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Cherubino Ribeiro TH, de Oliveira RR, das Neves TT, Santiago WD, Mansur BL, Saczk AA, Vilela de Resende ML, Chalfun-Junior A. Metabolic Pathway Reconstruction Indicates the Presence of Important Medicinal Compounds in Coffea Such as L-DOPA. Int J Mol Sci 2023; 24:12466. [PMID: 37569839 PMCID: PMC10419165 DOI: 10.3390/ijms241512466] [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: 06/27/2023] [Revised: 07/21/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The use of transcriptomic data to make inferences about plant metabolomes is a useful tool to help the discovery of important compounds in the available biodiversity. To unveil previously undiscovered metabolites of Coffea, of phytotherapeutic and economic value, we employed 24 RNAseq libraries. These libraries were sequenced from leaves exposed to a diverse range of environmental conditions. Subsequently, the data were meticulously processed to create models of putative metabolic networks, which shed light on the production of potential natural compounds of significant interest. Then, we selected one of the predicted compounds, the L-3,4-dihydroxyphenylalanine (L-DOPA), to be analyzed by LC-MS/MS using three biological replicates of flowers, leaves, and fruits from Coffea arabica and Coffea canephora. We were able to identify metabolic pathways responsible for producing several compounds of economic importance. One of the identified pathways involved in isoquinoline alkaloid biosynthesis was found to be active and producing L-DOPA, which is a common product of POLYPHENOL OXIDASES (PPOs, EC 1.14.18.1 and EC 1.10.3.1). We show that coffee plants are a natural source of L-DOPA, a widely used medicine for treatment of the human neurodegenerative condition called Parkinson's disease. In addition, dozens of other compounds with medicinal significance were predicted as potential natural coffee products. By further refining analytical chemistry techniques, it will be possible to enhance the characterization of coffee metabolites, enabling a deeper understanding of their properties and potential applications in medicine.
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Affiliation(s)
- Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-000, Brazil; (T.H.C.R.); (R.R.d.O.)
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-000, Brazil; (T.H.C.R.); (R.R.d.O.)
| | - Taís Teixeira das Neves
- Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-000, Brazil;
| | - Wilder Douglas Santiago
- National Institute of Coffee Science and Technology (INCT-CAFÉ), Federal University of Lavras (UFLA), Lavras 37200-000, Brazil;
| | - Bethania Leite Mansur
- Multiuser Instrumental Analysis Laboratory (LabMAI), Federal University of Lavras (UFLA), Lavras 37200-000, Brazil;
| | - Adelir Aparecida Saczk
- Analytical and Electroanalytical Laboratory (LAE), Federal University of Lavras (UFLA), Lavras 37200-000, Brazil;
| | | | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-000, Brazil; (T.H.C.R.); (R.R.d.O.)
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2
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Agunbiade M, Le Roes-Hill M. Application of bacterial tyrosinases in organic synthesis. World J Microbiol Biotechnol 2021; 38:2. [PMID: 34817696 DOI: 10.1007/s11274-021-03186-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/06/2021] [Indexed: 11/26/2022]
Abstract
Bacterial tyrosinases, as in the case of other bacterial oxidative enzymes, have been found to possess biochemical characteristics that typically make them more suited to applications requiring special operational conditions such as alkaline pH, high or low temperature, the presence of organic solvents, and the presence of inhibitors. Even though a great deal is known about fungal tyrosinases, bacterial tyrosinases still vastly remain underexplored for their potential application in organic synthesis. A literature survey in particular highlights the gaps in our knowledge pertaining to their biochemical properties. Bacterial tyrosinases have not only shown promise in the synthesis of medically important compounds such as L-3,4-dihydroxyphenylalanine (L-DOPA) and melanin but have also seen application in cross-linking reactions of proteins and the polymerization of environmental pollutants. Their ability to catalyse o-hydroxylation reactions have shown some degree of promise in the biocatalytic conversion of resveratrol to piceatannol, tyrosol to hydroxytyrosol, and many more. In this review, we will explore the world of bacterial tyrosinases, their current applications, and future perspectives for the application of these enzymes in organic synthesis.
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Affiliation(s)
- Mayowa Agunbiade
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, 7535, Bellville, South Africa
| | - Marilize Le Roes-Hill
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, 7535, Bellville, South Africa.
