Characterization of a bacterial pyranose 2-oxidase from Arthrobacter siccitolerans

Activity assays for flavoprotein oxidases: an overview

Flavoprotein oxidases have found many biotechnological applications. For identifying and improving their characteristics, it is essential to have reliable and robust assay methodology available. The methodologies used to monitor their activity seem to be scattered in the literature and seem often selected based on convenience. Due to the diversity of reactions catalyzed by flavoprotein oxidases, it is virtually impossible to recommend a single activity assay. A literature analysis of 60 recent papers describing flavoprotein oxidases revealed that continuous spectrophotometric assays, in particular colorimetric assays, are the preferred choice, as they are facile, scalable and allow for better interpretation of data than discontinuous assays. Colorimetric assays typically rely on the extinction coefficient of a monitored chromogenic product, which can be highly variable depending on the experimental conditions. Therefore, it is important to determine the extinction coefficient under the specific experimental conditions used, rather than taking it directly from the literature. To provide a guideline and assist in standardization, this review describes the most commonly utilized activity assays for flavoprotein oxidases, along with their respective merits and limitations. KEY POINTS: • Researchers should be more aware of limitations of activity assays. • Extinction coefficients should be determined for the appropriate experimental setup. • New robust activity assays are desired.

Characterization of a Pyranose Oxidase/C-Glycoside Oxidase from Microbacterium sp. 3H14, Belonging to the Unexplored Clade II of Actinobacterial POx/CGOx

Pyranose oxidase (POx) is an FAD-dependent oxidoreductase and belongs to the glucose-methanol-choline (GMC) superfamily of oxidoreductases. As recently reported, POxs and FAD-dependent C-glycoside oxidases (CGOxs) share the same sequence space, and phylogenetic analysis of actinobacterial sequences belonging to this shared sequence space showed that it can be divided into four clades. Here, we report the biochemical characterization of a POx/CGOx from Microbacterium sp. 3H14 (MPOx), belonging to the hitherto unexplored clade II of actinobacterial POx/CGOx. Overall, MPOx demonstrates comparable features to POxs/CGOxs of clades III and IV, including the preference for glycosides over monosaccharides as electron donors. However, as MPOx efficiently oxidizes the C-glycoside aspalathin as well as the O-glycoside phlorizin, it shows activity with yet another set of glycoside structures compared to other POx/CGOx members.

Identification of a robust bacterial pyranose oxidase that displays an unusual pH dependence

Pyranose oxidases are valuable biocatalysts, yet only a handful of bacterial pyranose oxidases are known. These bacterial enzymes exhibit noteworthy distinctions from their extensively characterized fungal counterparts, encompassing variations in substrate specificity and structural attributes. Herein a bacterial pyranose oxidase from Oscillatoria princeps (OPOx) was biochemically characterized in detail. In contrast to the fungal pyranose oxidases, OPOx could be well expressed in Escherichia coli as soluble, fully flavinylated, and active oxidase. It was found to be highly thermostable (melting temperature >90 °C) and showed activity on glucose, exhibiting an exceptionally low KM value (48 μM). Elucidation of its crystal structure revealed similarities with fungal pyranose oxidases, such as being a tetramer with a large central void leading to a narrow substrate access tunnel. In the active site, the FAD cofactor is covalently bound to a histidine. OPOx displays a relatively narrow pH optimum for activity with a sharp decline at relatively basic pH values which is accompanied by a drastic change in its flavin absorbance spectrum. The pH-dependent switch in flavin absorbance features and oxidase activity was shown to be fully reversible. It is hypothesized that a glutamic acid helps to stabilize the protonated form of the histidine that is tethered to the FAD. OPOx presents itself as a valuable biocatalyst as it is highly robust, well-expressed in E. coli, shows low KM values for monosaccharides, and has a peculiar pH-dependent "on-off switch".

