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Biomolecules
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Oxygenases: Exploiting Their Catalytic Power
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Oxygenases: Exploiting Their Catalytic Power

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Enzymology".

Deadline for manuscript submissions: closed (22 December 2021) | Viewed by 19113

Special Issue Editors

Dr. Marco van den Berg

E-Mail Website
Guest Editor
DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
Interests: enzyme engineering; redox enzymology; enzyme applications; pharmaceuticals; lignocellulosic ethanol; food processing; secondary metabolites; flavor
Prof. Dr. Ir. Marco Fraaije

E-Mail Website
Guest Editor
Faculty of Science and Engineering Biotechnology, Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 4, 9747 AG Groningen, The Netherlands
Interests: enzyme engineering; redox enzymology; enzyme applications; pharmaceuticals; lignocellulosic ethanol; food processing; secondary metabolites; flavor

Special Issue Information

Dear Colleagues,

Oxygenases are a diverse group of enzymes that carry out the regio-, stereo-, and chemoselective introduction of oxygen into a large range of organic molecules under mild conditions, and thus catalyse crucial reactions in nature. This versatility is of the utmost interest for industrial processes that include oxidative transformations (e.g., food, textile, pharmaceutical, and biorefinery processes), as the industrial use of oxygenases represents an environmentally friendly alternative to harsh chemical processes for the production of bulk and fine chemicals, including pharmaceuticals and other value-added products.

Despite their versatility in the catalysed reactions, compared to other enzyme classes, the application of oxygenases in industrial processes is not very widespread. This is mainly due to a relatively poor availability of industrially suitable biocatalysts and the methodology to apply them. Therefore, to fully exploit the catalytic power of oxygenases, not only a deeper understanding of abilities and limitations is needed, but also technical aspects of their industrial application need to be solved. This Special Issue aims to highlight the recent progress made in the fundamental understanding of oxygenases of all major classes (i.e., flavin-, heme-, and copper-dependent as well as co-factor-independent), towards applying them in industrial processes.

Dr. Marco van den Berg
Prof. Dr. Ir. Marco Fraaije
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Enzymes
  • Biotechnology
  • Enzyme engineering
  • Oxygenases
  • Electron donor
  • Redox cycle
  • Biocatalysis
  • Industrial application

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Published Papers (5 papers)