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3
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Nikolaivits E, Valmas A, Dedes G, Topakas E, Dimarogona M. Considerations Regarding Activity Determinants of Fungal Polyphenol Oxidases Based on Mutational and Structural Studies. Appl Environ Microbiol 2021; 87:e00396-21. [PMID: 33741634 PMCID: PMC8208164 DOI: 10.1128/aem.00396-21] [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: 02/25/2021] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Polyphenol oxidases (PPOs) are an industrially relevant family of enzymes, being involved in the postharvest browning of fruits and vegetables, as well as in human melanogenesis. Their involvement lies in their ability to oxidize phenolic or polyphenolic compounds, which subsequently form pigments. The PPO family includes tyrosinases and catechol oxidases, which, in spite of their high structural similarity, exhibit different catalytic activities. Long-standing research efforts have not yet managed to decipher the structural determinants responsible for this differentiation, as every new theory is disproved by a more recent study. In the present work, we combined biochemical along with structural data in order to better understand the function of a previously characterized PPO from Thermothelomyces thermophila (TtPPO). The crystal structure of a TtPPO variant, determined at 1.55 Å resolution, represents the second known structure of an ascomycete PPO. Kinetic data for structure-guided mutants prove the implication of "gate" residue L306, residue HB1+1 (G292), and HB2+1 (Y296) in TtPPO function against various substrates. Our findings demonstrate the role of L306 in the accommodation of bulky substrates and show that residue HB1+1 is unlikely to determine monophenolase activity, as was suggested from previous studies.IMPORTANCE PPOs are enzymes of biotechnological interest. They have been extensively studied both biochemically and structurally, with a special focus on the plant-derived counterparts. Even so, explicit description of the molecular determinants of their substrate specificity is still pending. For ascomycete PPOs, only one crystal structure has been determined so far, thus limiting our knowledge on this tree branch of the family. In the present study, we report the second crystal structure of an ascomycete PPO. Combined with site-directed mutagenesis and biochemical studies, we depict the amino acids in the vicinity of the active site that affect enzyme activity and perform a detailed analysis on a variety of substrates. Our findings improve current understanding of structure-function relations of microbial PPOs, which is a prerequisite for the engineering of biocatalysts of desired properties.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | | | - Grigorios Dedes
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Maria Dimarogona
- Laboratory of Structural Biology and Biotechnology, Department of Chemical Engineering, University of Patras, Patras, Greece
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4
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Oates NC, Abood A, Schirmacher AM, Alessi AM, Bird SM, Bennett JP, Leadbeater DR, Li Y, Dowle AA, Liu S, Tymokhin VI, Ralph J, McQueen-Mason SJ, Bruce NC. A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1. Proc Natl Acad Sci U S A 2021; 118:e2008888118. [PMID: 33903229 PMCID: PMC8106297 DOI: 10.1073/pnas.2008888118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. Here, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major β-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.
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Affiliation(s)
- Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Alexandra M Schirmacher
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Anna M Alessi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Susannah M Bird
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Joseph P Bennett
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Sarah Liu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - Vitaliy I Tymokhin
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI 53726
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom;
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Davies KM, Jibran R, Zhou Y, Albert NW, Brummell DA, Jordan BR, Bowman JL, Schwinn KE. The Evolution of Flavonoid Biosynthesis: A Bryophyte Perspective. FRONTIERS IN PLANT SCIENCE 2020; 11:7. [PMID: 32117358 PMCID: PMC7010833 DOI: 10.3389/fpls.2020.00007] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/07/2020] [Indexed: 05/04/2023]
Abstract
The flavonoid pathway is one of the best characterized specialized metabolite pathways of plants. In angiosperms, the flavonoids have varied roles in assisting with tolerance to abiotic stress and are also key for signaling to pollinators and seed dispersal agents. The pathway is thought to be specific to land plants and to have arisen during the period of land colonization around 550-470 million years ago. In this review we consider current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornworts, and mosses. The pathway is less characterized for bryophytes than angiosperms, and the first genetic and molecular studies on bryophytes are finding both commonalities and significant differences in flavonoid biosynthesis and pathway regulation between angiosperms and bryophytes. This includes biosynthetic pathway branches specific to each plant group and the apparent complete absence of flavonoids from the hornworts.
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Affiliation(s)
- Kevin M. Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Brian R. Jordan
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Kathy E. Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
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Prexler SM, Frassek M, Moerschbacher BM, Dirks‐Hofmeister ME. Catechol Oxidase versus Tyrosinase Classification Revisited by Site‐Directed Mutagenesis Studies. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sarah M. Prexler
- Institut für Biologie und Biotechnologie der PflanzenWestfälische Wilhelms-Universität (WWU) Schlossplatz 8 48143 Münster Germany
| | - Martin Frassek
- Institut für Biologie und Biotechnologie der PflanzenWestfälische Wilhelms-Universität (WWU) Schlossplatz 8 48143 Münster Germany
| | - Bruno M. Moerschbacher
- Institut für Biologie und Biotechnologie der PflanzenWestfälische Wilhelms-Universität (WWU) Schlossplatz 8 48143 Münster Germany
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7
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Prexler SM, Frassek M, Moerschbacher BM, Dirks‐Hofmeister ME. Catechol Oxidase versus Tyrosinase Classification Revisited by Site‐Directed Mutagenesis Studies. Angew Chem Int Ed Engl 2019; 58:8757-8761. [DOI: 10.1002/anie.201902846] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Sarah M. Prexler