Evolution and separation of actinobacterial pyranose and C-glycoside-3-oxidases

FAD-dependent pyranose oxidase (POx) and C-glycoside-3-oxidase (CGOx) are both members of the glucose-methanol-choline superfamily of oxidoreductases and belong to the same sequence space. Pyranose oxidases had been studied for their oxidation of monosaccharides such as D-glucose, but recently, a bacterial C-glycoside-3-oxidase that is phylogenetically related to POx and that reacts with C-glycosides such as carminic acid, mangiferin or puerarin has been described. Since these actinobacterial CGOx enzymes belong to the same sequence space as bacterial POx, they must have evolved from the same ancestor. Here, we performed a phylogenetic analysis of actinobacterial sequences and resurrected seven ancestral enzymes of the POx/CGOx sequence space to study the evolutionary trajectory of substrate preferences for monosaccharides and C-glycosides. Clade I, with its dimeric member POx from Kitasatospora aureofaciens, shows strict preference for monosaccharides (D-glucose and D-xylose) and does not react with any of the glycosides tested. No extant member of clade II has been studied to date. The two extant members of clades III and IV, monomeric POx/CGOx from Pseudoarthrobacter siccitolerans and Streptomyces canus, oxidized both monosaccharides as well as various C-glycosides (homoorientin, isovitexin, mangiferin, and puerarin). Steady-state kinetic parameters of several clades III and IV ancestral enzymes indicate that the generalist ancestor N35 slowly evolved to present-day enzymes with a much higher preference for C-glycosides than monosaccharides. Based on structural predictions of ancestors, we hypothesize that the strict specificity of bacterial clade I POx (and also fungal POx) is the result of oligomerization, which in turn results from the evolution of protein segments that were shown to be important for oligomerization, the arm, and the head domain.IMPORTANCEC-Glycosides often form active compounds in various plants. Breakage of the C-C bond in these glycosides to release the aglycone is challenging and proceeds via a two-step reaction, the oxidation of the sugar and subsequent cleavage of the C-C bond. Recently, an enzyme from a soil bacterium, FAD-dependent C-glycoside-3-oxidase (CGOx), was shown to catalyze the initial oxidation reaction. Here, we show that CGOx belongs to the same sequence space as pyranose oxidase (POx), and that an actinobacterial ancestor of the POx/CGOx family evolved into four clades, two of which show a high preference for C-glycosides.

Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms

C-glycosides are natural products with important biological activities but are recalcitrant to degradation. Glycoside 3-oxidases (G3Oxs) are recently identified bacterial flavo-oxidases from the glucose-methanol-coline (GMC) superfamily that catalyze the oxidation of C-glycosides with the concomitant reduction of O2 to H2O2. This oxidation is followed by C-C acid/base-assisted bond cleavage in two-step C-deglycosylation pathways. Soil and gut microorganisms have different oxidative enzymes, but the details of their catalytic mechanisms are largely unknown. Here, we report that PsG3Ox oxidizes at 50,000-fold higher specificity (kcat/Km) the glucose moiety of mangiferin to 3-keto-mangiferin than free D-glucose to 2-keto-glucose. Analysis of PsG3Ox X-ray crystal structures and PsG3Ox in complex with glucose and mangiferin, combined with mutagenesis and molecular dynamics simulations, reveal distinctive features in the topology surrounding the active site that favor catalytically competent conformational states suitable for recognition, stabilization, and oxidation of the glucose moiety of mangiferin. Furthermore, their distinction to pyranose 2-oxidases (P2Oxs) involved in wood decay and recycling is discussed from an evolutionary, structural, and functional viewpoint.

