Germany
- * E-mail:
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16
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Ayala M, Verdin J, Vazquez-Duhalt R. The prospects for peroxidase-based biorefining of petroleum fuels. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701379015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Leak DJ, Sheldon RA, Woodley JM, Adlercreutz P. Biocatalysts for selective introduction of oxygen. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420802393519] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Pecyna MJ, Ullrich R, Bittner B, Clemens A, Scheibner K, Schubert R, Hofrichter M. Molecular characterization of aromatic peroxygenase from Agrocybe aegerita. Appl Microbiol Biotechnol 2009; 84:885-97. [DOI: 10.1007/s00253-009-2000-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/31/2009] [Accepted: 04/01/2009] [Indexed: 02/08/2023]
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19
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Increased PCP removal by Amylomyces rouxii transformants with heterologous Phanerochaete chrysosporium peroxidases supplementing their natural degradative pathway. Appl Microbiol Biotechnol 2009; 84:335-40. [DOI: 10.1007/s00253-009-1981-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 03/16/2009] [Accepted: 03/17/2009] [Indexed: 10/20/2022]
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20
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Heterologous expression of the msp2 gene from Marasmius scorodonius. Arch Microbiol 2009; 191:397-402. [DOI: 10.1007/s00203-009-0462-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 01/22/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
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21
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Borole AP, Davison BH. Techno-economic analysis of biocatalytic processes for production of alkene epoxides. Appl Biochem Biotechnol 2008; 137-140:437-49. [PMID: 18478407 DOI: 10.1007/s12010-007-9070-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A techno-economic analysis of two different bioprocesses was conducted, one for the conversion of propylene to propylene oxide (PO) and other for conversion of styrene to styrene epoxide (SO). The first process was a lipase-mediated chemo-enzymatic reaction, whereas the second one was a one-step enzymatic process using chloroperoxidase. The PO produced through the chemo-enzymatic process is a racemic product, whereas the latter process (based on chloroperoxidase) produces an enantio-pure product. The former process thus falls under the category of high-volume commodity chemical (PO); whereas the latter is a low-volume, high-value product (SO).A simulation of the process was conducted using the bioprocess engineering software SuperPro Designer v6.0 (Intelligen, Inc., Scotch Plains, NJ) to determine the economic feasibility of the process. The purpose of the exercise was to compare biocatalytic processes with existing chemical processes for production of alkene expoxides. The results show that further improvements are needed in improving biocatalyst stability to make these bioprocesses competitive with chemical processes.
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Affiliation(s)
- Abhijeet P Borole
- Life Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6226, USA.
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22
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Eibes GM, Lú-Chau TA, Ruiz-Dueñas FJ, Feijoo G, Martínez MJ, Martínez AT, Lema JM. Effect of culture temperature on the heterologous expression of Pleurotus eryngii versatile peroxidase in Aspergillus hosts. Bioprocess Biosyst Eng 2008; 32:129-34. [PMID: 18481101 DOI: 10.1007/s00449-008-0231-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 04/29/2008] [Indexed: 10/22/2022]
Abstract
Production of recombinant versatile peroxidase in Aspergillus hosts was optimized through the modification of temperature during bioreactor cultivations. To further this purpose, the cDNA encoding a versatile peroxidase of Pleurotus eryngii was expressed under control of the alcohol dehydrogenase (alcA) promoter of Aspergillus nidulans. A dependence of recombinant peroxidase production on cultivation temperature was found. Lowering the culture temperature from 28 to 19 degrees C enhanced the level of active peroxidase 5.8-fold and reduced the effective proteolytic activity twofold. Thus, a maximum peroxidase activity of 466 U L(-1) was reached. The same optimization scheme was applied to a recombinant Aspergillus niger that bore the alcohol dehydrogenase regulator (alcR), enabling transformation with the peroxidase cDNA under the same alcA promoter. However, with this strain, the peroxidase activity was not improved, while the effective proteolytic activity was increased between 3- and 11-fold compared to that obtained with A. nidulans.
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Affiliation(s)
- G M Eibes
- Department of Chemical Engineering, Institute of Technology, Santiago de Compostela, Spain.
