1
|
Shapira M, Dobysh A, Liaudanskaya A, Aucharova H, Dzichenka Y, Bokuts V, Jovanović-Šanta S, Yantsevich A. New insights into the substrate specificity of cholesterol oxidases for more aware application. Biochimie 2023; 220:1-10. [PMID: 38104713 DOI: 10.1016/j.biochi.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/20/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Cholesterol oxidases (ChOxes) are enzymes that catalyze the oxidation of cholesterol to cholest-4-en-3-one. These enzymes find wide applications across various diagnostic and industrial settings. In addition, as a pathogenic factor of several bacteria, they have significant clinical implications. The current classification system for ChOxes is based on the type of bond connecting FAD to the apoenzyme, which does not adequately illustrate the enzymatic and structural characteristics of these proteins. In this study, we have adopted an integrative approach, combining evolutionary analysis, classic enzymatic techniques and computational approaches, to elucidate the distinct features of four various ChOxes from Rhodococcus sp. (RCO), Cromobacterium sp. (CCO), Pseudomonas aeruginosa (PCO) and Burkhoderia cepacia (BCO). Comparative and evolutionary analysis of substrate-binding domain (SBD) and FAD-binding domain (FBD) helped to reveal the origin of ChOxes. We discovered that all forms of ChOxes had a common ancestor and that the structural differences evolved later during divergence. Further examination of amino acid variations revealed SBD as a more variable compared to FBD independently of FAD coupling mechanism. Revealed differences in amino acid positions turned out to be critical in determining common for ChOxes properties and those that account for the individual differences in substrate specificity. A novel look with the help of chemical descriptors on found distinct features were sufficient to attempt an alternative classification system aimed at application approach. While univocal characteristics necessary to establish such a system remain elusive, we were able to demonstrate the substrate and protein features that explain the differences in substrate profile.
Collapse
Affiliation(s)
- Michail Shapira
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus.
| | - Alexandra Dobysh
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Hanna Aucharova
- Technical University of Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Yaraslau Dzichenka
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Volha Bokuts
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Suzana Jovanović-Šanta
- University of Novi Sad Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Novi Sad, Serbia
| | - Aliaksey Yantsevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| |
Collapse
|
2
|
Malric-Garajova S, Fortuna F, Pion F, Martin E, Thottathil AR, Guillemain A, Doan A, Lomascolo A, Faulds CB, Baumberger S, Foulon L, Chabbert B, de Baynast H, Dubessay P, Audonnet F, Bertrand E, Sciara G, Tapin-Lingua S, Ducrot PH, Michaud P, Aguié-Béghin V, Record E. Modification of a Marine Pine Kraft Lignin Sample by Enzymatic Treatment with a Pycnoporus cinnabarinus Laccase. Molecules 2023; 28:4873. [PMID: 37375426 DOI: 10.3390/molecules28124873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Here, we report work on developing an enzymatic process to improve the functionalities of industrial lignin. A kraft lignin sample prepared from marine pine was treated with the high-redox-potential laccase from the basidiomycete fungus Pycnoporus cinnabarinus at three different concentrations and pH conditions, and with and without the chemical mediator 1-hydroxybenzotriazole (HBT). Laccase activity was tested in the presence and absence of kraft lignin. The optimum pH of PciLac was initially 4.0 in the presence and absence of lignin, but at incubation times over 6 h, higher activities were found at pH 4.5 in the presence of lignin. Structural changes in lignin were investigated by Fourier-transform infrared spectroscopy (FTIR) with differential scanning calorimetry (DSC), and solvent-extractable fractions were analyzed using high-performance size-exclusion chromatography (HPSEC) and gas chromatography-mass spectrometry (GC-MS). The FTIR spectral data were analyzed with two successive multivariate series using principal component analysis (PCA) and ANOVA statistical analysis to identify the best conditions for the largest range of chemical modifications. DSC combined with modulated DSC (MDSC) revealed that the greatest effect on glass transition temperature (Tg) was obtained at 130 U g cm-1 and pH 4.5, with the laccase alone or combined with HBT. HPSEC data suggested that the laccase treatments led to concomitant phenomena of oligomerization and depolymerization, and GC-MS revealed that the reactivity of the extractable phenolic monomers depended on the conditions tested. This study demonstrates that P. cinnabarinus laccase can be used to modify marine pine kraft lignin, and that the set of analytical methods implemented here provides a valuable tool for screening enzymatic treatment conditions.
