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Chemo-enzymatic synthesis of sugar acid by pyranose 2-oxidase. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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2
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Boverio A, Widodo WS, Santema LL, Rozeboom H, Xiang R, Guallar V, Mattevi A, Fraaije MW. Structural Elucidation and Engineering of a Bacterial Carbohydrate Oxidase. Biochemistry 2022; 62:429-436. [PMID: 35881507 PMCID: PMC9850908 DOI: 10.1021/acs.biochem.2c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Flavin-dependent carbohydrate oxidases are valuable tools in biotechnological applications due to their high selectivity in the oxidation of carbohydrates. In this study, we report the biochemical and structural characterization of a recently discovered carbohydrate oxidase from the bacterium Ralstonia solanacearum, which is a member of the vanillyl alcohol oxidase flavoprotein family. Due to its exceptionally high activity toward N-acetyl-d-galactosamine and N-acetyl-d-glucosamine, the enzyme was named N-acetyl-glucosamine oxidase (NagOx). In contrast to most known (fungal) carbohydrate oxidases, NagOx could be overexpressed in a bacterial host, which facilitated detailed biochemical and enzyme engineering studies. Steady state kinetic analyses revealed that non-acetylated hexoses were also accepted as substrates albeit with lower efficiency. Upon determination of the crystal structure, structural insights into NagOx were obtained. A large cavity containing a bicovalently bound FAD, tethered via histidyl and cysteinyl linkages, was observed. Substrate docking highlighted how a single residue (Leu251) plays a key role in the accommodation of N-acetylated sugars in the active site. Upon replacement of Leu251 (L251R mutant), an enzyme variant was generated with a drastically modified substrate acceptance profile, tuned toward non-N-acetylated monosaccharides and disaccharides. Furthermore, the activity toward bulkier substrates such as the trisaccharide maltotriose was introduced by this mutation. Due to its advantage of being overexpressed in a bacterial host, NagOx can be considered a promising alternative engineerable biocatalyst for selective oxidation of monosaccharides and oligosaccharides.
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Affiliation(s)
- Alessandro Boverio
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands,Department
of Biology and Biotechnology, University
of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Wahyu S. Widodo
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Lars L. Santema
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Henriëtte
J. Rozeboom
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Ruite Xiang
- Electronic
and Atomic Protein Modelling Group, Barcelona
Supercomputing Center, E-08034 Barcelona, Spain
| | - Víctor Guallar
- Electronic
and Atomic Protein Modelling Group, Barcelona
Supercomputing Center, E-08034 Barcelona, Spain
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University
of Pavia, via Ferrata 9, 27100 Pavia, Italy
| | - Marco W. Fraaije
- Molecular
Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands,
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3
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Wang L, Li C, Wang X, Wang G, Shang S, Dou Z, Luo Y. Gut Lignocellulose Activity and Microbiota in Asian Longhorned Beetle and Their Predicted Contribution to Larval Nutrition. Front Microbiol 2022; 13:899865. [PMID: 35615502 PMCID: PMC9124977 DOI: 10.3389/fmicb.2022.899865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Anoplophora glabripennis (Asian longhorned beetle) is a wood-boring pest that can inhabit a wide range of healthy deciduous host trees in native and invaded areas. The gut microbiota plays important roles in the acquisition of nutrients for the growth and development of A. glabripennis larvae. Herein, we investigated the larval gut structure and studied the lignocellulose activity and microbial communities of the larval gut following feeding on different host trees. The larval gut was divided into foregut, midgut, and hindgut, of which the midgut is the longest, forming a single loop under itself. Microbial community composition and lignocellulose activity in larval gut extracts were correlated with host tree species. A. glabripennis larvae fed on the preferred host (Populus gansuensis) had higher lignocellulose activity and microbial diversity than larvae reared on either a secondary host (Salix babylonica) or a resistant host (Populus alba var. pyramidalis). Wolbachia was the most dominant bacteria in the gut of larvae fed on S. babylonica and P. alba var. pyramidalis, while Enterococcus and Gibbsiella were the most dominant in larvae fed on P. gansuensis, followed by Wolbachia. The lignocellulose-degrading fungus Fusarium solani was dominant in the larval gut fed on different host trees. Functional predictions of microbial communities in the larval gut fed on different resistant host trees suggested that they all play a role in degrading lignocellulose, detoxification, and fixing nitrogen, which likely contribute to the ability of these larvae to thrive in a broad range of host tree species.
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Affiliation(s)
- Lixiang Wang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Lixiang Wang,
| | - Chunchun Li
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Xuan Wang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Gaijin Wang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Suqin Shang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Zhipeng Dou
- Chinese Academy of Forestry Sciences, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
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4
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Chen Z, Fei K, Hu Y, Xu X, Gao XD, Li Z. Identification of a Novel Alditol Oxidase from Thermopolyspora flexuosa with Potential Application in D-Glyceric Acid Production. Mol Biotechnol 2022; 64:804-813. [PMID: 35129810 DOI: 10.1007/s12033-022-00459-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/30/2022] [Indexed: 10/19/2022]
Abstract
Glycerol is a potential sustainable feedstock, and biorefining processes to convert glycerol into value-added chemicals have been developed over the past decade. Alditol oxidase (AldO) is capable of selectively oxidizing the primary hydroxyl groups of alditols such as glycerol. In this study, a new FAD-binding protein from Thermopolyspora flexuosa was expressed and identified as a novel alditol oxidase (AldOT. fle). AldOT. fle displayed the optimal activity at pH 8.0 and 25 °C. AldOT. fle was not metal-dependent, but the activity was completely inhibited by Fe3+. AldOT. fle had a wide substrate specificity and high catalytic efficiency for glycerol. Furthermore, the recombinant AldOT. fle could produce D-glyceric acid from glycerol with a conversion rate ranging from 86.6% (5 mM glycerol) to 20.5% (500 mM glycerol). The recombinant E. coli with AldOT. fle could also produce 23.8 mM D-glyceric acid from 100 mM glycerol. The recombinant AldOT. fle had the potential to produce other aldehyde products by selectively oxidizing the hydroxyl groups of alditols and many other commodity chemicals by redesigning glycerol metabolism.
