1
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Robinson WXQ, Mielke T, Melling B, Cuetos A, Parkin A, Unsworth WP, Cartwright J, Grogan G. Comparing the Catalytic and Structural Characteristics of a 'Short' Unspecific Peroxygenase (UPO) Expressed in Pichia pastoris and Escherichia coli. Chembiochem 2023; 24:e202200558. [PMID: 36374006 PMCID: PMC10098773 DOI: 10.1002/cbic.202200558] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/14/2022] [Indexed: 11/16/2022]
Abstract
Unspecific peroxygenases (UPOs) have emerged as valuable tools for the oxygenation of non-activated carbon atoms, as they exhibit high turnovers, good stability and depend only on hydrogen peroxide as the external oxidant for activity. However, the isolation of UPOs from their natural fungal sources remains a barrier to wider application. We have cloned the gene encoding an 'artificial' peroxygenase (artUPO), close in sequence to the 'short' UPO from Marasmius rotula (MroUPO), and expressed it in both the yeast Pichia pastoris and E. coli to compare the catalytic and structural characteristics of the enzymes produced in each system. Catalytic efficiency for the UPO substrate 5-nitro-1,3-benzodioxole (NBD) was largely the same for both enzymes, and the structures also revealed few differences apart from the expected glycosylation of the yeast enzyme. However, the glycosylated enzyme displayed greater stability, as determined by nano differential scanning fluorimetry (nano-DSF) measurements. Interestingly, while artUPO hydroxylated ethylbenzene derivatives to give the (R)-alcohols, also given by a variant of the 'long' UPO from Agrocybe aegerita (AaeUPO), it gave the opposite (S)-series of sulfoxide products from a range of sulfide substrates, broadening the scope for application of the enzymes. The structures of artUPO reveal substantial differences to that of AaeUPO, and provide a platform for investigating the distinctive activity of this and related'short' UPOs.
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Affiliation(s)
- Wendy X Q Robinson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Tamara Mielke
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Benjamin Melling
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Anibal Cuetos
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Alison Parkin
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - William P Unsworth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Jared Cartwright
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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2
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Walter RM, Zemella A, Schramm M, Kiebist J, Kubick S. Vesicle-based cell-free synthesis of short and long unspecific peroxygenases. Front Bioeng Biotechnol 2022; 10:964396. [PMID: 36394036 PMCID: PMC9663805 DOI: 10.3389/fbioe.2022.964396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal enzymes that catalyze the oxyfunctionalization of non-activated hydrocarbons, making them valuable biocatalysts. Despite the increasing interest in UPOs that has led to the identification of thousands of putative UPO genes, only a few of these have been successfully expressed and characterized. There is currently no universal expression system in place to explore their full potential. Cell-free protein synthesis has proven to be a sophisticated technique for the synthesis of difficult-to-express proteins. In this work, we aimed to establish an insect-based cell-free protein synthesis (CFPS) platform to produce UPOs. CFPS relies on translationally active cell lysates rather than living cells. The system parameters can thus be directly manipulated without having to account for cell viability, thereby making it highly adaptable. The insect-based lysate contains translocationally active, ER-derived vesicles, called microsomes. These microsomes have been shown to allow efficient translocation of proteins into their lumen, promoting post-translational modifications such as disulfide bridge formation and N-glycosylations. In this study the ability of a redox optimized, vesicle-based, eukaryotic CFPS system to synthesize functional UPOs was explored. The influence of different reaction parameters as well as the influence of translocation on enzyme activity was evaluated for a short UPO from Marasmius rotula and a long UPO from Agrocybe aegerita. The capability of the CFPS system described here was demonstrated by the successful synthesis of a novel UPO from Podospora anserina, thus qualifying CFPS as a promising tool for the identification and evaluation of novel UPOs and variants thereof.
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Affiliation(s)
- Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Marina Schramm
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jan Kiebist
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry – Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus – Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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3
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Li Z, Meng S, Nie K, Schwaneberg U, Davari MD, Xu H, Ji Y, Liu L. Flexibility Regulation of Loops Surrounding the Tunnel Entrance in Cytochrome P450 Enhanced Substrate Access Substantially. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Zhongyu Li
- Beijing Bioprocess Key Laboratory, Beijing University of Chemical Technology, Beijing100029, People’s Republic of China
- Institute of Biotechnology, RWTH Aachen University, Aachen52074, Germany
| | - Shuaiqi Meng
- Institute of Biotechnology, RWTH Aachen University, Aachen52074, Germany
| | - Kaili Nie
- Beijing Bioprocess Key Laboratory, Beijing University of Chemical Technology, Beijing100029, People’s Republic of China
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen52074, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen52074, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle06120, Germany
| | - Haijun Xu
- Beijing Bioprocess Key Laboratory, Beijing University of Chemical Technology, Beijing100029, People’s Republic of China
| | - Yu Ji
- Institute of Biotechnology, RWTH Aachen University, Aachen52074, Germany
| | - Luo Liu
- Beijing Bioprocess Key Laboratory, Beijing University of Chemical Technology, Beijing100029, People’s Republic of China
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4
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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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5
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Synthesis of Indigo-Dyes from Indole Derivatives by Unspecific Peroxygenases and Their Application for In-Situ Dyeing. Catalysts 2021. [DOI: 10.3390/catal11121495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tyrian purple (also known as royal or imperial purple) is the oldest known commercial pigment and still one of the most expensive dyes, often associated with the wardrobes of clergy and royalty. It is a brominated derivative of indigo, a natural dye that has been used since 4000 BC. Moreover, just recently, the therapeutic value of indigoids for the treatment of several disorders was discovered. The manufacturing of indigo derivatives by the existing chemical routes has become increasingly uninteresting due to the use of aggressive reagents, expensive starting materials and high-energy costs. Thus, both dyestuff manufacturers and the pharmaceutical industry are interested in the development of gentle preparation methods of indigoids from simple precursors. Here, we describe a simple enzymatic method for the one-step synthesis of Tyrian purple and other indigo derivatives with fungal peroxygenases (UPO, EC 1.11.2.1). The reaction does not require complex co-substrates and works well in phosphate buffers with H2O2 (<0.1 wt%) and less than 5% (v/v) acetonitrile as co-solvent. We demonstrate the scaling up of the reaction to 10 Liters and established thereupon an environmentally friendly combined synthesis and in-situ dyeing process, further simplifying the manufacturing of vat-dyed fabrics. Eventually, we screened a number of halogen-substituted indoles in the search for novel indigo derivatives, which may be of interest for pharmaceutical and/or dyeing purposes.