Collapse
Affiliation(s)
- Sona Malric-Garajova
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Florian Fortuna
- Université de Reims-Champagne-Ardenne, INRAE, Fractionnement des Agro-Ressources et Environnement (FARE), UMR A 614, 51097 Reims, France
| | - Florian Pion
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Elise Martin
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal (IP), 63000 Clermont-Ferrand, France
| | | | - Audrey Guillemain
- FCBA, InTechFibres Division, Domaine Universitaire CS 90125, Cedex 9, 38044 Grenoble, France
| | - Annick Doan
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Anne Lomascolo
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Craig B Faulds
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Stéphanie Baumberger
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Laurence Foulon
- Université de Reims-Champagne-Ardenne, INRAE, Fractionnement des Agro-Ressources et Environnement (FARE), UMR A 614, 51097 Reims, France
| | - Brigitte Chabbert
- Université de Reims-Champagne-Ardenne, INRAE, Fractionnement des Agro-Ressources et Environnement (FARE), UMR A 614, 51097 Reims, France
| | - Hélène de Baynast
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal (IP), 63000 Clermont-Ferrand, France
| | - Pascal Dubessay
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal (IP), 63000 Clermont-Ferrand, France
| | - Fabrice Audonnet
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal (IP), 63000 Clermont-Ferrand, France
| | - Emmanuel Bertrand
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Giuliano Sciara
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Sandra Tapin-Lingua
- FCBA, InTechFibres Division, Domaine Universitaire CS 90125, Cedex 9, 38044 Grenoble, France
| | - Paul-Henri Ducrot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Philippe Michaud
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal (IP), 63000 Clermont-Ferrand, France
| | - Véronique Aguié-Béghin
- Université de Reims-Champagne-Ardenne, INRAE, Fractionnement des Agro-Ressources et Environnement (FARE), UMR A 614, 51097 Reims, France
| | - Eric Record
- INRAE, Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| |
Collapse
|
3
|
The Maize Pathogen Ustilago maydis Secretes Glycoside Hydrolases and Carbohydrate Oxidases Directed toward Components of the Fungal Cell Wall. Appl Environ Microbiol 2022; 88:e0158122. [PMID: 36354345 PMCID: PMC9746322 DOI: 10.1128/aem.01581-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Filamentous fungi are keystone microorganisms in the regulation of many processes occurring on Earth, such as plant biomass decay and pathogenesis as well as symbiotic associations. In many of these processes, fungi secrete carbohydrate-active enzymes (CAZymes) to modify and/or degrade carbohydrates. Ten years ago, while evaluating the potential of a secretome from the maize pathogen Ustilago maydis to supplement lignocellulolytic cocktails, we noticed it contained many unknown or poorly characterized CAZymes. Here, and after reannotation of this data set and detailed phylogenetic analyses, we observed that several CAZymes (including glycoside hydrolases and carbohydrate oxidases) are predicted to act on the fungal cell wall (FCW), notably on β-1,3-glucans. We heterologously produced and biochemically characterized two new CAZymes, called UmGH16_1-A and UmAA3_2-A. We show that UmGH16_1-A displays β-1,3-glucanase activity, with a preference for β-1,3-glucans with short β-1,6 substitutions, and UmAA3_2-A is a dehydrogenase catalyzing the oxidation of β-1,3- and β-1,6-gluco-oligosaccharides into the corresponding aldonic acids. Working on model β-1,3-glucans, we show that the linear oligosaccharide products released by UmGH16_1-A are further oxidized by UmAA3_2-A, bringing to light a putative biocatalytic cascade. Interestingly, analysis of available transcriptomics data indicates that both UmGH16_1-A and UmAA3_2-A are coexpressed, only during early stages of U. maydis infection cycle. Altogether, our results suggest that both enzymes are connected and that additional accessory activities still need to be uncovered to fully understand the biocatalytic cascade at play and its physiological role. IMPORTANCE Filamentous fungi play a central regulatory role on Earth, notably in the global carbon cycle. Regardless of their lifestyle, filamentous fungi need to remodel their own cell wall (mostly composed of polysaccharides) to grow and proliferate. To do so, they must secrete a large arsenal of enzymes, most notably carbohydrate-active enzymes (CAZymes). However, research on fungal CAZymes over past decades has mainly focused on finding efficient plant biomass conversion processes while CAZymes directed at the fungus itself have remained little explored. In the present study, using the maize pathogen Ustilago maydis as model, we set off to evaluate the prevalence of CAZymes directed toward the fungal cell wall during growth of the fungus on plant biomass and characterized two new CAZymes active on fungal cell wall components. Our results suggest the existence of a biocatalytic cascade that remains to be fully understood.