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Affiliation(s)
- Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Kangqing Fei
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yangfan Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiangyang Xu
- Zaozhuang Jienuo Enzyme Co., Ltd, Zaozhuang, 277100, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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5
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Li J, Li C, Wang M, Wang L, Liu X, Gao C, Ren L, Luo Y. Gut Structure and Microbial Communities in Sirex noctilio (Hymenoptera: Siricidae) and Their Predicted Contribution to Larval Nutrition. Front Microbiol 2021; 12:641141. [PMID: 33897646 PMCID: PMC8060704 DOI: 10.3389/fmicb.2021.641141] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/15/2021] [Indexed: 12/25/2022] Open
Abstract
The European woodwasp, Sirex noctilio Fabricius, is a major invasive quarantine pest that attacks and kills pine trees outside of its native range. Insect gut structure and gut microbiota play crucial roles in various life activities. Despite a few reports in nutrition and survival, an extensive study on the S. noctilio larval gut microbiome is lacking. We studied the gut structure using a stereo microscope and used high throughput sequencing of the bacterial 16S rRNA genes and fungal internal transcribed spacer 2 (ITS2) regions to investigate gut microbiota in different developmental stages of S. noctilio, including larvae, adults, and larval frass. We used PICRUSt2 to predict the functional profiles. The larval gut was thin and thread-like from the oral cavity to the anus, carrying few xylem particles in the crop. Pseudomonas, Ralstonia, and Burkholderia s.l were the dominant bacteria in the guts of larvae, adults, and frass, respectively. Even though Pseudomonas was the most abundant among all bacteria, Zoogloea, Ruminobacter, and Nitrosospira, which might be involved in degrading organic matter and fixing nitrogen occurred exclusively in the larval gut indicating their possible role in the growth and development of larvae in pine tree xylem. Fungal communities did not change significantly across different developmental stages or the frass. Amylostereum was dominant in the woodwasp’s larval gut. Functional prediction of bacterial and fungal communities revealed that they may encod enzymes involved in degrading lignocellulose and fixing nitrogen. Ours is the first study that compares gut microbial communities present in S. noctilio larvae, adults, and frass. This study could provide an understanding of larval nutrient acquisition in nutrient-deficient host xylem to some extent. Our study may unlock novel strategies for the development of pest management approaches based on interfering with the gut microbiota and restricting their role in larval survival and development.
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Affiliation(s)
- Jiale Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Chengcheng Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ming Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lixiang Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Xiaobo Liu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Chenglong Gao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China.,Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China.,Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
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6
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Broberg M, Dubey M, Iqbal M, Gudmundssson M, Ihrmark K, Schroers H, Funck Jensen D, Brandström Durling M, Karlsson M. Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales). Evol Appl 2021; 14:476-497. [PMID: 33664789 PMCID: PMC7896725 DOI: 10.1111/eva.13134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/09/2020] [Accepted: 09/02/2020] [Indexed: 12/16/2022] Open
Abstract
Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p ≤ .05) in the Bionectria subgenus lineage. This was accompanied with gene copy number increases (p ≤ .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most Clonostachys species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the C. rosea genome included expansions (p ≤ .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter gene abcG6 in C. rosea was induced (p ≤ .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121-fold) and various fungicides. Deletion of abcG6 resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites in Clonostachys subgenus Bionectria.
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Affiliation(s)
- Martin Broberg
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mudassir Iqbal
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Gudmundssson
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsalaSweden
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Dan Funck Jensen
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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7
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Savino S, Fraaije MW. The vast repertoire of carbohydrate oxidases: An overview. Biotechnol Adv 2020; 51:107634. [PMID: 32961251 DOI: 10.1016/j.biotechadv.2020.107634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/06/2020] [Indexed: 01/01/2023]
Abstract
Carbohydrates are widely abundant molecules present in a variety of forms. For their biosynthesis and modification, nature has evolved a plethora of carbohydrate-acting enzymes. Many of these enzymes are of particular interest for biotechnological applications, where they can be used as biocatalysts or biosensors. Among the enzymes catalysing conversions of carbohydrates are the carbohydrate oxidases. These oxidative enzymes belong to different structural families and use different cofactors to perform the oxidation reaction of CH-OH bonds in carbohydrates. The variety of carbohydrate oxidases available in nature reflects their specificity towards different sugars and selectivity of the oxidation site. Thanks to their properties, carbohydrate oxidases have received a lot of attention in basic and applied research, such that nowadays their role in biotechnological processes is of paramount importance. In this review we provide an overview of the available knowledge concerning the known carbohydrate oxidases. The oxidases are first classified according to their structural features. After a description on their mechanism of action, substrate acceptance and characterisation, we report on the engineering of the different carbohydrate oxidases to enhance their employment in biocatalysis and biotechnology. In the last part of the review we highlight some practical applications for which such enzymes have been exploited.
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Affiliation(s)
- Simone Savino
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands.
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8
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Abstract
This review presents a historical outline of the research on vanillyl alcohol oxidase (VAO) from Penicillium simplicissimum, one of the canonical members of the VAO/PCMH flavoprotein family. After describing its discovery and initial biochemical characterization, we discuss the physiological role, substrate scope, and catalytic mechanism of VAO, and review its three-dimensional structure and mechanism of covalent flavinylation. We also explain how protein engineering provided a deeper insight into the role of certain amino acid residues in determining the substrate specificity and enantioselectivity of the enzyme. Finally, we summarize recent computational studies about the migration of substrates and products through the enzyme's structure and the phylogenetic distribution of VAO and related enzymes.
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Affiliation(s)
- Tom A Ewing
- Wageningen Food & Biobased Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Gudrun Gygli
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Wageningen, The Netherlands.
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9
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Sriwaiyaphram K, Punthong P, Sucharitakul J, Wongnate T. Structure and function relationships of sugar oxidases and their potential use in biocatalysis. Enzymes 2020; 47:193-230. [PMID: 32951824 DOI: 10.1016/bs.enz.2020.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Several sugar oxidases that catalyze the oxidation of sugars have been isolated and characterized. These enzymes can be classified as flavoenzyme due to the presence of flavin adenine dinucleotide (FAD) as a cofactor. Sugar oxidases have been proposed to be the key biocatalyst in biotransformation of carbohydrates which can potentially convert sugars to provide a pool of intermediates for synthesis of rare sugars, fine chemicals and drugs. Moreover, sugar oxidases have been applied in biosensing of various biomolecules in food industries, diagnosis of diseases and environmental pollutant detection. This review provides the discussions on general properties, current mechanistic understanding, structural determination, biocatalytic application, and biosensor integration of representative sugar oxidase enzymes, namely pyranose 2-oxidase (P2O), glucose oxidase (GO), hexose oxidase (HO), and oligosaccharide oxidase. The information regarding the relationship between structure and function of these sugar oxidases points out the key properties of this particular group of enzymes that can be modified by engineering, which had resulted in a remarkable economic importance.