Localization of Pyranose 2-Oxidase from Kitasatospora aureofaciens: A Step Closer to Elucidate a Biological Role

Lignin degradation in fungal systems is well characterized. Recently, a potential for lignin depolymerization and modification employing similar enzymatic activities by bacteria is increasingly recognized. The presence of genes annotated as peroxidases in Actinobacteria genomes suggests that these bacteria should contain auxiliary enzymes such as flavin-dependent carbohydrate oxidoreductases. The only auxiliary activity subfamily with significantly similar representatives in bacteria is pyranose oxidase (POx). A biological role of providing H2O2 for peroxidase activation and reduction of radical degradation products suggests an extracellular localization, which has not been established. Analysis of the genomic locus of POX from Kitasatospora aureofaciens (KaPOx), which is similar to fungal POx, revealed a start codon upstream of the originally annotated one, and the additional sequence was considered a putative Tat-signal peptide by computational analysis. We expressed KaPOx including this additional upstream sequence as well as fusion constructs consisting of the additional sequence, the KaPOx mature domain and the fluorescent protein mRFP1 in Streptomyces lividans. The putative signal peptide facilitated secretion of KaPOx and the fusion protein, suggesting a natural extracellular localization and supporting a potential role in providing H2O2 and reducing radical compounds derived from lignin degradation.

Biochemical Characterization of Pyranose Oxidase from Streptomyces canus-Towards a Better Understanding of Pyranose Oxidase Homologues in Bacteria

Pyranose oxidase (POx, glucose 2-oxidase; EC 1.1.3.10, pyranose:oxygen 2-oxidoreductase) is an FAD-dependent oxidoreductase and a member of the auxiliary activity (AA) enzymes (subfamily AA3_4) in the CAZy database. Despite the general interest in fungal POxs, only a few bacterial POxs have been studied so far. Here, we report the biochemical characterization of a POx from Streptomyces canus (ScPOx), the sequence of which is positioned in a separate, hitherto unexplored clade of the POx phylogenetic tree. Kinetic analyses revealed that ScPOx uses monosaccharide sugars (such as d-glucose, d-xylose, d-galactose) as its electron-donor substrates, albeit with low catalytic efficiencies. Interestingly, various C- and O-glycosides (such as puerarin) were oxidized by ScPOx as well. Some of these glycosides are characteristic substrates for the recently described FAD-dependent C-glycoside 3-oxidase from Microbacterium trichothecenolyticum. Here, we show that FAD-dependent C-glycoside 3-oxidases and pyranose oxidases are enzymes belonging to the same sequence space.

FAD-dependent C-glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis

C-glycosides have a unique structure, in which an anomeric carbon of a sugar is directly bonded to the carbon of an aglycone skeleton. One of the natural C-glycosides, carminic acid, is utilized by the food, cosmetic, and pharmaceutical industries, for a total of more than 200 tons/y worldwide. However, a metabolic pathway of carminic acid has never been identified. In this study, we isolated the previously unknown carminic acid-catabolizing microorganism and discovered a flavoenzyme "C-glycoside 3-oxidase" named CarA that catalyzes oxidation of the sugar moiety of carminic acid. A Basic Local Alignment Search Tool (BLAST) search demonstrated that CarA homologs were distributed in soil microorganisms but not intestinal ones. In addition to CarA, two CarA homologs were cloned and heterologously expressed, and their biochemical properties were determined. Furthermore, a crystal structure of one homolog was determined. Together with the biochemical analysis, the crystal structure and a mutagenesis analysis of CarA revealed the mechanisms underlying their substrate specificity and catalytic reaction. Our study suggests that CarA and its homologs play a crucial role in the metabolism of C-glycosides in nature.

Repurposing Inflatable Packaging Pillows as Bioreactors: a Convenient Synthesis of Glucosone by Whole-Cell Catalysis Under Oxygen