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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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7
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Rotilio L, Swoboda A, Ebner K, Rinnofner C, Glieder A, Kroutil W, Mattevi A. Structural and biochemical studies enlighten the unspecific peroxygenase from Hypoxylon sp. EC38 as an efficient oxidative biocatalyst. ACS Catal 2021; 11:11511-11525. [PMID: 34540338 DOI: 10.1021/acscatal.1c03065] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Unspecific peroxygenases (UPO) are glycosylated fungal enzymes that can selectively oxidize C-H bonds. UPOs employ hydrogen peroxide as oxygen donor and reductant. With such an easy-to-handle co-substrate and without the need of a reducing agent, UPOs are emerging as convenient oxidative biocatalysts. Here, an unspecific peroxygenase from Hypoxylon sp. EC38 (HspUPO) was identified in an activity-based screen of six putative peroxygenase enzymes that were heterologously expressed in Pichia pastoris. The enzyme was found to tolerate selected organic solvents such as acetonitrile and acetone. HspUPO is a versatile catalyst performing various reactions, such as the oxidation of prim- and sec-alcohols, epoxidations and hydroxylations. Semi-preparative biotransformations were demonstrated for the non-enantioselective oxidation of racemic 1-phenylethanol rac -1b (TON = 13000), giving the product with 88% isolated yield, and the oxidation of indole 6a to give indigo 6b (TON = 2800) with 98% isolated yield. HspUPO features a compact and rigid three-dimensional conformation that wraps around the heme and defines a funnel-shaped tunnel that leads to the heme iron from the protein surface. The tunnel extends along a distance of about 12 Å with a fairly constant diameter in its innermost segment. Its surface comprises both hydrophobic and hydrophilic groups for dealing with small-to-medium size substrates of variable polarities. The structural investigation of several protein-ligand complexes revealed that the active site of HspUPO is accessible to molecules of varying bulkiness and polarity with minimal or no conformational changes, explaining the relatively broad substrate scope of the enzyme. With its convenient expression system, robust operational properties, relatively small size, well-defined structural features, and diverse reaction scope, HspUPO is an exploitable candidate for peroxygenase-based biocatalysis.
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Affiliation(s)
- Laura Rotilio
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Alexander Swoboda
- Austrian Centre of Industrial Biotechnology, c/o Institute of Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Katharina Ebner
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Claudia Rinnofner
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Austrian Centre of Industrial Biotechnology, c/o Institute of Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Gaz, BioTechMed Graz, Heinrichstraße 28, 8010 Graz, Austria
- Field of Excellence BioHealth-University of Graz, 8010 Graz, Austria
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy
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8
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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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9
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Knorrscheidt A, Soler J, Hünecke N, Püllmann P, Garcia-Borràs M, Weissenborn MJ. Accessing Chemo- and Regioselective Benzylic and Aromatic Oxidations by Protein Engineering of an Unspecific Peroxygenase. ACS Catal 2021; 11:7327-7338. [PMID: 34631225 PMCID: PMC8496131 DOI: 10.1021/acscatal.1c00847] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/21/2021] [Indexed: 01/12/2023]
Abstract
![]()
Unspecific
peroxygenases (UPOs) enable oxyfunctionalizations of
a broad substrate range with unparalleled activities. Tailoring these
enzymes for chemo- and regioselective transformations represents a
grand challenge due to the difficulties in their heterologous productions.
Herein, we performed protein engineering in Saccharomyces
cerevisiae using the MthUPO from Myceliophthora thermophila. More than 5300 transformants
were screened. This protein engineering led to a significant reshaping
of the active site as elucidated by computational modelling. The reshaping
was responsible for the increased oxyfunctionalization activity, with
improved kcat/Km values of up to 16.5-fold for the model substrate 5-nitro-1,3-benzodioxole.
Moreover, variants were identified with high chemo- and regioselectivities
in the oxyfunctionalization of aromatic and benzylic carbons, respectively.
The benzylic hydroxylation was demonstrated to perform with enantioselectivities
of up to 95% ee. The proposed evolutionary protocol
and rationalization of the enhanced activities and selectivities acquired
by MthUPO variants represent a step forward toward
the use and implementation of UPOs in biocatalytic synthetic pathways
of industrial interest.
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Affiliation(s)
- Anja Knorrscheidt
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Nicole Hünecke
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Pascal Püllmann
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Martin J. Weissenborn
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Germany
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10
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Zhang W, Li H, Younes SHH, Gómez de Santos P, Tieves F, Grogan G, Pabst M, Alcalde M, Whitwood AC, Hollmann F. Biocatalytic Aromaticity-Breaking Epoxidation of Naphthalene and Nucleophilic Ring-Opening Reactions. ACS Catal 2021; 11:2644-2649. [PMID: 33763289 PMCID: PMC7976598 DOI: 10.1021/acscatal.0c05588] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/29/2021] [Indexed: 02/06/2023]
Abstract
![]()
Aromatic hydroxylation
reactions catalyzed by heme-thiolate enzymes
proceed via an epoxide intermediate. These aromatic epoxides could
be valuable building blocks for organic synthesis giving access to
a range of chiral trans-disubstituted cyclohexadiene synthons. Here,
we show that naphthalene epoxides generated by fungal peroxygenases
can be subjected to nucleophilic ring opening, yielding non-racemic
trans-disubstituted cyclohexadiene derivates, which in turn can be
used for further chemical transformations. This approach may represent
a promising shortcut for the synthesis of natural products and APIs.
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Affiliation(s)
- Wuyuan Zhang
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin 300308, China
| | - Huanhuan Li
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Sabry H. H. Younes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
- Department of Chemistry, Faculty of Sciences, Sohag University, Sohag 82524, Egypt
| | | | - Florian Tieves
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain
| | | | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
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11
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Advances in enzymatic oxyfunctionalization of aliphatic compounds. Biotechnol Adv 2021; 51:107703. [PMID: 33545329 DOI: 10.1016/j.biotechadv.2021.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as "dream biocatalysts" of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H2O2 for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases.