- Institut für Biologie und Biotechnologie der PflanzenWestfälische Wilhelms-Universität (WWU) Schlossplatz 8 48143 Münster Germany
| | - Martin Frassek
- Institut für Biologie und Biotechnologie der PflanzenWestfälische Wilhelms-Universität (WWU) Schlossplatz 8 48143 Münster Germany
| | - Bruno M. Moerschbacher
- Institut für Biologie und Biotechnologie der PflanzenWestfälische Wilhelms-Universität (WWU) Schlossplatz 8 48143 Münster Germany
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8
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Versatile Fungal Polyphenol Oxidase with Chlorophenol Bioremediation Potential: Characterization and Protein Engineering. Appl Environ Microbiol 2018; 84:AEM.01628-18. [PMID: 30266731 PMCID: PMC6238066 DOI: 10.1128/aem.01628-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/21/2018] [Indexed: 12/24/2022] Open
Abstract
Polyphenol oxidases (PPOs) have been mostly associated with the undesirable postharvest browning in fruits and vegetables and have implications in human melanogenesis. Nonetheless, they are considered useful biocatalysts in the food, pharmaceutical, and cosmetic industries. The aim of the present work was to characterize a novel PPO and explore its potential as a bioremediation agent. A gene encoding an extracellular tyrosinase-like enzyme was amplified from the genome of Thermothelomyces thermophila and expressed in Pichia pastoris The recombinant enzyme (TtPPO) was purified and biochemically characterized. Its production reached 40 mg/liter, and it appeared to be a glycosylated and N-terminally processed protein. TtPPO showed broad substrate specificity, as it could oxidize 28/30 compounds tested, including polyphenols, substituted phenols, catechols, and methoxyphenols. Its optimum temperature was 65°C, with a half-life of 18.3 h at 50°C, while its optimum pH was 7.5. The homology model of TtPPO was constructed, and site-directed mutagenesis was performed in order to increase its activity on mono- and dichlorophenols (di-CPs). The G292N/Y296V variant of TtPPO 5.3-fold increased activity on 3,5-dichlorophenol (3,5-diCP) compared to the wild type.IMPORTANCE A novel fungal PPO was heterologously expressed and biochemically characterized. Construction of single and double mutants led to the generation of variants with altered specificity against CPs. Through this work, knowledge is gained regarding the effect of mutations on the substrate specificity of PPOs. This work also demonstrates that more potent biocatalysts for the bioremediation of harmful CPs can be developed by applying site-directed mutagenesis.
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Penttinen L, Rutanen C, Jänis J, Rouvinen J, Hakulinen N. Unraveling Substrate Specificity and Catalytic Promiscuity of Aspergillus oryzae
Catechol Oxidase. Chembiochem 2018; 19:2348-2352. [DOI: 10.1002/cbic.201800387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Leena Penttinen
- Department of Chemistry; University of Eastern Finland; Yliopistokatu 7 80130 Joensuu Finland
| | - Chiara Rutanen
- Department of Chemistry; University of Eastern Finland; Yliopistokatu 7 80130 Joensuu Finland
| | - Janne Jänis
- Department of Chemistry; University of Eastern Finland; Yliopistokatu 7 80130 Joensuu Finland
| | - Juha Rouvinen
- Department of Chemistry; University of Eastern Finland; Yliopistokatu 7 80130 Joensuu Finland
| | - Nina Hakulinen
- Department of Chemistry; University of Eastern Finland; Yliopistokatu 7 80130 Joensuu Finland
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What causes the different functionality in type-III-copper enzymes? A state of the art perspective. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.04.041] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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11
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Decker H, Solem E, Tuczek F. Are glutamate and asparagine necessary for tyrosinase activity of type-3 copper proteins? Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.11.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes. PLoS One 2018; 13:e0196691. [PMID: 29715329 PMCID: PMC5929527 DOI: 10.1371/journal.pone.0196691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.
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13
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Hamann JN, Herzigkeit B, Jurgeleit R, Tuczek F. Small-molecule models of tyrosinase: From ligand hydroxylation to catalytic monooxygenation of external substrates. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.07.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Frommhagen M, Mutte SK, Westphal AH, Koetsier MJ, Hinz SWA, Visser J, Vincken JP, Weijers D, van Berkel WJH, Gruppen H, Kabel MA. Boosting LPMO-driven lignocellulose degradation by polyphenol oxidase-activated lignin building blocks. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:121. [PMID: 28491137 PMCID: PMC5424327 DOI: 10.1186/s13068-017-0810-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/03/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Many fungi boost the deconstruction of lignocellulosic plant biomass via oxidation using lytic polysaccharide monooxygenases (LPMOs). The application of LPMOs is expected to contribute to ecologically friendly conversion of biomass into fuels and chemicals. Moreover, applications of LPMO-modified cellulose-based products may be envisaged within the food or material industry. RESULTS Here, we show an up to 75-fold improvement in LPMO-driven cellulose degradation using polyphenol oxidase-activated lignin building blocks. This concerted enzymatic process involves the initial conversion of monophenols into diphenols by the polyphenol oxidase MtPPO7 from Myceliophthora thermophila C1 and the subsequent oxidation of cellulose by MtLPMO9B. Interestingly, MtPPO7 shows preference towards lignin-derived methoxylated monophenols. Sequence analysis of genomes of 336 Ascomycota and 208 Basidiomycota reveals a high correlation between MtPPO7 and AA9 LPMO genes. CONCLUSIONS The activity towards methoxylated phenolic compounds distinguishes MtPPO7 from well-known PPOs, such as tyrosinases, and ensures that MtPPO7 is an excellent redox partner of LPMOs. The correlation between MtPPO7 and AA9 LPMO genes is indicative for the importance of the coupled action of different monooxygenases in the concerted degradation of lignocellulosic biomass. These results will contribute to a better understanding in both lignin deconstruction and enzymatic lignocellulose oxidation and potentially improve the exploration of eco-friendly routes for biomass utilization in a circular economy.