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Affiliation(s)
- Kanokkan Sriwaiyaphram
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Pangrum Punthong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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Valdés García A, Juárez Serrano N, Beltrán Sanahuja A, Garrigós MC. Novel Antioxidant Packaging Films Based on Poly(ε-Caprolactone) and Almond Skin Extract: Development and Effect on the Oxidative Stability of Fried Almonds. Antioxidants (Basel) 2020; 9:E629. [PMID: 32708916 PMCID: PMC7402149 DOI: 10.3390/antiox9070629] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Antioxidant films based on poly(ε-caprolactone) (PCL) containing almond skin extract (ASE) were developed for food packaging applications. The effect of ASE incorporation on the morphological, structural, colour, mechanical, thermal, barrier and antioxidant properties of the prepared films were evaluated. The structural, tensile and thermal properties of the films were not altered due to ASE addition. Although no significant differences were observed for the oxygen permeability of samples, some increase in water absorption and water vapour permeability was observed for active films due to the hydrophilic character of ASE phenolic compounds, suggesting the suitability of this novel packaging for fatty foods conservation. ASE conferred antioxidant properties to PCL films as determined by the DPPH radical scavenging activity. The efficiency of the developed films was evaluated by the real packaging application of fried almonds at different ASE contents (0, 3, 6 wt.%) up to 56 days at 40 °C. The evolution of peroxide and p-anisidine values, hexanal content, fatty acid profile and characteristic spectroscopy bands showed that active films improved fried almonds stability. The results suggested the potential of PCL/ASE films as sustainable and antioxidant food packaging systems to offer protection against lipid oxidation in foods.
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Affiliation(s)
- Arantzazu Valdés García
- Analytical Chemistry, Nutrition and Food Science Department, University of Alicante, PO Box 99, E-03080 Alicante, Spain; (N.J.S.); (A.B.S.); (M.C.G.)
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11
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Savino S, Jensen S, Terwisscha van Scheltinga A, Fraaije MW. Analysis of the structure and substrate scope of chitooligosaccharide oxidase reveals high affinity for C2-modified glucosamines. FEBS Lett 2020; 594:2819-2828. [PMID: 32491191 DOI: 10.1002/1873-3468.13854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023]
Abstract
Chitooligosaccharide oxidase (ChitO) is a fungal carbohydrate oxidase containing a bicovalently bound FAD cofactor. The enzyme is known to catalyse the oxidation of chitooligosaccharides, oligomers of N-acetylated glucosamines derived from chitin degradation. In this study, the unique substrate acceptance was explored by testing a range of N-acetyl-d-glucosamine derivatives, revealing that ChitO preferentially accepts carbohydrates with a hydrophobic group attached to C2. The enzyme also accepts streptozotocin, a natural product used to treat tumours. Elucidation of the crystal structure provides an explanation for the high affinity towards C2-decorated glucosamines: the active site has a secondary binding pocket that accommodates groups attached at C2. Docking simulations are fully in line with the observed substrate preference. This work expands the knowledge on this versatile enzyme.
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Affiliation(s)
- Simone Savino
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | - Sonja Jensen
- Molecular Enzymology Group, University of Groningen, The Netherlands
| | | | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, The Netherlands
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12
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Kumar V, Hainaut M, Delhomme N, Mannapperuma C, Immerzeel P, Street NR, Henrissat B, Mellerowicz EJ. Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:589-609. [PMID: 31111606 PMCID: PMC6852159 DOI: 10.1111/tpj.14417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/06/2019] [Accepted: 05/13/2019] [Indexed: 05/20/2023]
Abstract
Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.
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Affiliation(s)
- Vikash Kumar
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Aix‐Marseille UniversityMarseilleFrance
- INRAUSC 1408 AFMBMarseilleFrance
| | - Nicolas Delhomme
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
| | | | - Peter Immerzeel
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
- Chemical EngineeringKarlstad UniversityKarlstad65188Sweden
| | - Nathaniel R. Street
- Umeå Plant Science CenterPlant Physiology DepartmentUmeå UniversityUmeåSweden
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Aix‐Marseille UniversityMarseilleFrance
- INRAUSC 1408 AFMBMarseilleFrance
| | - Ewa J. Mellerowicz
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
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13
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Dimakos V, Taylor MS. Site-Selective Functionalization of Hydroxyl Groups in Carbohydrate Derivatives. Chem Rev 2018; 118:11457-11517. [DOI: 10.1021/acs.chemrev.8b00442] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Victoria Dimakos
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Mark S. Taylor
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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14
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Mohammed WS, Ziganshina EE, Shagimardanova EI, Gogoleva NE, Ziganshin AM. Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae). Sci Rep 2018; 8:10073. [PMID: 29968731 PMCID: PMC6030058 DOI: 10.1038/s41598-018-27342-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/31/2018] [Indexed: 12/27/2022] Open
Abstract
The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.
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Affiliation(s)
- Waleed S Mohammed
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Elvira E Ziganshina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
| | - Elena I Shagimardanova
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Natalia E Gogoleva
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia.