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12
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Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I. Int J Mol Sci 2020; 21:ijms21165734. [PMID: 32785123 PMCID: PMC7460833 DOI: 10.3390/ijms21165734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 11/28/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are fungal heme-thiolate enzymes able to catalyze a wide range of oxidation reactions, such as peroxidase-like, catalase-like, haloperoxidase-like, and, most interestingly, cytochrome P450-like. One of the most outstanding properties of these enzymes is the ability to catalyze the oxidation a wide range of organic substrates (both aromatic and aliphatic) through cytochrome P450-like reactions (the so-called peroxygenase activity), which involves the insertion of an oxygen atom from hydrogen peroxide. To catalyze this reaction, the substrate must access a channel connecting the bulk solution to the heme group. The composition, shape, and flexibility of this channel surely modulate the catalytic ability of the enzymes in this family. In order to gain an understanding of the role of the residues comprising the channel, mutants derived from PaDa-I, a laboratory-evolved UPO variant from Agrocybe aegerita, were obtained. The two phenylalanine residues at the surface of the channel, which regulate the traffic towards the heme active site, were mutated by less bulky residues (alanine and leucine). The mutants were experimentally characterized, and computational studies (i.e., molecular dynamics (MD)) were performed. The results suggest that these residues are necessary to reduce the flexibility of the region and maintain the topography of the channel.
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13
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Yuan B, Mahor D, Fei Q, Wever R, Alcalde M, Zhang W, Hollmann F. Water-Soluble Anthraquinone Photocatalysts Enable Methanol-Driven Enzymatic Halogenation and Hydroxylation Reactions. ACS Catal 2020; 10:8277-8284. [PMID: 32802571 PMCID: PMC7418218 DOI: 10.1021/acscatal.0c01958] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/30/2020] [Indexed: 02/06/2023]
Abstract
![]()
Peroxyzymes
simply use H2O2 as a cosubstrate
to oxidize a broad range of inert C–H bonds. The lability of
many peroxyzymes against H2O2 can be addressed
by a controlled supply of H2O2, ideally in situ.
Here, we report a simple, robust, and water-soluble anthraquinone
sulfonate (SAS) as a promising organophotocatalyst to drive both haloperoxidase-catalyzed
halogenation and peroxygenase-catalyzed oxyfunctionalization reactions.
Simple alcohols, methanol in particular, can be used both as a cosolvent
and an electron donor for H2O2 generation. Very
promising turnover numbers for the biocatalysts of up to 318 000
have been achieved.
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Affiliation(s)
- Bo Yuan
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Durga Mahor
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Ron Wever
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain
| | - Wuyuan Zhang
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
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14
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Screening of Fungi Isolates for C-4 Hydroxylation of R-2-Phenoxypropionic Acid Based on a Novel 96-Well Microplate Assay Method. Appl Biochem Biotechnol 2020; 192:42-56. [PMID: 32212108 DOI: 10.1007/s12010-020-03303-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
R-2-(4-Hydroxyphenoxy)propionic acid (R-HPPA) is a pivotal intermediate for the synthesis of aryloxyphenoxypropionate (APP) herbicide. To rapidly screen microbial isolates with the capacity of hydroxylating R-2-phenoxypropionic acid to R-HPPA from various environmental samples, a convenient and safe 96-well microplate assay method with sodium nitrite (NaNO2) as chromogenic reagent was proposed and optimized. The optimum assay conditions were as follows: the detection wavelength was 420 nm, the concentration of NaNO2 solution was 6.0 g/L, color reaction temperature was 60 °C, the pH of the NaNO2 solution was 2.4, and the reaction time was 40 min. With the aid of this method, screening for microorganisms with C-4-specific hydroxylation activity of R-PPA was conducted. As a result, 23 strains among 3744 single colonies isolated from various samples exhibited the hydroxylation activity. Among these strains, the highest bioconversion rate was achieved by Penicillium oxalicum A5 and Aspergillus versicolor A12, respectively. After 72-h cultivation in shake flask, their conversion rates of R-HPPA from 10 g/L R-PPA reached 21.18% and 40.24%, respectively. The established method was effective in rapid screening of microbes capable of biosynthesizing R-HPPA through hydroxylation of R-PPA, and the obtained two fungi species could be potentially used for R-HPPA production.
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15
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Colloidal graphene oxide enhances the activity of a lipase and protects it from oxidative damage: Insights from physicochemical and molecular dynamics investigations. J Colloid Interface Sci 2020; 567:285-299. [PMID: 32062491 DOI: 10.1016/j.jcis.2020.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/26/2020] [Accepted: 02/04/2020] [Indexed: 01/17/2023]
Abstract
Physical adsorption of lipase from Thermomyces lanuginosus onto single-layer sheets of graphene oxide (GO) was studied using the response surface methodology to evaluate the physicochemical factors - temperature, pH, ionic strength, and concentration - affecting the enzymatic activity and the immobilization efficiency. The immobilization efficiency and the activity of the enzyme were inversely proportional to each other. Specifically, higher pH values increased the immobilization efficacy, but produced changes in the aggregation state and secondary structure of the enzyme, thus decreasing its activity. Lower pH values, in turn, reduced the immobilization efficacy, but increased the activity of the adsorbed lipase. The adsorbed and the free lipase were followed during 600 ns and 3.5 μs, respectively, in molecular dynamics (MD) simulations. MD trajectories showed that irreversible adsorption freezes the enzyme in a state with a correctly opened catalytic cavity, while the active site remains without a direct interaction with the GO adsorbent. In contrast to the interfacial activation of lipases in a hydrophobic environment, where the catalytic pocket attaches to the hydrophobic surface, the adsorption onto GO made the active site of the lipase accessible by altering the tertiary structure of the enzyme, leading to a higher catalytic efficiency. Experimental investigations confirmed that the physical adsorption onto GO induces tertiary structure changes in the lipase and protects it from H2O2 by accepting the oxidative damage upon itself. In summary, the physical adsorption of the lipase onto GO is mainly affected by pH and could possibly provide a spreadable and robust catalytic interface for biotechnological applications.