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Affiliation(s)
- Matthias Frommhagen
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Sumanth Kumar Mutte
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Sandra W. A. Hinz
- DuPont Industrial Biosciences, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Jaap Visser
- Fungal Genetics & Technology Consultancy, P.O. Box 39b, 6700 AJ Wageningen, The Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Willem J. H. van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Harry Gruppen
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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Wang Q, Gong J, Chisti Y, Sirisansaneeyakul S. Production of theabrownins using a crude fungal enzyme concentrate. J Biotechnol 2016; 231:250-259. [DOI: 10.1016/j.jbiotec.2016.06.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 11/16/2022]
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16
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Kludas J, Arvas M, Castillo S, Pakula T, Oja M, Brouard C, Jäntti J, Penttilä M, Rousu J. Machine Learning of Protein Interactions in Fungal Secretory Pathways. PLoS One 2016; 11:e0159302. [PMID: 27441920 PMCID: PMC4956264 DOI: 10.1371/journal.pone.0159302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/30/2016] [Indexed: 12/18/2022] Open
Abstract
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker's yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities.
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Affiliation(s)
- Jana Kludas
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | - Tiina Pakula
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Céline Brouard
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Juho Rousu
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
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Marková E, Kotik M, Křenková A, Man P, Haudecoeur R, Boumendjel A, Hardré R, Mekmouche Y, Courvoisier-Dezord E, Réglier M, Martínková L. Recombinant Tyrosinase from Polyporus arcularius: Overproduction in Escherichia coli, Characterization, and Use in a Study of Aurones as Tyrosinase Effectors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2925-2931. [PMID: 26961852 DOI: 10.1021/acs.jafc.6b00286] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Tyrosinases act in the development of organoleptic properties of tea, raisins, etc., but also cause unwanted browning of fruits, vegetables, and mushrooms. The tyrosinase from Agaricus bisporus has been used as a model to study tyrosinase inhibitors, which are also indispensable in the treatment of skin pigmentation disorders. However, this model has disadvantages such as side enzyme activities and the presence of multiple isoenzymes. Therefore, we aimed to introduce a new tyrosinase model. The pro-tyrosinase from Polyporus arcularius was overproduced in Escherichia coli. Trypsin digestion led to a cleavage after R388 and hence enzyme activation. The tyrosinase was a homodimer and transformed L-DOPA and tert-butylcatechol preferentially. Various aurons were examined as effectors of this enzyme. 2'- and 3'-hydroxyaurones acted as its activators and 2',4'-dihydroxyaurone as an inhibitor, whereas 4'-hydroxyaurones were its substrates. The enzyme is a promising model for tyrosinase effector studies, being a single isoenzyme and void of side enzyme activities.
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Affiliation(s)
- Eva Marková
- Institute of Microbiology, Czech Academy of Sciences , Vídeňská 1083, 142 20 Prague, Czech Republic
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague , Technická 3, 166 28 Prague, Czech Republic
| | - Michael Kotik
- Institute of Microbiology, Czech Academy of Sciences , Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Alena Křenková
- Institute of Microbiology, Czech Academy of Sciences , Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences , Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Romain Haudecoeur
- Université Grenoble Alpes, CNRS, DPM UMR 5063 , 38041 Grenoble, France
| | - Ahcène Boumendjel
- Université Grenoble Alpes, CNRS, DPM UMR 5063 , 38041 Grenoble, France
| | - Renaud Hardré
- Aix Marseille Université, Centrale Marseille, CNRS, ISm2 UMR 7313 , 13397 Marseille, France
| | - Yasmina Mekmouche
- Aix Marseille Université, Centrale Marseille, CNRS, ISm2 UMR 7313 , 13397 Marseille, France
| | | | - Marius Réglier
- Aix Marseille Université, Centrale Marseille, CNRS, ISm2 UMR 7313 , 13397 Marseille, France
| | - Ludmila Martínková
- Institute of Microbiology, Czech Academy of Sciences , Vídeňská 1083, 142 20 Prague, Czech Republic
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Martínková L, Kotik M, Marková E, Homolka L. Biodegradation of phenolic compounds by Basidiomycota and its phenol oxidases: A review. CHEMOSPHERE 2016; 149:373-382. [PMID: 26874626 DOI: 10.1016/j.chemosphere.2016.01.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/09/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
The phylum Basidiomycota include organisms with enormous bioremediation potential. A variety of processes were proposed at the lab scale for using these fungi and their phenol oxidases in the degradation of phenolics. Here we present a survey of this topic using literature published mostly over the last 10 years. First, the sources of the enzymes are summarized. The laccase and tyrosinase were mainly from Trametes versicolor and Agaricus bisporus, respectively. Recently, however, new promising wild-type producers of the enzymes have emerged and a number of recombinant strains were also constructed, based mainly on yeasts or Aspergillus strains as hosts. The next part of the study summarizes the enzyme and whole-cell applications for the degradation of phenols, polyphenols, cresols, alkylphenols, naphthols, bisphenols and halogenated (bis)phenols in model mixtures or real wastewaters from the food, paper and coal industries, or municipal and hospital sewage. The enzymes were applied as free (crude or purified) enzymes or as enzymes immobilized in various supports or CLEAs, and optionally recycled or used in continuous mode. Alternatively, growing cultures or harvested mycelia were used instead. The products, which were characterized as quinones and their polymers in some cases, could be eliminated by filtration, flocculation or adsorption onto chitosan. The purity of a treated wastewater was monitored using a sensitive aquatic organism. It is concluded that low-cost sources of these enzymes should be searched for and the benefits of enzymatic, biological and physico-chemical methods could be combined to make the processes fit for industrial use.