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15
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Massonnet M, Morales‐Cruz A, Figueroa‐Balderas R, Lawrence DP, Baumgartner K, Cantu D. Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. MOLECULAR PLANT PATHOLOGY 2018; 19:21-34. [PMID: 27608421 PMCID: PMC6637977 DOI: 10.1111/mpp.12491] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single-molecule real-time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression, followed by co-expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co-regulation of transcriptional networks contributes to multiple aspects of N. parvum virulence. In most of the co-expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co-regulation by the same transcription factor. Co-expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi-layered regulation of the virulence repertoire of N. parvum.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Kendra Baumgartner
- US Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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A Novel Colletotrichum graminicola Raffinose Oxidase in the AA5 Family. Appl Environ Microbiol 2017; 83:AEM.01383-17. [PMID: 28778886 DOI: 10.1128/aem.01383-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022] Open
Abstract
We describe here the identification and characterization of a copper radical oxidase from auxiliary activities family 5 (AA5_2) that was distinguished by showing preferential activity toward raffinose. Despite the biotechnological potential of carbohydrate oxidases from family AA5, very few members have been characterized. The gene encoding raffinose oxidase from Colletotrichum graminicola (CgRaOx; EC 1.1.3.-) was identified utilizing a bioinformatics approach based on the known modular structure of a characterized AA5_2 galactose oxidase. CgRaOx was expressed in Pichia pastoris, and the purified enzyme displayed the highest activity on the trisaccharide raffinose, whereas the activity on the disaccharide melibiose was three times lower and more than ten times lower activity was detected on d-galactose at a 300 mM substrate concentration. Thus, the substrate preference of CgRaOx was distinguished clearly from the substrate preferences of the known galactose oxidases. The site of oxidation for raffinose was studied by 1H nuclear magnetic resonance and mass spectrometry, and we confirmed that the hydroxyl group at the C-6 position was oxidized to an aldehyde and that in addition uronic acid was produced as a side product. A new electrospray ionization mass spectrometry method for the identification of C-6 oxidized products was developed, and the formation mechanism of the uronic acid was studied. CgRaOx presented a novel activity pattern in the AA5 family.IMPORTANCE Currently, there are only a few characterized members of the CAZy AA5 protein family. These enzymes are interesting from an application point of view because of their ability to utilize the cheap and abundant oxidant O2 without the requirement of complex cofactors such as FAD or NAD(P). Here, we present the identification and characterization of a novel AA5 member from Colletotrichum graminicola As discussed in the present study, the bioinformatics approach using the modular structure of galactose oxidase was successful in finding a C-6 hydroxyl carbohydrate oxidase having substrate preference for the trisaccharide raffinose. By the discovery of this activity, the diversity of the CAZy AA5 family is increasing.
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17
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Sonawane A, Manickam P, Bhansali S. Stability of Enzymatic Biosensors for Wearable Applications. IEEE Rev Biomed Eng 2017; 10:174-186. [PMID: 28541225 DOI: 10.1109/rbme.2017.2706661] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Technological evolution in wearable sensors accounts for major growth and transformation in a multitude of industries, ranging from healthcare to computing and informatics to communication and biomedical sciences. The major driver for this transformation is the new-found ability to continuously monitor and analyze the patients' physiology in patients' natural setting. Numerous wearable sensors are already on the market and are summarized. Most of the current technologies have focused on electrophysiological, electromechanical, or acoustic measurements. Wearable biochemical sensing devices are in their infancy. Traditional challenges in biochemical sensing such as reliability, repeatability, stability, and drift are amplified in wearable sensing systems due to variabilities in operating environment, sample/sensor handling, and motion artifacts. Enzymatic sensing technologies, due to reduced fluidic challenges, continue to be forerunners for converting into wearable sensors. This paper reviews the recent developments in wearable enzymatic sensors. The wearable sensors have been classified in three major groups based on sensor embodiment and placement relative to the human body: 1) on-body, 2) clothing/textile-based biosensors, and 3) biosensor accessories. The sensors, which come in the forms of stickers and tattoos, are categorized as on-body biosensors. The fabric-based biosensor comes in different models such as smart-shirts, socks, gloves, and smart undergarments with printed sensors for continuous monitoring.
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18
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Lacerda Júnior GV, Noronha MF, de Sousa STP, Cabral L, Domingos DF, Sáber ML, de Melo IS, Oliveira VM. Potential of semiarid soil from Caatinga biome as a novel source for mining lignocellulose-degrading enzymes. FEMS Microbiol Ecol 2016; 93:fiw248. [PMID: 27986827 DOI: 10.1093/femsec/fiw248] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/11/2016] [Accepted: 12/13/2016] [Indexed: 11/14/2022] Open
Abstract
The litterfall is the major organic material deposited in soil of Brazilian Caatinga biome, thus providing the ideal conditions for plant biomass-degrading microorganisms to thrive. Herein, the phylogenetic composition and lignocellulose-degrading capacity have been explored for the first time from a fosmid library dataset of Caatinga soil by sequence-based screening. A complex bacterial community dominated by Proteobacteria and Actinobacteria was unraveled. SEED subsystems-based annotations revealed a broad range of genes assigned to carbohydrate and aromatic compounds metabolism, indicating microbial ability to utilize plant-derived material. CAZy-based annotation identified 7275 genes encoding 37 glycoside hydrolases (GHs) families related to hydrolysis of cellulose, hemicellulose, oligosaccharides and other lignin-modifying enzymes. Taxonomic affiliation of genes showed high genetic potential of the phylum Acidobacteria for hemicellulose degradation, whereas Actinobacteria members appear to play an important role in celullose hydrolysis. Additionally, comparative analyses revealed greater GHs profile similarity among soils as compared to the digestive tract of animals capable of digesting plant biomass, particularly in the hemicellulases content. Combined results suggest a complex synergistic interaction of community members required for biomass degradation into fermentable sugars. This large repertoire of lignocellulolytic enzymes opens perspectives for mining potential candidates of biochemical catalysts for biofuels production from renewable resources and other environmental applications.
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Affiliation(s)
- Gileno V Lacerda Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
| | - Melline F Noronha
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
| | - Sanderson Tarciso P de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
| | - Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
| | - Daniela F Domingos
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA
| | - Mírian L Sáber
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, Jaguariúna, Zip code 13820-000, Brazil
| | - Itamar S de Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, Jaguariúna, Zip code 13820-000, Brazil
| | - Valéria M Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
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Ferrari AR, Rozeboom HJ, Dobruchowska JM, van Leeuwen SS, Vugts ASC, Koetsier MJ, Visser J, Fraaije MW. Discovery of a Xylooligosaccharide Oxidase from Myceliophthora thermophila C1. J Biol Chem 2016; 291:23709-23718. [PMID: 27629413 PMCID: PMC5095424 DOI: 10.1074/jbc.m116.741173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/12/2016] [Indexed: 11/06/2022] Open
Abstract
By inspection of the predicted proteome of the fungus Myceliophthora thermophila C1 for vanillyl-alcohol oxidase (VAO)-type flavoprotein oxidases, a putative oligosaccharide oxidase was identified. By homologous expression and subsequent purification, the respective protein could be obtained. The protein was found to contain a bicovalently bound FAD cofactor. By screening a large number of carbohydrates, several mono- and oligosaccharides could be identified as substrates. The enzyme exhibits a strong substrate preference toward xylooligosaccharides; hence it is named xylooligosaccharide oxidase (XylO). Chemical analyses of the product formed upon oxidation of xylobiose revealed that the oxidation occurs at C1, yielding xylobionate as product. By elucidation of several XylO crystal structures (in complex with a substrate mimic, xylose, and xylobiose), the residues that tune the unique substrate specificity and regioselectivity could be identified. The discovery of this novel oligosaccharide oxidase reveals that the VAO-type flavoprotein family harbors oxidases tuned for specific oligosaccharides. The unique substrate profile of XylO hints at a role in the degradation of xylan-derived oligosaccharides by the fungus M. thermophila C1.