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16
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Zhou HY, Li YZ, Jiang R, Hu HF, Wang YS, Liu ZQ, Xue YP, Zheng YG. A high-throughput screening method for improved R-2-(4-hydroxyphenoxy)propionic acid biosynthesis. Bioprocess Biosyst Eng 2019; 42:1573-1582. [PMID: 31190281 DOI: 10.1007/s00449-019-02154-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/27/2019] [Indexed: 01/12/2023]
Abstract
R-2-(4-hydroxyphenoxy)propionic acid (R-HPPA) is a key intermediate of the enantiomerically pure phenoxypropionic acid herbicides. R-HPPA could be biosynthesized through selective introduction of a hydroxyl group (-OH) into the substrate R-2-phenoxypropionic acid (R-PPA) at C-4 position, facilitated by microorganisms with hydroxylases. In this study, an efficient high-throughput screening method for improved R-HPPA biosynthesis through microbial hydroxylation was developed. As a hydroxylated aromatic product, R-HPPA could be oxidized by oxidant potassium dichromate to form brown-colored quinone-type compound. The concentration of R-HPPA can be quantified according to the absorbance of the colored compound at a suitable wavelength of 570 nm; and the R-HPPA biosynthetic capability of microorganism strains could also be rapidly evaluated. After optimization of the assay conditions, the high-throughput screening method was successfully used in identification of Beauveria bassiana mutants with enhanced R-HPPA biosynthesis capacity. A positive mutant C-7 with high tolerance to 20 g/L R-PPA was rapidly selected from 1920 mutants. The biomass and R-HPPA titer were 12.5- and 38.19-fold higher compared with the original strain at 20 g/L R-PPA. This high-throughput screening method developed in this work could also be a potential tool for screening strains producing other important phenolic compounds.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yi-Zuo Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Rui Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Hai-Feng Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yuan-Shan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China. .,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, 310014, Zhejiang Province, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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17
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18
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Burek BO, de Boer SR, Tieves F, Zhang W, van Schie M, Bormann S, Alcalde M, Holtmann D, Hollmann F, Bahnemann DW, Bloh JZ. Photoenzymatic Hydroxylation of Ethylbenzene Catalyzed by Unspecific Peroxygenase: Origin of Enzyme Inactivation and the Impact of Light Intensity and Temperature. ChemCatChem 2019. [DOI: 10.1002/cctc.201900610] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Bastien O. Burek
- Chemical Technology Group and Industrial Biotechnology GroupDECHEMA Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Germany
- Institut für Technische ChemieLeibniz Universität Hannover Callinstraße 3 30167 Hannover Germany
| | - Sabrina R. de Boer
- Chemical Technology Group and Industrial Biotechnology GroupDECHEMA Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Germany
| | - Florian Tieves
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 2629HZ Delft (The Netherlands
| | - Wuyuan Zhang
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 2629HZ Delft (The Netherlands
| | - Morten van Schie
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 2629HZ Delft (The Netherlands
| | - Sebastian Bormann
- Chemical Technology Group and Industrial Biotechnology GroupDECHEMA Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Germany
| | - Miguel Alcalde
- Department of BiocatalysisInstitute of Catalysis, CSIC 28049 Madrid Spain
| | - Dirk Holtmann
- Chemical Technology Group and Industrial Biotechnology GroupDECHEMA Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technology Van der Maasweg 9 2629HZ Delft (The Netherlands
| | - Detlef W. Bahnemann
- Institut für Technische ChemieLeibniz Universität Hannover Callinstraße 3 30167 Hannover Germany
- Laboratory “Photoactive Nanocomposite Materials”Saint-Petersburg State University Ulyanovskaya str. 1, Peterhof Saint-Petersburg 198504 Russia
| | - Jonathan Z. Bloh
- Chemical Technology Group and Industrial Biotechnology GroupDECHEMA Forschungsinstitut Theodor-Heuss-Allee 25 60486 Frankfurt am Main Germany
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19
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Karich A, Ullrich R, Scheibner K, Hofrichter M. Fungal Unspecific Peroxygenases Oxidize the Majority of Organic EPA Priority Pollutants. Front Microbiol 2017; 8:1463. [PMID: 28848501 PMCID: PMC5552789 DOI: 10.3389/fmicb.2017.01463] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/20/2017] [Indexed: 11/18/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are secreted fungal enzymes with promiscuity for oxygen transfer and oxidation reactions. Functionally, they represent hybrids of P450 monooxygenases and heme peroxidases; phylogenetically they belong to the family of heme-thiolate peroxidases. Two UPOs from the basidiomycetous fungi Agrocybe aegerita (AaeUPO) and Marasmius rotula (MroUPO) converted 35 out of 40 compounds listed as EPA priority pollutants, including chlorinated benzenes and their derivatives, halogenated biphenyl ethers, nitroaromatic compounds, polycyclic aromatic hydrocarbons (PAHs) and phthalic acid derivatives. These oxygenations and oxidations resulted in diverse products and—if at all—were limited for three reasons: (i) steric hindrance caused by multiple substitutions or bulkiness of the compound as such (e.g., hexachlorobenzene or large PAHs), (ii) strong inactivation of aromatic rings (e.g., nitrobenzene), and (iii) low water solubility (e.g., complex arenes). The general outcome of our study is that UPOs can be considered as extracellular counterparts of intracellular monooxygenases, both with respect to catalyzed reactions and catalytic versatility. Therefore, they should be taken into consideration as a relevant biocatalytic detoxification and biodegradation tool used by fungi when confronted with toxins, xenobiotics and pollutants in their natural environments.