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Affiliation(s)
- L Martínková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic.
| | - M Kotik
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - E Marková
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic; Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 3, CZ-166 28 Prague, Czech Republic
| | - L Homolka
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
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Kanteev M, Goldfeder M, Fishman A. Structure-function correlations in tyrosinases. Protein Sci 2015; 24:1360-9. [PMID: 26104241 DOI: 10.1002/pro.2734] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 06/19/2015] [Indexed: 11/08/2022]
Abstract
Tyrosinases are metalloenzymes belonging to the type-3 copper protein family which contain two copper ions in the active site. They are found in various prokaryotes as well as in plants, fungi, arthropods, and mammals and are responsible for pigmentation, wound healing, radiation protection, and primary immune response. Tyrosinases perform two sequential enzymatic reactions: hydroxylation of monophenols and oxidation of diphenols to form quinones which polymerize spontaneously to melanin. Two other members of this family are catechol oxidases, which are prevalent mainly in plants and perform only the second oxidation step, and hemocyanins, which lack enzymatic activity and are oxygen carriers. In the last decade, several structures of plant and bacterial tyrosinases were determined, some with substrates or inhibitors, highlighting features and residues which are important for copper uptake and catalysis. This review summarizes the updated information on structure-function correlations in tyrosinases along with comparison to other type-3 copper proteins.
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Affiliation(s)
- Margarita Kanteev
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Mor Goldfeder
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
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Kaintz C, Mayer RL, Jirsa F, Halbwirth H, Rompel A. Site-directed mutagenesis around the CuA site of a polyphenol oxidase from Coreopsis grandiflora (cgAUS1). FEBS Lett 2015; 589:789-97. [PMID: 25697959 PMCID: PMC4364613 DOI: 10.1016/j.febslet.2015.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 11/09/2022]
Abstract
Site-directed mutations of AUS1 around the CuA site were generated and verified. All mutations led to loss of diphenolase activity with butein as substrate. Exchange of histidines in the CuA resulted in enzymes containing only one Cu. F273 mutation to alanine did not increase the monophenolase activity. C97 mutation eliminated the diphenolase activity, but 2 Cu atoms were incorporated.
Aurone synthase from Coreopsis grandiflora (cgAUS1), catalyzing conversion of butein to sulfuretin in a type-3 copper center, is a rare example of a polyphenol oxidase involved in anabolism. Site-directed mutagenesis around the CuA site of AUS1 was performed, and recombinant enzymes were analyzed by mass spectrometry. Replacement of the coordinating CuA histidines with alanine resulted in the presence of a single copper and loss of diphenolase activity. The thioether bridge-building cysteine and a phenylalanine over the CuA site, exchanged to alanine, have no influence on copper content but appear to play an important role in substrate binding.
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Affiliation(s)
- Cornelia Kaintz
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria.
| | - Rupert L Mayer
- Universität Wien, Department of Analytical Chemistry, Währinger Straße 38, 1090 Vienna, Austria.
| | - Franz Jirsa
- Universität Wien, Department of Inorganic Chemistry, Althanstraße 14, 1090 Vienna, Austria.
| | - Heidi Halbwirth
- University of Technology Vienna, Institute of Chemical Engineering, Getreidemarkt 9, 1060 Vienna, Austria.
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien, Austria.