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Affiliation(s)
| | | | - Justyna M Dobruchowska
- Microbial Physiology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen
| | - Sander S van Leeuwen
- Microbial Physiology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen
| | | | | | - Jaap Visser
- the Fungal Genetics and Technology Consultancy, 6700 AJ Wageningen, The Netherlands
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20
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Frandsen KEH, Lo Leggio L. Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes. IUCRJ 2016; 3:448-467. [PMID: 27840684 PMCID: PMC5094447 DOI: 10.1107/s2052252516014147] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/05/2016] [Indexed: 05/05/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are a new class of microbial copper enzymes involved in the degradation of recalcitrant polysaccharides. They have only been discovered and characterized in the last 5-10 years and have stimulated strong interest both in biotechnology and in bioinorganic chemistry. In biotechnology, the hope is that these enzymes will finally help to make enzymatic biomass conversion, especially of lignocellulosic plant waste, economically attractive. Here, the role of LPMOs is likely to be in attacking bonds that are not accessible to other enzymes. LPMOs have attracted enormous interest since their discovery. The emphasis in this review is on the past and present contribution of crystallographic studies as a guide to functional understanding, with a final look towards the future.
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Affiliation(s)
- Kristian E. H. Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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21
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Rubio MV, Zubieta MP, Franco Cairo JPL, Calzado F, Paes Leme AF, Squina FM, Prade RA, de Lima Damásio AR. Mapping N-linked glycosylation of carbohydrate-active enzymes in the secretome of Aspergillus nidulans grown on lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:168. [PMID: 27508003 PMCID: PMC4977673 DOI: 10.1186/s13068-016-0580-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/27/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND The genus Aspergillus includes microorganisms that naturally degrade lignocellulosic biomass, secreting large amounts of carbohydrate-active enzymes (CAZymes) that characterize their saprophyte lifestyle. Aspergillus has the capacity to perform post-translational modifications (PTM), which provides an additional advantage for the use of these organisms as a host for the production of heterologous proteins. In this study, the N-linked glycosylation of CAZymes identified in the secretome of Aspergillus nidulans grown on lignocellulose was mapped. RESULTS Aspergillus nidulans was grown in glucose, xylan and pretreated sugarcane bagasse (SCB) for 96 h, after which glycoproteomics and glycomics were carried out on the extracellular proteins (secretome). A total of 265 proteins were identified, with 153, 210 and 182 proteins in the glucose, xylan and SCB substrates, respectively. CAZymes corresponded to more than 50 % of the total secretome in xylan and SCB. A total of 182 N-glycosylation sites were identified, of which 121 were detected in 67 CAZymes. A prevalence of the N-glyc sequon N-X-T (72.2 %) was observed in N-glyc sites compared with N-X-S (27.8 %). The amino acids flanking the validated N-glyc sites were mainly composed of hydrophobic and polar uncharged amino acids. Selected proteins were evaluated for conservation of the N-glyc sites in Aspergilli homologous proteins, but a pattern of conservation was not observed. A global analysis of N-glycans released from the proteins secreted by A. nidulans was also performed. While the proportion of N-glycans with Hex5 to Hex9 was similar in the xylan condition, a prevalence of Hex5 was observed in the SCB and glucose conditions. CONCLUSIONS The most common and frequent N-glycosylated motifs, an overview of the N-glycosylation of the CAZymes and the number of mannoses found in N-glycans were analyzed. There are many bottlenecks in protein production by filamentous fungi, such as folding, transport by vesicles and secretion, but N-glycosylation in the correct context is a fundamental event for defining the high levels of secretion of target proteins. A comprehensive analysis of the protein glycosylation processes in A. nidulans will assist with a better understanding of glycoprotein structures, profiles, activities and functions. This knowledge can help in the optimization of heterologous expression and protein secretion in the fungal host.
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Affiliation(s)
- Marcelo Ventura Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Mariane Paludetti Zubieta
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - João Paulo Lourenço Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Felipe Calzado
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
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Gonaus C, Kittl R, Sygmund C, Haltrich D, Peterbauer C. Transcription analysis of pyranose dehydrogenase from the basidiomycete Agaricus bisporus and characterization of the recombinantly expressed enzyme. Protein Expr Purif 2015; 119:36-44. [PMID: 26616098 DOI: 10.1016/j.pep.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/22/2015] [Accepted: 11/04/2015] [Indexed: 01/25/2023]
Abstract
Agaricus bisporus is a litter degrading basidiomycete commonly found in humic-rich environments. It is used as model organism and cultivated in large scale for food industry. Due to its ecological niche it produces a variety of enzymes for detoxification and degradation of humified plant litter. One of these, pyranose dehydrogenase, is thought to play a role in detoxification and lignocellulose degradation. It is a member of the glucose-methanol-choline family of flavin-dependent enzymes and oxidizes a wide range of sugars with concomitant reduction of electron acceptors like quinones. In this work, transcription of pdh in A. bisporus was investigated with real-time PCR revealing influence of the carbon source on pdh expression levels. The gene was isolated and heterologously expressed in Pichia pastoris. Characterization of the recombinant enzyme showed a higher affinity towards disaccharides compared to other tested pyranose dehydrogenases from related Agariceae. Homology modeling and sequence alignments indicated that two loops of high sequence variability at substrate access site could play an important role in modulating these substrate specificities.
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Affiliation(s)
- Christoph Gonaus
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Roman Kittl
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Peterbauer
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, University of Natural Resources and Life Sciences, Vienna, Austria.