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Affiliation(s)
- Alexander Karich
- Department of Bio-and Environmental Sciences, Technische Universität Dresden-International Institute ZittauZittau, Germany
| | - René Ullrich
- Department of Bio-and Environmental Sciences, Technische Universität Dresden-International Institute ZittauZittau, Germany
| | - Katrin Scheibner
- Enzyme Technology Unit, Brandenburg University of TechnologyCottbus, Germany
| | - Martin Hofrichter
- Department of Bio-and Environmental Sciences, Technische Universität Dresden-International Institute ZittauZittau, Germany
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20
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Zhou P, Lan D, Popowicz GM, Wang X, Yang B, Wang Y. Enhancing H2O2 resistance of an esterase from Pyrobaculum calidifontis by structure-guided engineering of the substrate binding site. Appl Microbiol Biotechnol 2017; 101:5689-5697. [DOI: 10.1007/s00253-017-8299-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/06/2017] [Accepted: 04/12/2017] [Indexed: 11/28/2022]
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21
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Wang Y, Lan D, Durrani R, Hollmann F. Peroxygenases en route to becoming dream catalysts. What are the opportunities and challenges? Curr Opin Chem Biol 2017; 37:1-9. [DOI: 10.1016/j.cbpa.2016.10.007] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023]
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22
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Chen W, Hasegawa DK, Kaur N, Kliot A, Pinheiro PV, Luan J, Stensmyr MC, Zheng Y, Liu W, Sun H, Xu Y, Luo Y, Kruse A, Yang X, Kontsedalov S, Lebedev G, Fisher TW, Nelson DR, Hunter WB, Brown JK, Jander G, Cilia M, Douglas AE, Ghanim M, Simmons AM, Wintermantel WM, Ling KS, Fei Z. The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biol 2016; 14:110. [PMID: 27974049 PMCID: PMC5157087 DOI: 10.1186/s12915-016-0321-y] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/28/2016] [Indexed: 12/04/2022] Open
Abstract
Background The whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is among the 100 worst invasive species in the world. As one of the most important crop pests and virus vectors, B. tabaci causes substantial crop losses and poses a serious threat to global food security. Results We report the 615-Mb high-quality genome sequence of B. tabaci Middle East-Asia Minor 1 (MEAM1), the first genome sequence in the Aleyrodidae family, which contains 15,664 protein-coding genes. The B. tabaci genome is highly divergent from other sequenced hemipteran genomes, sharing no detectable synteny. A number of known detoxification gene families, including cytochrome P450s and UDP-glucuronosyltransferases, are significantly expanded in B. tabaci. Other expanded gene families, including cathepsins, large clusters of tandemly duplicated B. tabaci-specific genes, and phosphatidylethanolamine-binding proteins (PEBPs), were found to be associated with virus acquisition and transmission and/or insecticide resistance, likely contributing to the global invasiveness and efficient virus transmission capacity of B. tabaci. The presence of 142 horizontally transferred genes from bacteria or fungi in the B. tabaci genome, including genes encoding hopanoid/sterol synthesis and xenobiotic detoxification enzymes that are not present in other insects, offers novel insights into the unique biological adaptations of this insect such as polyphagy and insecticide resistance. Interestingly, two adjacent bacterial pantothenate biosynthesis genes, panB and panC, have been co-transferred into B. tabaci and fused into a single gene that has acquired introns during its evolution. Conclusions The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0321-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenbo Chen
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel K Hasegawa
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,US Department of Agriculture-Agricultural Research Service, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - Navneet Kaur
- US Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research, Salinas, CA, 93905, USA
| | - Adi Kliot
- Department of Entomology, The Volcani Center, Bet Dagan, 50250, Israel
| | - Patricia Valle Pinheiro
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,EMBRAPA Rice and Beans, Santo Antônio de Goiás, GO, 75375-000, Brazil.,Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Junbo Luan
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Wenli Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Yimin Xu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Yuan Luo
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Angela Kruse
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xiaowei Yang
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Galina Lebedev
- Department of Entomology, The Volcani Center, Bet Dagan, 50250, Israel
| | - Tonja W Fisher
- Department of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Wayne B Hunter
- US Department of Agriculture-Agricultural Research Service, US Horticultural Laboratory, Fort Pierce, FL, 34945, USA
| | - Judith K Brown
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Michelle Cilia
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,Department of Biology, Lund University, Lund, SE-223 62, Sweden.,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, Bet Dagan, 50250, Israel
| | - Alvin M Simmons
- US Department of Agriculture-Agricultural Research Service, US Vegetable Laboratory, Charleston, SC, 29414, USA
| | - William M Wintermantel
- US Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research, Salinas, CA, 93905, USA.
| | - Kai-Shu Ling
- US Department of Agriculture-Agricultural Research Service, US Vegetable Laboratory, Charleston, SC, 29414, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. .,US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
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23
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Exploring the catalase activity of unspecific peroxygenases and the mechanism of peroxide-dependent heme destruction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Verloop AJW, Vincken JP, Gruppen H. Peroxidase Can Perform the Hydroxylation Step in the "Oxidative Cascade" during Oxidation of Tea Catechins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:8002-8009. [PMID: 27723327 DOI: 10.1021/acs.jafc.6b03029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The formation of black tea thearubigins involves at least two of the following oxidation steps: (i) oligomerization, (ii) rearrangement, and (iii) hydroxylation. The first two are mainly catalyzed by polyphenol oxidase (PPO), whereas the enzyme responsible for hydroxylation has not yet been identified. Two main oxidative activities, peroxidase (POD) and PPO, occur in tea leaves. POD was hypothesized to be responsible for hydroxylation. Model systems with horseradish POD and mushroom tyrosinase were used investigating hydroxylation of theaflavins (TFs). POD was found capable of hydroxylation. TFs with up to five extra hydroxyl groups were annotated by their MS2 data. Hydroxylation by POD was also shown for theanaphtoquinones, theatridimensins, and dehydrodicatechins. The H2O2 concentration influenced the extent of hydroxylation, decreasing it at concentrations above 0.01 mM. TFs with up to five extra hydroxyl groups and traces of other hydroxylated oligomeric catechins could be annotated in black tea without any sample pretreatment, using a selective screening method with reversed-phase ultrahigh-performance liquid chromatography mass spectrometry.
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Affiliation(s)
- Annewieke J W Verloop
- Laboratory of Food Chemistry, Wageningen University , Post Office Box 17, 6700 AA Wageningen, Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University , Post Office Box 17, 6700 AA Wageningen, Netherlands
| | - Harry Gruppen
- Laboratory of Food Chemistry, Wageningen University , Post Office Box 17, 6700 AA Wageningen, Netherlands
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25
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Naphthalenes Oxidation by Aqueous Sodium Hypochlorite Catalyzed by Ruthenium Salts Under Phase-Transfer Catalytic Conditions. Catal Letters 2016. [DOI: 10.1007/s10562-016-1717-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Molina-Espeja P, Cañellas M, Plou FJ, Hofrichter M, Lucas F, Guallar V, Alcalde M. Synthesis of 1-Naphthol by a Natural Peroxygenase Engineered by Directed Evolution. Chembiochem 2016; 17:341-9. [DOI: 10.1002/cbic.201500493] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Patricia Molina-Espeja
- Department of Biocatalysis; Institute of Catalysis; CSIC; C/Marie Curie n° 2L10 28049 Madrid Spain
| | | | - Francisco J. Plou
- Department of Biocatalysis; Institute of Catalysis; CSIC; C/Marie Curie n° 2L10 28049 Madrid Spain
| | - Martin Hofrichter
- TU Dresden; International Institute Zittau; Department of Bio- and Environmental Sciences; Markt 23 02763 Zittau Germany
| | - Fatima Lucas
- Anaxomics Biotech; Balmes 89 08008 Barcelona Spain
- Joint BSC-CRG-IRB Research Program in Computational Biology; Barcelona Supercomputing Center; Jordi Girona 29 08034 Barcelona Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology; Barcelona Supercomputing Center; Jordi Girona 29 08034 Barcelona Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats; Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Miguel Alcalde
- Department of Biocatalysis; Institute of Catalysis; CSIC; C/Marie Curie n° 2L10 28049 Madrid Spain
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27
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Lucas F, Babot ED, Cañellas M, del Río JC, Kalum L, Ullrich R, Hofrichter M, Guallar V, Martínez AT, Gutiérrez A. Molecular determinants for selective C25-hydroxylation of vitamins D2and D3by fungal peroxygenases. Catal Sci Technol 2016. [DOI: 10.1039/c5cy00427f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regioselective hydroxylation of vitamin D byAgrocybe aegeritaandCoprinopsis cinereaperoxygenases was investigated in an experimental and computational study.