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Isolation and bioelectrochemical characterization of novel fungal sources with oxidasic activity applied in situ for the cathodic oxygen reduction in microbial fuel cells. Enzyme Microb Technol 2014; 66:20-7. [DOI: 10.1016/j.enzmictec.2014.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/14/2014] [Accepted: 07/25/2014] [Indexed: 11/18/2022]
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Partial purification and characterization of a novel extracellular tyrosinase from Auricularia auricula. Appl Biochem Biotechnol 2013; 172:1460-9. [PMID: 24218185 DOI: 10.1007/s12010-013-0638-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
Abstract
Extracellular tyrosinase from Auricularia auricula RF201 was purified in a three-step procedure involving ammonium sulfate precipitation, Sephadex G-100, and DEAE-Sepharose column chromatography. The partially purified enzyme showed a single protein band of 12.6 kDa on SDS-PAGE. The optimum pH for tyrosinase activity was 7, and the enzyme was stable between pH 6 and 9. Tyrosinase has optimal activity at 40 °C and retained most of its activity between 4 and 50 °C. A. auricula tyrosinase could oxidize L-tyrosine, L-DOPA, catechol, and caffeic acid and displayed dark brown or peach color. However, the enzyme was unable to catalyze L-phenylalanine and ferulic acid. In comparison with other substrates, L-tyrosine displayed the highest affinity (K m of 0.11 mM) and the maximal reaction velocity (V max of 102.58 μmol/min). Tyrosinase activity was reduced in the presence of numerous tested compounds. Particularly SDS, it significantly inhibited enzyme activity. CuSO4 and NaCl showed an activation effect on enzyme activity, with the maximum activation found in the presence of CuSO4.
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The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae. J Biol Inorg Chem 2013; 18:917-29. [PMID: 24043469 DOI: 10.1007/s00775-013-1038-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
Abstract
Catechol oxidases (EC 1.10.3.1) catalyse the oxidation of o-diphenols to their corresponding o-quinones. These oxidases contain two copper ions (CuA and CuB) within the so-called coupled type 3 copper site as found in tyrosinases (EC 1.14.18.1) and haemocyanins. The crystal structures of a limited number of bacterial and fungal tyrosinases and plant catechol oxidases have been solved. In this study, we present the first crystal structure of a fungal catechol oxidase from Aspergillus oryzae (AoCO4) at 2.5-Å resolution. AoCO4 belongs to the newly discovered family of short-tyrosinases, which are distinct from other tyrosinases and catechol oxidases because of their lack of the conserved C-terminal domain and differences in the histidine pattern for CuA. The sequence identity of AoCO4 with other structurally known enzymes is low (less than 30 %), and the crystal structure of AoCO4 diverges from that of enzymes belonging to the conventional tyrosinase family in several ways, particularly around the central α-helical core region. A diatomic oxygen moiety was identified as a bridging molecule between the two copper ions CuA and CuB separated by a distance of 4.2-4.3 Å. The UV/vis absorption spectrum of AoCO4 exhibits a distinct maximum of absorbance at 350 nm, which has been reported to be typical of the oxy form of type 3 copper enzymes.
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Hildén K, Mäkelä MR, Lankinen P, Lundell T. Agaricus bisporus and related Agaricus species on lignocellulose: Production of manganese peroxidase and multicopper oxidases. Fungal Genet Biol 2013; 55:32-41. [DOI: 10.1016/j.fgb.2013.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 01/30/2013] [Accepted: 02/10/2013] [Indexed: 11/26/2022]
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Ren Q, Henes B, Fairhead M, Thöny-Meyer L. High level production of tyrosinase in recombinant Escherichia coli. BMC Biotechnol 2013; 13:18. [PMID: 23442796 PMCID: PMC3598836 DOI: 10.1186/1472-6750-13-18] [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: 09/24/2012] [Accepted: 02/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tyrosinase is a bifunctional enzyme that catalyzes both the hydroxylation of monophenols to o-diphenols (monophenolase activity) and the subsequent oxidation of the diphenols to o-quinones (diphenolase activity). Due to the potential applications of tyrosinase in biotechnology, in particular in biocatalysis and for biosensors, it is desirable to develop a suitable low-cost process for efficient production of this enzyme. So far, the best production yield reported for tyrosinase was about 1 g L(-1), which was achieved by cultivating the filamentous fungus Trichoderma reesei for 6 days. RESULTS In this work, tyrosinase from Verrucomicrobium spinosum was expressed in Escherichia coli and its production was studied in both batch and fed-batch cultivations. Effects of various key cultivation parameters on tyrosinase production were first examined in batch cultures to identify optimal conditions. It was found that a culture temperature of 32 °C and induction at the late growth stage were favorable, leading to a highest tyrosinase activity of 0.76 U mL(-1). The fed-batch process was performed by using an exponential feeding strategy to achieve high cell density. With the fed-batch process, a final biomass concentration of 37 g L(-1) (based on optical density) and a tyrosinase activity of 13 U mL(-1) were obtained in 28 hours, leading to a yield of active tyrosinase of about 3 g L(-1). The highest overall volumetric productivity of 103 mg of active tyrosinase per liter and hour (corresponding to 464 mU L(-1) h(-1)) was determined, which is approximately 15 times higher than that obtained in batch cultures. CONCLUSIONS We have successfully expressed and produced gram quantities per liter of active tyrosinase in recombinant E. coli by optimizing the expression conditions and fed-batch cultivation strategy. Exponential feed of substrate helped to prolong the exponential phase of growth, to reduce the fermentation time and thus the cost. A specific tyrosinase production rate of 103 mg L(-1) h(-1) and a maximum volumetric activity of 464 mU L(-1) h(-1) were achieved in this study. These levels have not been reported previously.