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Research

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12 pages, 2103 KiB  
Article
Enzyme-Mediated Quenching of the Pseudomonas Quinolone Signal (PQS): A Comparison between Naturally Occurring and Engineered PQS-Cleaving Dioxygenases
by Alba Arranz San Martín, Jan Vogel, Sandra C. Wullich, Wim J. Quax and Susanne Fetzner
Biomolecules 2022, 12(2), 170; https://doi.org/10.3390/biom12020170 - 21 Jan 2022
Cited by 5 | Viewed by 2669
Abstract
The opportunistic pathogen Pseudomonas aeruginosa employs quorum sensing to govern the production of many virulence factors. Interference with quorum sensing signaling has therefore been put forward as an attractive approach to disarm this pathogen. Here, we analyzed the quorum quenching properties of natural [...] Read more.
The opportunistic pathogen Pseudomonas aeruginosa employs quorum sensing to govern the production of many virulence factors. Interference with quorum sensing signaling has therefore been put forward as an attractive approach to disarm this pathogen. Here, we analyzed the quorum quenching properties of natural and engineered (2-alkyl-)3-hydroxy-4(1H)-quinolone 2,4-dioxygenases (HQDs) that inactivate the P. aeruginosa signal molecule PQS (Pseudomonas quinolone signal; 2-heptyl-3-hydroxy-4(1H)-quinolone). When added exogenously to P. aeruginosa cultures, all HQDs tested significantly reduced the levels of PQS and other alkylquinolone-type secondary metabolites deriving from the biosynthetic pathway, such as the respiratory inhibitor 2-heptyl-4-hydroxyquinoline N-oxide. HQDs from Nocardia farcinica and Streptomyces bingchenggensis, which combine low KM values for PQS with thermal stability and resilience in the presence of P. aeruginosa exoproducts, respectively, attenuated production of the virulence factors pyocyanin and pyoverdine. A delay in mortality was observed when Galleria mellonella larvae were infected with P. aeruginosa suspensions treated with the S. bingchenggensis HQD or with inhibitors of alkylquinolone biosynthesis. Our data indicate that quenching of PQS signaling has potential as an anti-virulence strategy; however, an efficient anti-virulence therapy against P. aeruginosa likely requires a combination of agents addressing multiple targets. Full article
(This article belongs to the Special Issue Oxygenases: Exploiting Their Catalytic Power)
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12 pages, 2620 KiB  
Article
Preparative Production of Functionalized (N- and O-Heterocyclic) Polycyclic Aromatic Hydrocarbons by Human Cytochrome P450 3A4 in a Bioreactor
by Matic Srdič, Nico D. Fessner, Deniz Yildiz, Anton Glieder, Markus Spiertz and Ulrich Schwaneberg
Biomolecules 2022, 12(2), 153; https://doi.org/10.3390/biom12020153 - 18 Jan 2022
Cited by 3 | Viewed by 2386
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and their N- and O-containing derivatives (N-/O-PAHs) are environmental pollutants and synthetically attractive building blocks in pharmaceuticals. Functionalization of PAHs can be achieved via C-H activation by cytochrome P450 enzymes (e.g., P450 CYP3A4) in an environmentally friendly manner. Despite [...] Read more.
Polycyclic aromatic hydrocarbons (PAHs) and their N- and O-containing derivatives (N-/O-PAHs) are environmental pollutants and synthetically attractive building blocks in pharmaceuticals. Functionalization of PAHs can be achieved via C-H activation by cytochrome P450 enzymes (e.g., P450 CYP3A4) in an environmentally friendly manner. Despite its broad substrate scope, the contribution of CYP3A4 to metabolize common PAHs in humans was found to be small. We recently showcased the potential of CYP3A4 in whole-cell biocatalysis with recombinant yeast Komagataella phaffii (Pichia pastoris) catalysts for the preparative-scale synthesis of naturally occurring metabolites in humans. In this study, we aimed at exploring the substrate scope of CYP3A4 towards (N-/O)-PAHs and conducted a bioconversion experiment at 10 L scale to validate the synthetic potential of CYP3A4 for the preparative-scale production of functionalized PAH metabolites. Hydroxylated products were purified and characterized using HPLC and NMR analysis. In total, 237 mg of fluorenol and 48 mg of fluorenone were produced from 498 mg of fluorene, with peak productivities of 27.7 μmol/L/h for fluorenol and 5.9 μmol/L/h for fluorenone; the latter confirmed that CYP3A4 is an excellent whole-cell biocatalyst for producing authentic human metabolites. Full article
(This article belongs to the Special Issue Oxygenases: Exploiting Their Catalytic Power)
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13 pages, 1260 KiB  
Article
Late-Stage Functionalisation of Polycyclic (N-Hetero-) Aromatic Hydrocarbons by Detoxifying CYP5035S7 Monooxygenase of the White-Rot Fungus Polyporus arcularius
by Nico D. Fessner, Christopher Grimm, Wolfgang Kroutil and Anton Glieder
Biomolecules 2021, 11(11), 1708; https://doi.org/10.3390/biom11111708 - 17 Nov 2021
Cited by 4 | Viewed by 3484
Abstract
Functionalisation of polycyclic aromatic hydrocarbons (PAHs) and their N-heteroarene analogues (NPAHs) is a tedious synthetic endeavour that requires diverse bottom-up approaches. Cytochrome P450 enzymes of white-rot fungi were shown to participate in the fungal detoxification of xenobiotics and environmental hazards via hydroxylation [...] Read more.
Functionalisation of polycyclic aromatic hydrocarbons (PAHs) and their N-heteroarene analogues (NPAHs) is a tedious synthetic endeavour that requires diverse bottom-up approaches. Cytochrome P450 enzymes of white-rot fungi were shown to participate in the fungal detoxification of xenobiotics and environmental hazards via hydroxylation of PAH compounds. In this paper, the recently discovered activity of the monooxygenase CYP5035S7 towards (N)PAHs was investigated in detail, and products formed from the substrates azulene, acenaphthene, fluorene, anthracene, and phenanthrene by whole-cell biocatalysis were isolated and characterised. The observed regioselectivity of CYP5035S7 could be explained by a combination of the substrate’s electron density and steric factors influencing the substrate orientation giving insight into the active-site geometry of the enzyme. Full article
(This article belongs to the Special Issue Oxygenases: Exploiting Their Catalytic Power)
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10 pages, 918 KiB  
Article
Modular Assembly of Phosphite Dehydrogenase and Phenylacetone Monooxygenase for Tuning Cofactor Regeneration
by Ni Nyoman Purwani, Caterina Martin, Simone Savino and Marco W. Fraaije
Biomolecules 2021, 11(6), 905; https://doi.org/10.3390/biom11060905 - 17 Jun 2021
Cited by 6 | Viewed by 3768
Abstract
The use of multienzyme complexes can facilitate biocatalytic cascade reactions by employing fusion enzymes or protein tags. In this study, we explored the use of recently developed peptide tags that promote complex formation of the targeted proteins: the dimerization-docking and anchoring domain (RIDD–RIAD) [...] Read more.
The use of multienzyme complexes can facilitate biocatalytic cascade reactions by employing fusion enzymes or protein tags. In this study, we explored the use of recently developed peptide tags that promote complex formation of the targeted proteins: the dimerization-docking and anchoring domain (RIDD–RIAD) system. These peptides allow self-assembly based on specific protein–protein interactions between both peptides and allow tuning of the ratio of the targeted enzymes as the RIAD peptide binds to two RIDD peptides. Each of these tags were added to the C-terminus of a NADPH-dependent Baeyer–Villiger monooxygenase (phenylacetone monooxygenase, PAMO) and a NADPH-regenerating enzyme (phosphite dehydrogenase, PTDH). Several RIDD/RIAD-tagged PAMO and PTDH variants were successfully overproduced in E. coli and subsequently purified. Complementary tagged enzymes were mixed and analyzed for their oligomeric state, stability, and activity. Complexes were formed in the case of some specific combinations (PAMORIAD–PTDHRIDD and PAMORIAD/RIAD–PTDHRIDD). These enzyme complexes displayed similar catalytic activity when compared with the PTDH–PAMO fusion enzyme. The thermostability of PAMO in these complexes was retained while PTDH displayed somewhat lower thermostability. Evaluation of the biocatalytic performance by conducting conversions revealed that with a self-assembled PAMO–PTDH complex less PTDH was required for the same performance when compared with the PTDH–PAMO fusion enzyme. Full article
(This article belongs to the Special Issue Oxygenases: Exploiting Their Catalytic Power)
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Review