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Affiliation(s)
- Fátima Lucas
- Joint BSC-CRG-IRB Research Program in Computational Biology
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
| | - Esteban D. Babot
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | - Marina Cañellas
- Joint BSC-CRG-IRB Research Program in Computational Biology
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
- Anaxomics Biotech
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | | | - René Ullrich
- TU Dresden
- Department of Bio- and Environmental Sciences
- 02763 Zittau
- Germany
| | - Martin Hofrichter
- TU Dresden
- Department of Bio- and Environmental Sciences
- 02763 Zittau
- Germany
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
- ICREA
| | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
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28
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Hofrichter M, Kellner H, Pecyna MJ, Ullrich R. Fungal Unspecific Peroxygenases: Heme-Thiolate Proteins That Combine Peroxidase and Cytochrome P450 Properties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:341-68. [DOI: 10.1007/978-3-319-16009-2_13] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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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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30
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Peng R, Fu X, Tian Y, Zhao W, Zhu B, Xu J, Wang B, Wang L, Yao Q. Metabolic engineering of Arabidopsis for remediation of different polycyclic aromatic hydrocarbons using a hybrid bacterial dioxygenase complex. Metab Eng 2014; 26:100-110. [PMID: 25305469 DOI: 10.1016/j.ymben.2014.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022]
Abstract
The widespread presence of polycyclic aromatic hydrocarbons (PAHs) and their potential harm to various organisms has generated interest in efficiently eliminating these compounds from the environment. Phytoremediation is an efficient technology for cleaning up pollutants. However, unlike microorganisms, plants lack the catabolic pathway for complete degradation of these dangerous groups of compounds. One way to enhance the potential of plants for remediation of these compounds is by transferring genes involved in xenobiotic degradation from microbes to plants. In this paper, four genes, namely nidA and nidB (encoding the large and small subunits of naphthalene dioxygenase of Mycobacterium vanbaalenii PYR-1) as well as NahAa and NahAb (encoding flavoprotein reductase and ferredoxin of the electron-transport chain of the Pseudomonas putida G7 naphthalene dioxygenase system), were transferred and ectopically expressed in Arabidopsis thaliana. Transgenic Arabidopsis plants overexpressing the heterozygous naphthalene dioxygenase system exhibited enhanced tolerance toward 2-4 rings PAHs. Transgenic plants assimilated PAHs from the culture media faster and accumulated less in vivo than wild-type plants. Furthermore, examination of metabolic intermediates by gas chromatography-mass spectrometry revealed that the naphthalene metabolic pathway in transgenic plants mainly involves the dioxygenase pathway. Taken together, our findings suggest that grafting the naphthalene dioxygenase complex into plants is a possible strategy to breed PAH-tolerant plants to efficiently degrade PAHs in the environment.
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Affiliation(s)
- Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Bo Zhu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Jing Xu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research institute, Shanghai Academy of Agricultural Sciences, National Center for Plant Gene Research, Shanghai, PR China.
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31
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Peter S, Karich A, Ullrich R, Gröbe G, Scheibner K, Hofrichter M. Enzymatic one-pot conversion of cyclohexane into cyclohexanone: Comparison of four fungal peroxygenases. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Formation of naphthalene hydrates in the enzymatic conversion of 1,2-dihydronaphthalene by two fungal peroxygenases and subsequent naphthalene formation. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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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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34
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Hofrichter M, Ullrich R. Oxidations catalyzed by fungal peroxygenases. Curr Opin Chem Biol 2014; 19:116-25. [PMID: 24607599 DOI: 10.1016/j.cbpa.2014.01.015] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 11/28/2022]
Abstract
The enzymatic oxyfunctionalization of organic molecules under physiological conditions has attracted keen interest from the chemical community. Unspecific peroxygenases (EC 1.11.2.1) secreted by fungi represent an intriguing enzyme type that selectively transfers peroxide-borne oxygen with high efficiency to diverse substrates including unactivated hydrocarbons. They are glycosylated heme-thiolate enzymes that form a separate superfamily of heme proteins. Among the catalyzed reactions are hydroxylations, epoxidations, dealkylations, oxidations of organic hetero atoms and inorganic halides as well as one-electron oxidations. The substrate spectrum of fungal peroxygenases and the product patterns show similarities both to cytochrome P450 monooxygenases and classic heme peroxidases. Given that selective oxyfunctionalizations are among the most difficult to realize chemical reactions and that respectively transformed molecules are of general importance in organic and pharmaceutical syntheses, it will be worth developing peroxygenase biocatalysts for industrial applications.