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Affiliation(s)
- Qun Ren
- Laboratory for Biomaterials, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014 St, Gallen, Switzerland.
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Faccio G, Arvas M, Thöny-Meyer L, Saloheimo M. Experimental and bioinformatic investigation of the proteolytic degradation of the C-terminal domain of a fungal tyrosinase. J Inorg Biochem 2012; 121:37-45. [PMID: 23333757 DOI: 10.1016/j.jinorgbio.2012.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 10/27/2022]
Abstract
Proteolytic processing is a key step in the production of polyphenol oxidases such as tyrosinases, converting the inactive proenzyme to an active form. In general, the fungal tyrosinase gene codes for a ~60 kDa protein that is, however, isolated as an active enzyme of ~40 kDa, lacking the C-terminal domain. Using the secreted tyrosinase 2 from Trichoderma reesei as a model protein, we performed a mutagenesis study of the residues in proximity of the experimentally determined cleavage site which are possibly involved in the proteolytic process. However, the mutant forms of tyrosinase 2 were not secreted in a full-length form retaining the C-terminal domain, but they were processed to give a ~45 kDa active form. Aiming at explaining this phenomenon, we analysed in silico the properties of the C-terminal domain of tyrosinase 2, of 23 previously retrieved homologous tyrosinase sequences from fungi (C. Gasparetti, G. Faccio, M. Arvas, J. Buchert, M. Saloheimo, K. Kruus, Appl. Microbiol. Biotechnol. 86 (2010) 213-226) and of nine well-characterised polyphenol oxidases. Based on the results of our study, we exclude the key role of specific amino acids at the cleavage site in the proteolytic process and report an overall higher sensitivity to proteolysis of the linker region and of the whole C-terminal domain of fungal tyrosinases.
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Affiliation(s)
- Greta Faccio
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomaterials, Lerchenfeldstrasse 5, CH-9014 St. Gallen, Switzerland.
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28
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Häkkinen M, Arvas M, Oja M, Aro N, Penttilä M, Saloheimo M, Pakula TM. Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. Microb Cell Fact 2012; 11:134. [PMID: 23035824 PMCID: PMC3526510 DOI: 10.1186/1475-2859-11-134] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. About 30 carbohydrate active enzymes (CAZymes) of T. reesei have been biochemically characterised. Genome sequencing has revealed a large number of novel candidates for CAZymes, thus increasing the potential for identification of enzymes with novel activities and properties. Plenty of data exists on the carbon source dependent regulation of the characterised hydrolytic genes. However, information on the expression of the novel CAZyme genes, especially on complex biomass material, is very limited. RESULTS In this study, the CAZyme gene content of the T. reesei genome was updated and the annotations of the genes refined using both computational and manual approaches. Phylogenetic analysis was done to assist the annotation and to identify functionally diversified CAZymes. The analyses identified 201 glycoside hydrolase genes, 22 carbohydrate esterase genes and five polysaccharide lyase genes. Updated or novel functional predictions were assigned to 44 genes, and the phylogenetic analysis indicated further functional diversification within enzyme families or groups of enzymes. GH3 β-glucosidases, GH27 α-galactosidases and GH18 chitinases were especially functionally diverse. The expression of the lignocellulose degrading enzyme system of T. reesei was studied by cultivating the fungus in the presence of different inducing substrates and by subjecting the cultures to transcriptional profiling. The substrates included both defined and complex lignocellulose related materials, such as pretreated bagasse, wheat straw, spruce, xylan, Avicel cellulose and sophorose. The analysis revealed co-regulated groups of CAZyme genes, such as genes induced in all the conditions studied and also genes induced preferentially by a certain set of substrates. CONCLUSIONS In this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined. Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates. Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.
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Affiliation(s)
- Mari Häkkinen
- VTT Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044, VTT, Finland.
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Barakat KM, Gohar YM. Antimicrobial Agents Produced by Marine Aspergillus terreus var. africanus Against Some Virulent Fish Pathogens. Indian J Microbiol 2012; 52:366-72. [PMID: 23997326 PMCID: PMC3460127 DOI: 10.1007/s12088-012-0255-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 01/29/2012] [Indexed: 11/26/2022] Open
Abstract
Screening of fungal isolates collected from different locations of Alexandria coast, Egypt, was carried out to obtain new biologically active metabolites against some virulent fish pathogens (Edwardsiella tarda, Aeromonas hydrophila, Vibrio ordalli and Vibrio angularuim). Among 26 fungal isolates, Aspergillus terreus var. africanus was identified as the most potent isolate. Production of the bioactive material was optimized using response surface methodology including fermentation media, incubation period, temperature, pH, and thermo-stability. Spectral properties of the gas chromatography/mass spectrum of the ethyl acetate crude extract were determined. Partially purified components of the crude extract were chromatographically separated and bioassayed. Out of ten separated compounds, five were with considerable antibacterial agent. The bio-toxicity of crude showed a slight toxicity against the brine shrimp Artemia salina (LC50 = 1,500 μg/l). Antibacterial activity of the crude was compared with some known standard antibiotics and found to be superior over many where its MIC against some pathogen reached 1 μg/ml.