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23
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Ferrari AR, Lee M, Fraaije MW. Expanding the substrate scope of chitooligosaccharide oxidase fromFusarium graminearumby structure-inspired mutagenesis. Biotechnol Bioeng 2015; 112:1074-80. [DOI: 10.1002/bit.25532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/23/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Alessandro R. Ferrari
- Molecular Enzymology Group; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen The Netherlands
| | - Misun Lee
- Molecular Enzymology Group; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen The Netherlands
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24
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Vuong TV, Vesterinen AH, Foumani M, Juvonen M, Seppälä J, Tenkanen M, Master ER. Xylo- and cello-oligosaccharide oxidation by gluco-oligosaccharide oxidase from Sarocladium strictum and variants with reduced substrate inhibition. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:148. [PMID: 24119501 PMCID: PMC4015748 DOI: 10.1186/1754-6834-6-148] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/04/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND The oxidation of carbohydrates from lignocellulose can facilitate the synthesis of new biopolymers and biochemicals, and also reduce sugar metabolism by lignocellulolytic microorganisms, reserving aldonates for fermentation to biofuels. Although oxidoreductases that oxidize cellulosic hydrolysates have been well characterized, none have been reported to oxidize substituted or branched xylo-oligosaccharides. Moreover, this is the first report that identifies amino acid substitutions leading to GOOX variants with reduced substrate inhibition. RESULTS The recombinant wild type gluco-oligosaccharide oxidase (GOOX) from the fungus Sarocladium strictum, along with variants that were generated by site-directed mutagenesis, retained the FAD cofactor, and showed high activity on cello-oligosaccharide and xylo-oligosaccharides, including substituted and branched xylo-oligosaccharides. Mass spectrometric analyses confirmed that GOOX introduces one oxygen atom to oxidized products, and 1H NMR and tandem mass spectrometry analysis confirmed that oxidation was restricted to the anomeric carbon. The A38V mutation, which is close to a predicted divalent ion-binding site in the FAD-binding domain of GOOX but 30 Å away from the active site, significantly increased the kcat and catalytic efficiency of the enzyme on all oligosaccharides. Eight amino acid substitutions were separately introduced to the substrate-binding domain of GOOX-VN (at positions Y72, E247, W351, Q353 and Q384). In all cases, the Km of the enzyme variant was higher than that of GOOX, supporting the role of corresponding residues in substrate binding. Most notably, W351A increased Km values by up to two orders of magnitude while also increasing kcat up to 3-fold on cello- and xylo-oligosaccharides and showing no substrate inhibition. CONCLUSIONS This study provides further evidence that S. strictum GOOX has broader substrate specificity than the enzyme name implies, and that substrate inhibition can be reduced by removing aromatic side chains in the -2 binding subsite. Of the enzyme variants, W351A might be particularly advantageous when oxidizing oligosaccharides present at high substrate concentrations often experienced in industrial processes.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Arja-Helena Vesterinen
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1 D1, Espoo 02150, Finland
| | - Maryam Foumani
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Minna Juvonen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Jukka Seppälä
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1 D1, Espoo 02150, Finland
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
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Wongnate T, Chaiyen P. The substrate oxidation mechanism of pyranose 2-oxidase and other related enzymes in the glucose-methanol-choline superfamily. FEBS J 2013; 280:3009-27. [DOI: 10.1111/febs.12280] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/01/2013] [Accepted: 04/04/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science; Mahidol University; Bangkok; Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science; Mahidol University; Bangkok; Thailand
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Hervás M, Bashir Q, Leferink NGH, Ferreira P, Moreno-Beltrán B, Westphal AH, Dίaz-Moreno I, Medina M, de la Rosa MA, Ubbink M, Navarro JA, van Berkel WJH. Communication between L-galactono-1,4-lactone dehydrogenase and cytochromec. FEBS J 2013; 280:1830-40. [DOI: 10.1111/febs.12207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/08/2013] [Accepted: 02/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | - Qamar Bashir
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | | | - Patricia Ferreira
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Physics of Complex Systems; University of Zaragoza; Spain
| | - Blas Moreno-Beltrán
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | | | - Irene Dίaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cell Biology and Institute for Biocomputation and Physics of Complex Systems; University of Zaragoza; Spain
| | - Miguel A. de la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
| | - Marcellus Ubbink
- Gorlaeus Laboratories; Leiden Institute of Chemistry; Leiden University; The Netherlands
| | - José A. Navarro
- Instituto de Bioquímica Vegetal y Fotosíntesis; CSIC and University of Sevilla; Spain
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27
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Scheele S, Oertel D, Bongaerts J, Evers S, Hellmuth H, Maurer KH, Bott M, Freudl R. Secretory production of an FAD cofactor-containing cytosolic enzyme (sorbitol-xylitol oxidase from Streptomyces coelicolor) using the twin-arginine translocation (Tat) pathway of Corynebacterium glutamicum. Microb Biotechnol 2012; 6:202-6. [PMID: 23163932 PMCID: PMC3917463 DOI: 10.1111/1751-7915.12005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/08/2012] [Accepted: 10/13/2012] [Indexed: 12/02/2022] Open
Abstract
Carbohydrate oxidases are biotechnologically interesting enzymes that require a tightly or covalently bound cofactor for activity. Using the industrial workhorse Corynebacterium glutamicum as the expression host, successful secretion of a normally cytosolic FAD cofactor-containing sorbitol–xylitol oxidase from Streptomyces coelicolor was achieved by using the twin-arginine translocation (Tat) protein export machinery for protein translocation across the cytoplasmic membrane. Our results demonstrate for the first time that, also for cofactor-containing proteins, a secretory production strategy is a feasible and promising alternative to conventional intracellular expression strategies.
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Affiliation(s)
- Sandra Scheele
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich, Germany
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28
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Winter RT, Heuts DPHM, Rijpkema EMA, van Bloois E, Wijma HJ, Fraaije MW. Hot or not? Discovery and characterization of a thermostable alditol oxidase from Acidothermus cellulolyticus 11B. Appl Microbiol Biotechnol 2012; 95:389-403. [PMID: 22231860 PMCID: PMC3371188 DOI: 10.1007/s00253-011-3750-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/01/2011] [Accepted: 11/17/2011] [Indexed: 11/26/2022]
Abstract
We describe the discovery, isolation and characterization of a highly thermostable alditol oxidase from Acidothermus cellulolyticus 11B. This protein was identified by searching the genomes of known thermophiles for enzymes homologous to Streptomyces coelicolor A3(2) alditol oxidase (AldO). A gene (sharing 48% protein sequence identity to AldO) was identified, cloned and expressed in Escherichia coli. Following 6xHis tag purification, characterization revealed the protein to be a covalent flavoprotein of 47 kDa with a remarkably similar reactivity and substrate specificity to that of AldO. A steady-state kinetic analysis with a number of different polyol substrates revealed lower catalytic rates but slightly altered substrate specificity when compared to AldO. Thermostability measurements revealed that the novel AldO is a highly thermostable enzyme with an unfolding temperature of 84 °C and an activity half-life at 75 °C of 112 min, prompting the name HotAldO. Inspired by earlier studies, we attempted a straightforward, exploratory approach to improve the thermostability of AldO by replacing residues with high B-factors with corresponding residues from HotAldO. None of these mutations resulted in a more thermostable oxidase; a fact that was corroborated by in silico analysis.