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Affiliation(s)
- Martin Hofrichter
- TU Dresden - International Institute Zittau, Department of Bio- and Environmental Sciences, Markt 23, 02763 Zittau, Germany.
| | - René Ullrich
- TU Dresden - International Institute Zittau, Department of Bio- and Environmental Sciences, Markt 23, 02763 Zittau, Germany
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35
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Poraj-Kobielska M, Atzrodt J, Holla W, Sandvoss M, Gröbe G, Scheibner K, Hofrichter M. Preparation of labeled human drug metabolites and drug-drug interaction-probes with fungal peroxygenases. J Labelled Comp Radiopharm 2013; 56:513-9. [PMID: 24285530 DOI: 10.1002/jlcr.3103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 01/15/2023]
Abstract
Enzymatic conversion of a drug can be an efficient alternative for the preparation of a complex metabolite compared with a multi-step chemical synthesis approach. Limitations exist for chemical methods for direct oxygen incorporation into organic molecules often suffering from low yields and unspecific oxidation and also for alternative whole-cell biotransformation processes, which require specific fermentation know-how. Stable oxygen-transferring biocatalysts such as unspecific peroxygenases (UPOs) could be an alternative for the synthesis of human drug metabolites and related stable isotope-labeled analogues. This work shows that UPOs can be used in combination with hydrogen/deuterium exchange for an efficient one-step process for the preparation of 4'-OH-diclofenac-d6. The scope of the reaction was investigated by screening of different peroxygenase subtypes for the transformation of selected deuterium-labeled substrates such as phenacetin-d3 or lidocaine-d3. Experiments with diclofenac-d7 revealed that the deuterium-labeling does not affect the kinetic parameters. By using the latter substrate and H2 (18) O2 as cosubstrate, it was possible to prepare a doubly isotope-labeled metabolite (4'-(18) OH-diclofenac-d6). UPOs offer certain practical advantages compared with P450 enzyme systems in terms of stability and ease of handling. Given these advantages, future work will expand the existing 'monooxygenation toolbox' of different fungal peroxygenases that mimic P450 in vitro reactions.
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Affiliation(s)
- Marzena Poraj-Kobielska
- Department of Biological and Environmental Sciences, TU Dresden - International Institute Zittau, Markt 23, 02763, Zittau, Germany
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36
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Peter S, Kinne M, Ullrich R, Kayser G, Hofrichter M. Epoxidation of linear, branched and cyclic alkenes catalyzed by unspecific peroxygenase. Enzyme Microb Technol 2013; 52:370-6. [DOI: 10.1016/j.enzmictec.2013.02.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
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37
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Karich A, Kluge M, Ullrich R, Hofrichter M. Benzene oxygenation and oxidation by the peroxygenase of Agrocybe aegerita. AMB Express 2013; 3:5. [PMID: 23327645 PMCID: PMC3565944 DOI: 10.1186/2191-0855-3-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/14/2013] [Indexed: 11/10/2022] Open
Abstract
Aromatic peroxygenase (APO) is an extracellular enzyme produced by the agaric basidiomycete Agrocybe aegerita that catalyzes diverse peroxide-dependent oxyfunctionalization reactions. Here we describe the oxygenation of the unactivated aromatic ring of benzene with hydrogen peroxide as co-substrate. The optimum pH of the reaction was around 7 and it proceeded via an initial epoxide intermediate that re-aromatized in aqueous solution to form phenol. Identity of the epoxide intermediate as benzene oxide was proved by a freshly prepared authentic standard using GC-MS and LC-MS analyses. Second and third [per]oxygenation was also observed and resulted in the formation of further hydroxylation and following [per]oxidation products: hydroquinone and p-benzoquinone, catechol and o-benzoquinone as well as 1,2,4-trihydroxybenzene and hydroxy-p-benzoquinone, respectively. Using H218O2 as co-substrate and ascorbic acid as radical scavenger, inhibiting the formation of peroxidation products (e.g., p-benzoquinone), the origin of the oxygen atom incorporated into benzene or phenol was proved to be the peroxide. Apparent enzyme kinetic constants (kcat, Km) for the peroxygenation of benzene were estimated to be around 8 s-1 and 3.6 mM. These results raise the possibility that peroxygenases may be useful for enzymatic syntheses of hydroxylated benzene derivatives under mild conditions.
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38
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Krishna H, Nagaraja P, Shivakumar A, Avinash K, Lingaiah V. Hydroxylation of 4-Amino-5-hydroxynaphthalene-2,7-disulfonic Acid Monosodium Salt Catalysed by Horseradish Peroxidase and Hydrogen Peroxide: Computation of Kinetic Parameters Including Its Application to Crude Plant Extracts. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201200351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Poraj-Kobielska M, Kinne M, Ullrich R, Scheibner K, Hofrichter M. A spectrophotometric assay for the detection of fungal peroxygenases. Anal Biochem 2012; 421:327-9. [DOI: 10.1016/j.ab.2011.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/19/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
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40
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Poraj-Kobielska M, Kinne M, Ullrich R, Scheibner K, Kayser G, Hammel KE, Hofrichter M. Preparation of human drug metabolites using fungal peroxygenases. Biochem Pharmacol 2011; 82:789-96. [DOI: 10.1016/j.bcp.2011.06.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 06/14/2011] [Accepted: 06/14/2011] [Indexed: 11/29/2022]
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41
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Peter S, Kinne M, Wang X, Ullrich R, Kayser G, Groves JT, Hofrichter M. Selective hydroxylation of alkanes by an extracellular fungal peroxygenase. FEBS J 2011; 278:3667-75. [PMID: 21812933 DOI: 10.1111/j.1742-4658.2011.08285.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fungal peroxygenases are novel extracellular heme-thiolate biocatalysts that are capable of catalyzing the selective monooxygenation of diverse organic compounds, using only H(2)O(2) as a cosubstrate. Little is known about the physiological role or the catalytic mechanism of these enzymes. We have found that the peroxygenase secreted by Agrocybe aegerita catalyzes the H(2)O(2)-dependent hydroxylation of linear alkanes at the 2-position and 3-position with high efficiency, as well as the regioselective monooxygenation of branched and cyclic alkanes. Experiments with n-heptane and n-octane showed that the hydroxylation proceeded with complete stereoselectivity for the (R)-enantiomer of the corresponding 3-alcohol. Investigations with a number of model substrates provided information about the route of alkane hydroxylation: (a) the hydroxylation of cyclohexane mediated by H(2)(18)(2) resulted in complete incorporation of (18)O into the hydroxyl group of the product cyclohexanol; (b) the hydroxylation of n-hexane-1,1,1,2,2,3,3-D(7) showed a large intramolecular deuterium isotope effect [(k(H)/k(D))(obs)] of 16.0 ± 1.0 for 2-hexanol and 8.9 ± 0.9 for 3-hexanol; and (c) the hydroxylation of the radical clock norcarane led to an estimated radical lifetime of 9.4 ps and an oxygen rebound rate of 1.06 × 10(11) s(-1). These results point to a hydrogen abstraction and oxygen rebound mechanism for alkane hydroxylation. The peroxygenase appeared to lack activity on long-chain alkanes (> C(16)) and highly branched alkanes (e.g. tetramethylpentane), but otherwise exhibited a broad substrate range. It may accordingly have a role in the bioconversion of natural and anthropogenic alkane-containing structures (including alkyl chains of complex biomaterials) in soils, plant litter, and wood.