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23
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Hofrichter M, Ullrich R. Heme-thiolate haloperoxidases: versatile biocatalysts with biotechnological and environmental significance. Appl Microbiol Biotechnol 2006; 71:276-88. [PMID: 16628447 DOI: 10.1007/s00253-006-0417-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 03/06/2006] [Accepted: 03/06/2006] [Indexed: 11/24/2022]
Abstract
Heme-thiolate haloperoxidases are undoubtedly the most versatile biocatalysts of the hemeprotein family and share catalytic properties with at least three further classes of heme-containing oxidoreductases, namely, classic plant and fungal peroxidases, cytochrome P450 monooxygenases, and catalases. For a long time, only one enzyme of this type--the chloroperoxidase (CPO) of the ascomycete Caldariomyces fumago--has been known. The enzyme is commercially available as a fine chemical and catalyzes the unspecific chlorination, bromination, and iodation (but no fluorination) of a variety of electrophilic organic substrates via hypohalous acid as actual halogenating agent. In the absence of halide, CPO resembles cytochrome P450s and epoxidizes and hydroxylates activated substrates such as organic sulfides and olefins; aromatic rings, however, are not susceptible to CPO-catalyzed oxygen-transfer. Recently, a second fungal haloperoxidase of the heme-thiolate type has been discovered in the agaric mushroom Agrocybe aegerita. The UV-Vis adsorption spectrum of the isolated enzyme shows little similarity to that of CPO but is almost identical to a resting-state P450. The Agrocybe aegerita peroxidase (AaP) has strong brominating as well as weak chlorinating and iodating activities, and catalyzes both benzylic and aromatic hydroxylations (e.g., of toluene and naphthalene). AaP and related fungal peroxidases could become promising biocatalysts in biotechnological applications because they seemingly fill the gap between CPO and P450 enzymes and act as "self-sufficient" peroxygenases. From the environmental point of view, the existence of a halogenating mushroom enzyme is interesting because it could be linked to the multitude of halogenated compounds known from these organisms.
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Affiliation(s)
- Martin Hofrichter
- Unit of Environmental Biotechnology, International Graduate School of Zittau, Germany.
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24
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Weenink XO, Punt PJ, van den Hondel CAMJJ, Ram AFJ. A new method for screening and isolation of hypersecretion mutants in Aspergillus niger. Appl Microbiol Biotechnol 2006; 69:711-7. [PMID: 16021486 DOI: 10.1007/s00253-005-0013-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 04/21/2005] [Accepted: 04/23/2005] [Indexed: 10/25/2022]
Abstract
Although filamentous fungi have a unique property of secreting a large amount of homologous extracellular proteins, the use of filamentous fungi as hosts for the production of heterologous proteins is limited because of the low production levels that are generally reached. Here, we report a general screening method for the isolation of mutants with increased protein production levels. The screening method makes use of an Aspergillus niger strain that lacks the two major amylolytic enzymes, glucoamylase (GlaA) and acid amylase (AamA). The double-mutant strain grows poorly on starch and its growth is restored after reintroducing the catalytic part of the glucoamylase gene (GlaA512). We show that the fusion of a heterologous protein, a laccase from Pleurotus ostreatus (Pox2), to the catalytic part of glucoamylase (GlaA512-Pox2) severely hampers efficient production of the glucoamylase protein, resulting in a slow-growth phenotype on starch. Laccase-hypersecreting mutants were obtained by isolating mutants that displayed improved growth on starch plates. The mutant with the highest growth rate on starch displayed the highest laccase activity, indicating that increased glucoamylase protein levels are correlated with higher laccase production levels. In principle, our method can be applied to any low-produced heterologous protein that is secreted as a fusion with the glucoamylase protein.
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Affiliation(s)
- Xavier O Weenink
- Clusius Laboratory, Fungal Genetics Research Group, Institute of Biology, Leiden University, Wassenaarseweg 64, 2333 AL, Leiden, The Netherlands
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Ullrich R, Nüske J, Scheibner K, Spantzel J, Hofrichter M. Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Appl Environ Microbiol 2004; 70:4575-81. [PMID: 15294788 PMCID: PMC492325 DOI: 10.1128/aem.70.8.4575-4581.2004] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrocybe aegerita, a bark mulch- and wood-colonizing basidiomycete, was found to produce a peroxidase (AaP) that oxidizes aryl alcohols, such as veratryl and benzyl alcohols, into the corresponding aldehydes and then into benzoic acids. The enzyme also catalyzed the oxidation of typical peroxidase substrates, such as 2,6-dimethoxyphenol (DMP) or 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS). A. aegerita peroxidase production depended on the concentration of organic nitrogen in the medium, and highest enzyme levels were detected in the presence of soybean meal. Two fractions of the enzyme, AaP I and AaP II, which had identical molecular masses (46 kDa) and isoelectric points of 4.6 to 5.4 and 4.9 to 5.6, respectively (corresponding to six different isoforms), were identified after several steps of purification, including anion- and cation-exchange chromatography. The optimum pH for the oxidation of aryl alcohols was found to be around 7, and the enzyme required relatively high concentrations of H(2)O(2) (2 mM) for optimum activity. The apparent K(m) values for ABTS, DMP, benzyl alcohol, veratryl alcohol, and H(2)O(2) were 37, 298, 1,001, 2,367 and 1,313 microM, respectively. The N-terminal amino acid sequences of the main AaP II spots blotted after two-dimensional gel electrophoresis were almost identical and exhibited almost no homology to the sequences of other peroxidases from basidiomycetes, but they shared the first three amino acids, as well as two additional amino acids, with the heme chloroperoxidase (CPO) from the ascomycete Caldariomyces fumago. This finding is consistent with the fact that AaP halogenates monochlorodimedone, the specific substrate of CPO. The existence of haloperoxidases in basidiomycetous fungi may be of general significance for the natural formation of chlorinated organic compounds in forest soils.