Collapse
|
4
|
Bauer JA, Zámocká M, Majtán J, Bauerová-Hlinková V. Glucose Oxidase, an Enzyme "Ferrari": Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications. Biomolecules 2022; 12:472. [PMID: 35327664 PMCID: PMC8946809 DOI: 10.3390/biom12030472] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 01/25/2023] Open
Abstract
Glucose oxidase (GOx) is an important oxidoreductase enzyme with many important roles in biological processes. It is considered an "ideal enzyme" and is often called an oxidase "Ferrari" because of its fast mechanism of action, high stability and specificity. Glucose oxidase catalyzes the oxidation of β-d-glucose to d-glucono-δ-lactone and hydrogen peroxide in the presence of molecular oxygen. d-glucono-δ-lactone is sequentially hydrolyzed by lactonase to d-gluconic acid, and the resulting hydrogen peroxide is hydrolyzed by catalase to oxygen and water. GOx is presently known to be produced only by fungi and insects. The current main industrial producers of glucose oxidase are Aspergillus and Penicillium. An important property of GOx is its antimicrobial effect against various pathogens and its use in many industrial and medical areas. The aim of this review is to summarize the structure, function, production strains and biophysical and biochemical properties of GOx in light of its various industrial, biotechnological and medical applications.
Collapse
Affiliation(s)
- Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia; (J.A.B.); (M.Z.); (J.M.)
| | - Monika Zámocká
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia; (J.A.B.); (M.Z.); (J.M.)
| | - Juraj Majtán
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia; (J.A.B.); (M.Z.); (J.M.)
- Department of Microbiology, Faculty of Medicine, Slovak Medical University, Limbová 12, 833 03 Bratislava, Slovakia
| | - Vladena Bauerová-Hlinková
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia; (J.A.B.); (M.Z.); (J.M.)
| |
Collapse
|
5
|
Monclaro AV, Gorgulho Silva CDO, Gomes HAR, Moreira LRDS, Filho EXF. The enzyme interactome concept in filamentous fungi linked to biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126200. [PMID: 34710591 DOI: 10.1016/j.biortech.2021.126200] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Biomass represents an abundant and inexpensive source of sugars and aromatic compounds that can be used as raw materials for conversion into value-added bioproducts. Filamentous fungi are sources of plant cell wall degrading enzymes in nature. Understanding the interactions between enzymes is crucial for optimizing biomass degradation processes. Herein, the concept of the interactome is presented as a holistic approach that depicts the interactions among enzymes, substrates, metabolites, and inhibitors. The interactome encompasses several stages of biomass degradation, starting with the sensing of the substrate and the subsequent synthesis of hydrolytic and oxidative enzymes (fungus-substrate interaction). Enzyme-enzyme interactions are exemplified in the complex processes of lignocellulosic biomass degradation. The enzyme-substrate-metabolite-inhibitor interaction also provides a better understanding of biomass conversion, allowing bioproduct production from recalcitrant agro-industrial residues, thus bringing greater value to residual biomass. Finally, technological applications are presented for optimizing the interactome at various levels.
Collapse
Affiliation(s)
- Antonielle Vieira Monclaro
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology and Urban Resource Efficiency (CAPTURE), Frieda Saeysstraat, 9052 Ghent, Belgium
| | - Caio de Oliveira Gorgulho Silva
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway; Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Helder Andrey Rocha Gomes
- Health Science School, University Center of the Federal District (UDF), DF, Brasília 70390045, Brazil
| | | | | |
Collapse
|
6
|
Characterization of Fungal FAD-Dependent AA3_2 Glucose Oxidoreductases from Hitherto Unexplored Phylogenetic Clades. J Fungi (Basel) 2021; 7:jof7100873. [PMID: 34682294 PMCID: PMC8537048 DOI: 10.3390/jof7100873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 01/29/2023] Open
Abstract
The CAZy auxiliary activity family 3 (AA3) comprises FAD-dependent enzymes belonging to the superfamily of glucose-methanol-choline (GMC) oxidoreductases. Glucose oxidase (GOx; EC 1.1.3.4) and glucose dehydrogenase (GDH; EC 1.1.5.9) are part of subfamily AA3_2 and catalyze the oxidation of β-D-glucose at its anomeric carbon to D-glucono-1,5-lactone. Recent phylogenetic analysis showed that AA3_2 glucose oxidoreductases can be grouped into four major clades, GOx I and GDH I–III, and in minor clades such as GOx II or distinct subclades. This wide sequence space of AA3_2 glucose oxidoreductases has, however, not been studied in detail, with mainly members of GOx I and GDH I studied biochemically or structurally. Here, we report the biochemical characterization of four fungal glucose oxidoreductases from distinct, hitherto unexplored clades or subclades. The enzyme from Aureobasidium subglaciale, belonging to the minor GOx II clade, showed a typical preference for oxygen and glucose, confirming the correct annotation of this clade. The other three enzymes exhibited strict dehydrogenase activity with different substrate specificities. GDH II from Trichoderma virens showed an almost six-fold higher catalytic efficiency for maltose compared to glucose. The preferred substrate for the two GDH III enzymes from Rhizoctonia solani and Ustilago maydis was gentiobiose, a β(1→6) disaccharide, as judged from the catalytic efficiency. Overall, the newly studied AA3_2 glucose oxidoreductases showed a much broader substrate spectrum than the archetypal GOx from Aspergillus niger, which belongs to clade GOx I.
Collapse
|