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Affiliation(s)
- Sebastian Peter
- Department of Bio- and Environmental Sciences, International Graduate School of Zittau, Zittau, Germany
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42
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Yarman A, Peng L, Wu Y, Bandodkar A, Gajovic-Eichelmann N, Wollenberger U, Hofrichter M, Ullrich R, Scheibner K, Scheller FW. Can peroxygenase and microperoxidase substitute cytochrome P450 in biosensors. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s12566-011-0023-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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43
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44
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Peroxygenase based sensor for aromatic compounds. Biosens Bioelectron 2010; 26:1432-6. [DOI: 10.1016/j.bios.2010.07.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 07/06/2010] [Accepted: 07/07/2010] [Indexed: 11/17/2022]
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45
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Peng L, Wollenberger U, Hofrichter M, Ullrich R, Scheibner K, Scheller FW. Bioelectrocatalytic properties of Agrocybe aegerita peroxygenase. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2009.12.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Kinne M, Zeisig C, Ullrich R, Kayser G, Hammel KE, Hofrichter M. Stepwise oxygenations of toluene and 4-nitrotoluene by a fungal peroxygenase. Biochem Biophys Res Commun 2010; 397:18-21. [DOI: 10.1016/j.bbrc.2010.05.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
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47
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Piontek K, Ullrich R, Liers C, Diederichs K, Plattner DA, Hofrichter M. Crystallization of a 45 kDa peroxygenase/peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:693-8. [PMID: 20516602 PMCID: PMC2882772 DOI: 10.1107/s1744309110013515] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 04/12/2010] [Indexed: 11/10/2022]
Abstract
Some litter-decaying fungi secrete haem-thiolate peroxygenases that oxidize numerous organic compounds and therefore have a high potential for applications such as the detoxification of recalcitrant organic waste and chemical synthesis. Like P450 enzymes, they transfer oxygen functionalities to aromatic and aliphatic substrates. However, in contrast to this class of enzymes, they only require H(2)O(2) for activity. Furthermore, they exhibit halogenation activity, as in the well characterized fungal chloroperoxidase, and display ether-cleavage activity. The major form of a highly glycosylated peroxygenase was produced from Agrocybe aegerita culture media, purified to apparent SDS homogeneity and crystallized under three different pH conditions. One crystal form containing two molecules per asymmetric unit was solved at 2.2 A resolution by SAD using the anomalous signal of the haem iron. Subsequently, two other crystal forms with four molecules per asymmetric unit were determined at 2.3 and 2.6 A resolution by molecular replacement.
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Affiliation(s)
- Klaus Piontek
- Institute of Organic Chemistry and Biochemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.
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48
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Hofrichter M, Ullrich R, Pecyna MJ, Liers C, Lundell T. New and classic families of secreted fungal heme peroxidases. Appl Microbiol Biotechnol 2010; 87:871-97. [PMID: 20495915 DOI: 10.1007/s00253-010-2633-0] [Citation(s) in RCA: 333] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/14/2010] [Accepted: 04/14/2010] [Indexed: 01/15/2023]
Abstract
Heme-containing peroxidases secreted by fungi are a fascinating group of biocatalysts with various ecological and biotechnological implications. For example, they are involved in the biodegradation of lignocelluloses and lignins and participate in the bioconversion of other diverse recalcitrant compounds as well as in the natural turnover of humic substances and organohalogens. The current review focuses on the most recently discovered and novel types of heme-dependent peroxidases, aromatic peroxygenases (APOs), and dye-decolorizing peroxidases (DyPs), which catalyze remarkable reactions such as peroxide-driven oxygen transfer and cleavage of anthraquinone derivatives, respectively, and represent own separate peroxidase superfamilies. Furthermore, several aspects of the "classic" fungal heme-containing peroxidases, i.e., lignin, manganese, and versatile peroxidases (LiP, MnP, and VP), phenol-oxidizing peroxidases as well as chloroperoxidase (CPO), are discussed against the background of recent scientific developments.
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Affiliation(s)
- Martin Hofrichter
- Department of Environmental Biotechnology, International Graduate School of Zittau, Markt 23, 02763, Zittau, Germany.
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49
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Ullrich R, Liers C, Schimpke S, Hofrichter M. Purification of homogeneous forms of fungal peroxygenase. Biotechnol J 2009; 4:1619-26. [DOI: 10.1002/biot.200900076] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Mori T, Nakamura K, Kondo R. Fungal hydroxylation of polychlorinated naphthalenes with chlorine migration by wood rotting fungi. CHEMOSPHERE 2009; 77:1230-1235. [PMID: 19800097 DOI: 10.1016/j.chemosphere.2009.08.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 08/12/2009] [Accepted: 08/27/2009] [Indexed: 05/28/2023]
Abstract
Biodegradation of the polychlorinated naphthalenes (PCNs) 1,4-dichloronaphthalene (1,4-DCN), 2,7-dichloronaphthalene (2,7-DCN), and 1,2,3,4-tetrachloronaphthalene (1,2,3,4-TCN), by the white-rot fungus Phlebia lindtneri was investigated. 1,4-DCN was metabolized to form six metabolites by the fungus. It was estimated from GC-MS fragment patterns that the metabolites were four putative hydroxylated and two dihydrodihydroxylated compounds. One of the hydroxylated products was identified as 2,4-dichloro-1-naphthol by GC-MS analysis using an authentic standard. This intermediate indicated chlorine migration in a biological system of P. lindtneri. 2,7-DCN was metabolized to five hydroxylated metabolites and a dihydrodihydroxylated metabolite. Significant inhibition of the degradation of DCNs and formation of their metabolic products was observed in incubation with the cytochrome P-450 monooxygenase inhibitor piperonyl butoxide. The formation of the dihydrodiol-like metabolites, chlorine migration and the experiment with P-450 inhibitor suggested that P. lindtneri provides hydroxyl metabolites via benzene oxide intermediates of DCNs by a cytochrome P450 monooxygenase. In addition, P. lindtneri degraded 1,2,3,4-TCN; two hydroxylated compounds and a dihydrodihydroxylated compound were formed.
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Affiliation(s)
- Toshio Mori
- Department of Forest and Forest Products Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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