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Affiliation(s)
- René Ullrich
- Unit of Environmental Biotechnology, International Graduate School of Zittau, Markt 23, D-02763 Zittau, Germany.
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Yi X, Conesa A, Punt PJ, Hager LP. Examining the role of glutamic acid 183 in chloroperoxidase catalysis. J Biol Chem 2003; 278:13855-9. [PMID: 12576477 DOI: 10.1074/jbc.m210906200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Site-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in facilitating the reaction between the peroxidase and hydrogen peroxide with the formation of Compound I. In contrast, the other members of the heme peroxidase family use a histidine residue in this role. Plasmids have now been constructed in which the codon for Glu-183 is replaced with a histidine codon. The mutant recombinant gene has been expressed in Aspergillus niger. An analysis of the produced mutant gene shows that the substitution of Glu-183 with a His residue is detrimental to the chlorination and dismutation activity of chloroperoxidase. The activity is reduced by 85 and 50% of wild type activity, respectively. However, quite unexpectedly, the epoxidation activity of the mutant enzyme is significantly enhanced approximately 2.5-fold. These results show that Glu-183 is important but not essential for the chlorination activity of chloroperoxidase. It is possible that the increased epoxidation of the mutant enzyme is based on an increase in the hydrophobicity of the active site.
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Affiliation(s)
- Xianwen Yi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 61801, USA
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27
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Bar-Nun N, Shcolnick S, Mayer AM. Presence of a vanadium-dependent haloperoxidase in Botrytis cinerea. FEMS Microbiol Lett 2002; 217:121-4. [PMID: 12445655 DOI: 10.1111/j.1574-6968.2002.tb11465.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The presence of a haloperoxidase in the mycelium of Botrytis cinerea, extractable with buffer, is demonstrated. A low level of extracellular enzyme activity was also detected. The haloperoxidase from the fungus is a vanadium-dependent glycoprotein, with a pH optimum of about 5.5. Native gel electrophoresis indicates that it is a high molecular mass protein. It appears to react with antibodies against haloperoxidase from Caldariomyces fumago. Enzyme activity is increased 3.5-fold and 15-fold by culture of the fungus in the presence of NaCl or vanadium, respectively. Activity is partly reduced by removal of vanadium and activity can be restored by the addition of vanadium to the enzyme. The possible function of this haloperoxidase is discussed.
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Affiliation(s)
- Nurit Bar-Nun
- Department of Botany, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
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Punt PJ, van Biezen N, Conesa A, Albers A, Mangnus J, van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol 2002; 20:200-6. [PMID: 11943375 DOI: 10.1016/s0167-7799(02)01933-9] [Citation(s) in RCA: 314] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Filamentous fungi have been used as sources of metabolites and enzymes for centuries. For about two decades, molecular genetic tools have enabled us to use these organisms to express extra copies of both endogenous and exogenous genes. This review of current practice reveals that molecular tools have enabled several new developments. But it has been process development that has driven the final breakthrough to achieving commercially relevant quantities of protein. Recent research into gene expression in filamentous fungi has explored their wealth of genetic diversity with a view to exploiting them as expression hosts and as a source of new genes. Inevitably, the progress in the 'genomics' technology will further develop high-throughput technologies for these organisms.
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Affiliation(s)
- Peter J Punt
- TNO Nutrition and Food Research Institute, Dept of Applied Microbiology and Gene Technology, P.O. Box 360, 3700 AJ, Zeist, The Netherlands.
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29
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Abstract
Oxygenase enzymes have seen limited practical applications because of their complexity, poor stabilities, and often low catalytic rates. However, their ability to perform difficult chemistry with high selectivity and specificity has kept oxygenases at the forefront of engineering efforts. Growing understanding of structure-function relationships and improved protein engineering methods are paving the way for applications of oxygenases in chemical synthesis and bioremediation.
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Affiliation(s)
- Patrick C Cirino
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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Abstract
Peroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze oxidative reactions. A large number of peroxidases have been identified in fungal species and are being characterized at the molecular level. In this manuscript we review the current knowledge on the molecular aspects of this type of enzymes. We present an overview of the research efforts undertaken in deciphering the structural basis of the catalytic properties of fungal peroxidases and discuss molecular genetics and protein homology aspects of this enzyme class. Finally, we summarize the potential biotechnological applications of these enzymes and evaluate recent advances on their expression in heterologous systems for production purposes.
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Affiliation(s)
- Ana Conesa
- Department of Applied Microbiology and Gene Technology, TNO Nutrition and Food Research Institute, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
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