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Affiliation(s)
- Remko T. Winter
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dominic P. H. M. Heuts
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Egon M. A. Rijpkema
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Edwin van Bloois
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Xin Y, Yang H, Xiao X, Zhang L, Zhang Y, Tong Y, Wang W. Preparation and characterization of affinity sorbents based on isoalloxazine-like ligands for separation of flavoenzymes. J Sep Sci 2011; 34:2940-9. [DOI: 10.1002/jssc.201100474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/25/2011] [Accepted: 07/26/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Xin
- School of Biotechnology, Jiangnan University, Key Laboratory of Industry Biotechnology, Ministry of Education, Wuxi, Jiangsu, P R China.
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30
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Affiliation(s)
- Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K
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31
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Rannes JB, Ioannou A, Willies SC, Grogan G, Behrens C, Flitsch SL, Turner NJ. Glycoprotein Labeling Using Engineered Variants of Galactose Oxidase Obtained by Directed Evolution. J Am Chem Soc 2011; 133:8436-9. [DOI: 10.1021/ja2018477] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Julie B. Rannes
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, U.K
| | - Avgousta Ioannou
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, U.K
| | - Simon C. Willies
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, U.K
| | - Gideon Grogan
- Department of Chemistry, University of York, York, YO10 5YW, U.K
| | - Carsten Behrens
- Department of Protein and Peptide Chemistry, Novo Nordisk A/S, Maaløv, Denmark
| | - Sabine L. Flitsch
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, U.K
| | - Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, U.K
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32
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Monti D, Ottolina G, Carrea G, Riva S. Redox Reactions Catalyzed by Isolated Enzymes. Chem Rev 2011; 111:4111-40. [DOI: 10.1021/cr100334x] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
| | - Gianluca Ottolina
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
| | - Giacomo Carrea
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
| | - Sergio Riva
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
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33
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Foumani M, Vuong TV, Master ER. Altered substrate specificity of the gluco-oligosaccharide oxidase from Acremonium strictum. Biotechnol Bioeng 2011; 108:2261-9. [PMID: 21455933 DOI: 10.1002/bit.23149] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 03/05/2011] [Accepted: 03/14/2011] [Indexed: 11/08/2022]
Abstract
A gluco-oligosaccharide oxidase (GOOX) from Acremonium strictum type strain CBS 346.70 was cloned and expressed in Pichia pastoris. The recombinant protein, GOOX-VN, contained fifteen amino acid substitutions compared with the previously reported A. strictum GOOX. These two enzymes share 97% sequence identity; however, only GOOX-VN oxidized xylose, galactose, and N-acetylglucosamine. Besides monosaccharides, GOOX-VN oxidized xylo-oligosaccharides, including xylobiose and xylotriose with similar catalytic efficiency as for cello-oligosaccharides. Of three mutant enzymes that were created in GOOX-VN to improve substrate specificity, Y300A and Y300N doubled kcat values for monosaccharide and oligosaccharide substrates. With this novel substrate specificity, GOOX-VN and its variants are particularly valuable for oxidative modification of cello- and xylo-oligosaccharides.
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Affiliation(s)
- Maryam Foumani
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5; telephone: +1-416-946-7861; fax: +1-416-978-8605
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34
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Teichert JF, den Hartog T, Hanstein M, Smit C, ter Horst B, Hernandez-Olmos V, Feringa BL, Minnaard AJ. Organocatalytic Reduction of Carbon−Carbon Double Bonds in Racemization-Sensitive Compounds. ACS Catal 2011. [DOI: 10.1021/cs100121m] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johannes F. Teichert
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Tim den Hartog
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Miriam Hanstein
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christian Smit
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bjorn ter Horst
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Victor Hernandez-Olmos
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ben L. Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Adriaan J. Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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35
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Sucharitakul J, Wongnate T, Chaiyen P. Kinetic Isotope Effects on the Noncovalent Flavin Mutant Protein of Pyranose 2-Oxidase Reveal Insights into the Flavin Reduction Mechanism. Biochemistry 2010; 49:3753-65. [DOI: 10.1021/bi100187b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Patumwan, Bangkok 10330, Thailand
| | - Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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36
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Peterbauer CK, Volc J. Pyranose dehydrogenases: biochemical features and perspectives of technological applications. Appl Microbiol Biotechnol 2009; 85:837-48. [PMID: 19768457 DOI: 10.1007/s00253-009-2226-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 11/25/2022]
Abstract
Pyranose dehydrogenase is a fungal flavin-dependent sugar oxidoreductase which is structurally and catalytically related to fungal pyranose oxidase and cellobiose dehydrogenase and probably fulfills similar biological functions in lignocellulose breakdown. It is a monomeric secretory glycoprotein and is limited to a rather small group of litter-decomposing basidiomycetes. Compared with pyranose oxidase, it displays broader substrate specificity and a variable regioselectivity and is unable to utilize oxygen as electron acceptor using substituted benzoquinones and (organo) metallic ions instead. Depending on the structure of the sugar in pyranose form (mono/di/oligosaccharide or glycoside) and the enzyme source, selective monooxidations at C-1, C-2, C-3, or dioxidations at C-2,3 or C-3,4 of the molecule to the corresponding aldonolactones (C-1), or (di)dehydrosugars (aldos(di)uloses) can be performed. These features make pyranose dehydrogenase a promising and versatile biocatalyst for production of highly reactive, sometimes unique, di- and tri-carbonyl sugar derivatives that may serve as interesting chiral intermediates for the synthesis of rare sugars, novel drugs, and fine chemicals.
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Affiliation(s)
- Clemens K Peterbauer
- Department of Food Sciences and Technology, BOKU-University of Natural Resources and Applied Life Sciences, Vienna, Austria.