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21 pages, 3477 KiB  
Review
Oxidative Power: Tools for Assessing LPMO Activity on Cellulose
by Federica Calderaro, Loes E. Bevers and Marco A. van den Berg
Biomolecules 2021, 11(8), 1098; https://doi.org/10.3390/biom11081098 - 26 Jul 2021
Cited by 13 | Viewed by 5806
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have sparked a lot of research regarding their fascinating mode-of-action. Particularly, their boosting effect on top of the well-known cellulolytic enzymes in lignocellulosic hydrolysis makes them industrially relevant targets. As more characteristics of LPMO and its key role have [...] Read more.
Lytic polysaccharide monooxygenases (LPMOs) have sparked a lot of research regarding their fascinating mode-of-action. Particularly, their boosting effect on top of the well-known cellulolytic enzymes in lignocellulosic hydrolysis makes them industrially relevant targets. As more characteristics of LPMO and its key role have been elucidated, the need for fast and reliable methods to assess its activity have become clear. Several aspects such as its co-substrates, electron donors, inhibiting factors, and the inhomogeneity of lignocellulose had to be considered during experimental design and data interpretation, as they can impact and often hamper outcomes. This review provides an overview of the currently available methods to measure LPMO activity, including their potential and limitations, and it is illustrated with practical examples. Full article
(This article belongs to the Special Issue Oxygenases: Exploiting Their Catalytic Power)
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