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Affiliation(s)
- Khouloud M. Barakat
- Microbiology Lab, National Institute of Oceanography and Fisheries, Alexandria, Egypt
| | - Yousry M. Gohar
- Botany and Microbiology Department, Faculty of Science, Alexandria Univ, Alexandria, Egypt
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Arvas M, Pakula T, Smit B, Rautio J, Koivistoinen H, Jouhten P, Lindfors E, Wiebe M, Penttilä M, Saloheimo M. Correlation of gene expression and protein production rate - a system wide study. BMC Genomics 2011; 12:616. [PMID: 22185473 PMCID: PMC3266662 DOI: 10.1186/1471-2164-12-616] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/20/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on Saccharomyces cerevisiae chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus Trichoderma reesei (Hypocrea jecorina) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype. RESULTS We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of T. reesei. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response. CONCLUSIONS Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).
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Affiliation(s)
- Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
| | - Tiina Pakula
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
| | - Bart Smit
- NIZO food research, Kernhemseweg 2, 6718ZB Ede, the Netherlands
| | - Jari Rautio
- Plexpress, Viikinkaari 6, 00790 Helsinki, Finland
| | | | - Paula Jouhten
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
| | - Erno Lindfors
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
| | - Marilyn Wiebe
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
| | - Markku Saloheimo
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT, Espoo, Finland
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Cloning and expression of a tyrosinase from Aspergillus oryzae in Yarrowia lipolytica: application in l-DOPA biotransformation. Appl Microbiol Biotechnol 2011; 92:951-9. [DOI: 10.1007/s00253-011-3400-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 04/22/2011] [Accepted: 05/17/2011] [Indexed: 10/18/2022]
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Kaljunen H, Gasparetti C, Kruus K, Rouvinen J, Hakulinen N. Crystallization and preliminary X-ray analysis of Aspergillus oryzae catechol oxidase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:672-4. [PMID: 21636908 PMCID: PMC3107139 DOI: 10.1107/s1744309111010141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/17/2011] [Indexed: 11/11/2022]
Abstract
Catechol oxidase is an enzyme that catalyzes the oxidation of o-diphenols to the corresponding o-quinones. It is a copper-containing enzyme with a binuclear copper active site. Here, the crystallization and multiple-wavelength anomalous dispersion data collection of catechol oxidase from the mould fungus Aspergillus oryzae are described. During the purification, three forms of the enzyme (39.3, 40.5 and 44.3 kDa) were obtained. A mixture of these three forms was initially crystallized and gave crystals that diffracted to 2.5 Å resolution and belonged to space group P3(2)21, with unit-cell parameters a = b = 118.9, c = 84.5 Å, α = β = 90, γ = 120°. A preparation containing only the shorter form (39.3 kDa) produced crystals that diffracted to 2.9 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.8, b = 95.3, c = 139.5 Å, α = β = γ = 90°.
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Affiliation(s)
- Heidi Kaljunen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
| | - Chiara Gasparetti
- VTT Technical Research Center of Finland, PO Box 1000, FIN-02044 VTT, Finland
| | - Kristiina Kruus
- VTT Technical Research Center of Finland, PO Box 1000, FIN-02044 VTT, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
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Muñoz-Muñoz JL, Garcia-Molina F, Varon R, Garcia-Ruíz PA, Tudela J, Garcia-Cánovas F, Rodríguez-López JN. Suicide inactivation of the diphenolase and monophenolase activities of tyrosinase. IUBMB Life 2010; 62:539-47. [PMID: 20552645 DOI: 10.1002/iub.348] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The suicide inactivation mechanism of tyrosinase acting on its phenolic substrates has been studied. Kinetic analysis of the proposed mechanism during the transition phase provides explicit analytical expressions for the concentrations of o-quinone versus time. The electronic, steric, and hydrophobic effects of the phenolic substrates influence the enzymatic reaction, increasing the catalytic speed by three orders of magnitude and the inactivation by one order of magnitude. To explain this suicide inactivation, we propose a mechanism in which the enzymatic form oxy-tyrosinase is responsible for the inactivation. In this mechanism, the rate constant of the reaction would be directly related with the strength of the nucleophilic attack of the C-1 hydroxyl group, which depends on the chemical shift of the carbon C-1 (delta(1)) obtained by (13)C-NMR. The suicide inactivation would occur if the C-2 hydroxyl group transferred the proton to the protonated peroxide, which would again act as a general base. In this case, the coplanarity between the copper atom, the oxygen of the C-1 and the ring would only permit the oxidation/reduction of one copper atom, giving rise to copper (0), hydrogen peroxide, and an o-quinone, which would be released, thus inactivating the enzyme. One possible application of this property could be the use of these suicide substrates as skin depigmenting agents.
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Affiliation(s)
- Jose Luis Muñoz-Muñoz
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Biologia, Universidad de Murcia, Espinardo, Murcia, Spain
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