Biocatalysis using molecular oxygen as the electron acceptor has significant potential for selective oxidations at low cost. However, oxygen is poorly soluble in water, and its slow rate of mass transfer in the aqueous phase is a major obstacle, even for laboratory-scale syntheses. Oxygen transfer can be accelerated by vigorous mechanical methods, but these are often incompatible with biological catalysts. Gentler conditions can be achieved with shallow, high surface area bag reactors that are designed for single use and generally for specialized cell culture applications. As a less-expensive alternative to these high-end bioreactors, we describe repurposing inflatable shipping pillows with resealable valves to provide high surface area mixing under oxygen for preparative synthesis of glucosone (D-arabino-hexos-2-ulose) from D-glucose using non-growing Escherichia coli whole cells containing recombinant pyranose 2-oxidase (POX) as catalyst. Parallel reactions permitted systematic study of the effects of headspace composition (i.e., air vs 100% oxygen), cell density, exogenous catalase, and reaction volume in the oxidation of 10% glucose. Importantly, only a single charge of 100% oxygen is required for stoichiometric conversion on a multi-gram scale in 18 h with resting cells, and the conversion was successfully repeated with recycled cells.

The vast repertoire of carbohydrate oxidases: An overview

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.

Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases

Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.

Pyranose oxidase: A versatile sugar oxidoreductase for bioelectrochemical applications

Pyranose oxidase (POx) is an FAD-dependent oxidoreductase, and like glucose oxidase (GOx) it is a member of the glucose-methanol-choline (GMC) superfamily of oxidoreductases. POx oxidizes several monosaccharides including D-glucose, D-galactose, and D-xylose, while concurrently oxygen is reduced to hydrogen peroxide. In addition to this oxidase activity, POx shows pronounced activity with alternative electron acceptors that include various quinones or (complexed) metal ions. Even though POx in general shows properties that are more favourable than those of GOx (e.g., a considerably higher catalytic efficiency (k_cat/K_m) for D-glucose, significantly lower Michaelis constants K_m for D-glucose, reactivity with both anomeric forms of D-glucose) it is much less frequently used for both biosensor and biofuel cell applications than GOx. POx has been applied in biosensing of D-glucose, D-galactose, and D-xylose, and in combination with α-glucosidase also maltose. An attractive application is in biosensors constructed for the measurement of 1,5-anhydro-D-glucitol, a recognised biomarker in diabetes. Bioelectrochemical applications of POx had been restricted to enzymes of fungal origin. The recent discovery and characterisation of POx from bacterial sources, which show properties that are very distinct from the fungal enzymes, might open new possibilities for further applications in bioelectrochemistry.

Characterization of pyranose oxidase variants for bioelectrocatalytic applications

Pyranose oxidase (POx) catalyzes the oxidation of d-glucose to 2-ketoglucose with concurrent reduction of oxygen to H₂O₂. POx from Trametes ochracea (ToPOx) is known to react with alternative electron acceptors including 1,4-benzoquinone (1,4-BQ), 2,6-dichlorophenol indophenol (DCPIP), and the ferrocenium ion. In this study, enzyme variants with improved electron acceptor turnover and reduced oxygen turnover were characterized as potential anode biocatalysts. Pre-steady-state kinetics of the oxidative half-reaction of ToPOx variants T166R, Q448H, L545C, and L547R with these alternative electron acceptors were evaluated using stopped-flow spectrophotometry. Higher kinetic constants were observed as compared to the wild-type ToPOx for some of the variants. Subsequently, the variants were immobilized on glassy carbon electrodes. Cyclic voltammetry measurements were performed to measure the electrochemical responses of these variants with glucose as substrate in the presence of 1,4-BQ, DCPIP, or ferrocene methanol as redox mediators. High catalytic efficiencies (I_max^app/K_M^app) compared to the wild-type POx proved the potential of these variants for future bioelectrocatalytic applications, in biosensors or biofuel cells. Among the variants, L545C showed the most desirable properties as determined kinetically and electrochemically.

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Pyranose oxidase (POx) shows attractive features for bioelectrocatalysis.

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Trametes ochracea POx variant L545C is most promising for these applications.

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Rapid kinetics experiments give good predictions for performance on an electrode.

Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase In Vitro

Pyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacterium Kitasatospora aureofaciens (KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substrates in vitro A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene from K. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus, KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds between KaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity in KaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCE Establishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase from Kitasatospora aureofaciens is of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively small K. aureofaciens proteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.