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37
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van Hellemond E, Vermote L, Koolen W, Sonke T, Zandvoort E, Heuts DP, Janssen D, Fraaije M. Exploring the Biocatalytic Scope of Alditol Oxidase fromStreptomyces coelicolor. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900176] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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38
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Prongjit M, Sucharitakul J, Wongnate T, Haltrich D, Chaiyen P. Kinetic mechanism of pyranose 2-oxidase from trametes multicolor. Biochemistry 2009; 48:4170-80. [PMID: 19317444 DOI: 10.1021/bi802331r] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoprotein oxidase that catalyzes the oxidation of aldopyranoses by molecular oxygen to yield the corresponding 2-keto-aldoses and hydrogen peroxide. P2O is the first enzyme in the class of flavoprotein oxidases, for which a C4a-hydroperoxy-flavin adenine dinucleotide (FAD) intermediate has been detected during the oxidative half-reaction. In this study, the reduction kinetics of P2O by d-glucose and 2-d-d-glucose at pH 7.0 was investigated using stopped-flow techniques. The results indicate that d-glucose binds to the enzyme with a two-step binding process; the first step is the initial complex formation, while the second step is the isomerization to form an active Michaelis complex (E-Fl(ox):G). Interestingly, the complex (E-Fl(ox):G) showed greater absorbance at 395 nm than the oxidized enzyme, and the isomerization process showed a significant inverse isotope effect, implying that the C2-H bond of d-glucose is more rigid in the E-Fl(ox):G complex than in the free form. A large normal primary isotope effect (k(H)/k(D) = 8.84) was detected in the flavin reduction step. Steady-state kinetics at pH 7.0 shows a series of parallel lines. Kinetics of formation and decay of C-4a-hydroperoxy-FAD is the same in absence and presence of 2-keto-d-glucose, implying that the sugar does not bind to P2O during the oxidative half-reaction. This suggests that the kinetic mechanism of P2O is likely to be the ping-pong-type where the sugar product leaves prior to the oxygen reaction. The movement of the active site loop when oxygen is present is proposed to facilitate the release of the sugar product. Correlation between data from pre-steady-state and steady-state kinetics has shown that the overall turnover of the reaction is limited by the steps of flavin reduction and decay of C4a-hydroperoxy-FAD.
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Affiliation(s)
- Methinee Prongjit
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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39
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Export of functional Streptomyces coelicolor alditol oxidase to the periplasm or cell surface of Escherichia coli and its application in whole-cell biocatalysis. Appl Microbiol Biotechnol 2009; 83:679-87. [PMID: 19224207 PMCID: PMC2690846 DOI: 10.1007/s00253-009-1904-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/30/2009] [Accepted: 01/30/2009] [Indexed: 11/30/2022]
Abstract
Streptomyces coelicolor A3(2) alditol oxidase (AldO) is a soluble monomeric flavoprotein in which the flavin cofactor is covalently linked to the polypeptide chain. AldO displays high reactivity towards different polyols such as xylitol and sorbitol. These characteristics make AldO industrially relevant, but full biotechnological exploitation of this enzyme is at present restricted by laborious and costly purification steps. To eliminate the need for enzyme purification, this study describes a whole-cell AldO biocatalyst system. To this end, we have directed AldO to the periplasm or cell surface of Escherichia coli. For periplasmic export, AldO was fused to endogenous E. coli signal sequences known to direct their passenger proteins into the SecB, signal recognition particle (SRP), or Twin-arginine translocation (Tat) pathway. In addition, AldO was fused to an ice nucleation protein (INP)-based anchoring motif for surface display. The results show that Tat-exported AldO and INP-surface-displayed AldO are active. The Tat-based system was successfully employed in converting xylitol by whole cells, whereas the use of the INP-based system was most likely restricted by lipopolysaccharide LPS in wild-type cells. It is anticipated that these whole-cell systems will be a valuable tool for further biological and industrial exploitation of AldO and other cofactor-containing enzymes.
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40
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Heuts DPHM, Janssen DB, Fraaije MW. Changing the substrate specificity of a chitooligosaccharide oxidase fromFusarium graminearumby model-inspired site-directed mutagenesis. FEBS Lett 2007; 581:4905-9. [PMID: 17900572 DOI: 10.1016/j.febslet.2007.09.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 09/04/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
Abstract
Chitooligosaccharide oxidase (ChitO) catalyzes the oxidation of C1 hydroxyl moieties on chitooligosaccharides and in this way displays a different substrate preference as compared to other known oligosaccharide oxidases. ChitO was identified in the genome of Fusarium graminearum and a structural model revealed that one active site residue (Q268) was likely to be involved in the recognition of the N-acetyl moiety on the chitooligosaccharide substrates. The substrate specificity of wild type ChitO and the Q268R mutant were examined and confirmed that Q268 is indeed involved in N-acetyl recognition.
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Affiliation(s)
- Dominic P H M Heuts
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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41
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Heuts DPHM, van Hellemond EW, Janssen DB, Fraaije MW. Discovery, characterization, and kinetic analysis of an alditol oxidase from Streptomyces coelicolor. J Biol Chem 2007; 282:20283-91. [PMID: 17517896 DOI: 10.1074/jbc.m610849200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A gene encoding an alditol oxidase was found in the genome of Streptomyces coelicolor A3(2). This newly identified oxidase, AldO, was expressed at extremely high levels in Escherichia coli when fused to maltose-binding protein. AldO is a soluble monomeric flavoprotein with subunits of 45.1 kDa, each containing a covalently bound FAD cofactor. From sequence alignments with other flavoprotein oxidases, it was found that AldO contains a conserved histidine (His(46)) that is typically involved in covalent FAD attachment. Covalent FAD binding is not observed in the H46A AldO mutant, confirming its role in covalent attachment of the flavin cofactor. Steady-state kinetic analyses revealed that wild-type AldO is active with several polyols. The alditols xylitol (K(m) = 0.32 mm, k(cat) = 13 s(-1)) and sorbitol (K(m) = 1.4 mm, k(cat) = 17 s(-1)) are the preferred substrates. From pre-steady-state kinetic analyses, using xylitol as substrate, it can be concluded that AldO mainly follows a ternary complex kinetic mechanism. Reduction of the flavin cofactor by xylitol occurs at a relatively high rate (99 s(-1)), after which a second kinetic event is observed, which is proposed to represent ring closure of the formed aldehyde product, yielding the hemiacetal of d-xylose. Reduced AldO readily reacts with molecular oxygen (1.7 x 10(5) m(-1) s(-1)), which confirms that the enzyme represents a true flavoprotein oxidase.
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Affiliation(s)
- Dominic P H M Heuts
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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42
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Abstract
Flavoenzymes are colourful oxidoreductases that catalyze a large variety of different types of reactions. Flavoenzymes have been extensively studied for their structural and mechanistic properties and are gaining momentum in industrial biocatalytic applications. Some of these enzymes catalyze the oxidative modification of protein substrates. New insights in oxidative flavoenzymes and in particular in novel family members point towards their potential application in the pharmaceutical, fine-chemical and food industries.
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Affiliation(s)
- Vivi Joosten
- Laboratory of Biochemistry, Wageningen University Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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