The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases

BACKGROUND

The glucose-methanol-choline (GMC) superfamily is a large and functionally diverse family of oxidoreductases that share a common structural fold. Fungal members of this superfamily that are characterised and relevant for lignocellulose degradation include aryl-alcohol oxidoreductase, alcohol oxidase, cellobiose dehydrogenase, glucose oxidase, glucose dehydrogenase, pyranose dehydrogenase, and pyranose oxidase, which together form family AA3 of the auxiliary activities in the CAZy database of carbohydrate-active enzymes. Overall, little is known about the extant sequence space of these GMC oxidoreductases and their phylogenetic relations. Although some individual forms are well characterised, it is still unclear how they compare in respect of the complete enzyme class and, therefore, also how generalizable are their characteristics.

RESULTS

To improve the understanding of the GMC superfamily as a whole, we used sequence similarity networks to cluster large numbers of fungal GMC sequences and annotate them according to functionality. Subsequently, different members of the GMC superfamily were analysed in detail with regard to their sequences and phylogeny. This allowed us to define the currently characterised sequence space and show that complete clades of some enzymes have not been studied in any detail to date. Finally, we interpret our results from an evolutionary perspective, where we could show, for example, that pyranose dehydrogenase evolved from aryl-alcohol oxidoreductase after a change in substrate specificity and that the cytochrome domain of cellobiose dehydrogenase was regularly lost during evolution.

CONCLUSIONS

This study offers new insights into the sequence variation and phylogenetic relationships of fungal GMC/AA3 sequences. Certain clades of these GMC enzymes identified in our phylogenetic analyses are completely uncharacterised to date, and might include enzyme activities of varying specificities and/or activities that are hitherto unstudied.

Identification and characterization of a novel bacterial pyranose 2-oxidase from the lignocellulolytic bacterium Pantoea ananatis Sd-1

OBJECTIVE

To identify and characterize a novel bacterial pyranose 2-oxidase (P2Ox) and investigate its potential use in lignin degradation applications.

RESULTS

A new bacterial P2Ox (PaP2Ox) enzyme was identified in the lignocellulolytic bacterium Pantoea ananatis Sd-1. The PaP2Ox open reading frame was cloned, and the encoded protein was heterologously expressed in an Escherichia coli expression system. Unlike another reported bacterial P2Ox enzyme, the purified PaP2Ox exhibits a homotetrameric spatial conformation that is similar to fungal P2Oxs, with each subunit having a molecular mass of 65 kDa. The recombinant PaP2Ox exhibits maximum activity at 50 °C and pH 6.5 with D-glucose as its preferred substrate. In addition, this enzyme was shown to work in combination with bacterial laccase in lignin degradation.

CONCLUSIONS

The bacterial enzyme PaP2Ox has potential use in ligninolytic systems and shows promising value in industrial biotechnological applications.

Multiplicity of enzymatic functions in the CAZy AA3 family

The CAZy auxiliary activity family 3 (AA3) comprises enzymes from the glucose-methanol-choline (GMC) family of oxidoreductases, which assist the activity of other AA family enzymes via their reaction products or support the action of glycoside hydrolases in lignocellulose degradation. The AA3 family is further divided into four subfamilies, which include cellobiose dehydrogenase, glucose oxidoreductases, aryl-alcohol oxidase, alcohol (methanol) oxidase, and pyranose oxidoreductases. These different enzymes catalyze a wide variety of redox reactions with respect to substrates and co-substrates. The common feature of AA3 family members is the formation of key metabolites such as H2O2 or hydroquinones, which are required by other AA enzymes. The multiplicity of enzymatic functions in the AA3 family is reflected by the multigenicity of AA3 genes in fungi, which also depends on their lifestyle. We provide an overview of the phylogenetic, molecular, and catalytic properties of AA3 enzymes and discuss their interactions with other carbohydrate-active enzymes.