Exploring the biocatalytic potential of a DyP-type peroxidase by profiling the substrate acceptance of Thermobifida fusca DyP peroxidase

Structural and Biochemical Insights into Lignin-Oxidizing Activity of Bacterial Peroxidases against Soluble Substrates and Kraft Lignin

Great interest has recently been drawn to the production of value-added products from lignin; however, its recalcitrance and high chemical complexity have made this challenging. Dye-decolorizing peroxidases and catalase-peroxidases are among the enzymes that are recognized to play important roles in environmental lignin oxidation. However, bacterial lignin-oxidizing enzymes remain less characterized compared to related proteins from fungi. In this study, screening of 18 purified bacterial peroxidases against the general chromogenic substrate 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS) revealed the presence of peroxidase activity in all proteins. Agarose plate-based screens with kraft lignin identified detectable and high lignin oxidation activity in 15 purified proteins. Crystal structures were determined for the DyP-type peroxidases FC2591 from Frankia casuarinae, PF3257 from Pseudomonas fluorescens, and PR9465 from Pseudomonas rhizosphaerae. The structures revealed the presence of hemes with bound oxygens coordinated by conserved His, Arg, and Asp residues as well as three molecular tunnels connecting the heme with the protein surface. Structure-based site-directed mutagenesis of FC2591 identified at least five active site residues as essential for oxidase activity against both ABTS and lignin, whereas the S370A mutant protein showed a three- to 4-fold activity increase with both substrates. HPLC analysis of reaction products of the wild-type FC2591 and S370A mutant proteins with the model lignin dimer guaiacylglycerol-β-guaiacyl ether and kraft lignin revealed the formation of products consistent with the radical coupling of the reaction intermediates. Thus, this study identified novel bacterial heme peroxidases with lignin oxidation activity and provided further insights into our understanding of these enzymes.

A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics

Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of "biological funneling," which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.

Characterization of Amycolatopsis 75iv2 dye-decolorizing peroxidase on O-glycosides

Dye-decolorizing peroxidases are heme peroxidases with a broad range of substrate specificity. Their physiological function is still largely unknown, but a role in the depolymerization of plant cell wall polymers has been widely proposed. Here, a new expression system for bacterial dye-decolorizing peroxidases as well as the activity with previously unexplored plant molecules are reported. The dye-decolorizing peroxidase from Amycolatopsis 75iv2 (DyP2) was heterologously produced in the Gram-positive bacterium Streptomyces lividans TK24 in both intracellular and extracellular forms without external heme supplementation. The enzyme was tested on a series of O-glycosides, which are plant secondary metabolites with a phenyl glycosidic linkage. O-glycosides are of great interest, both for studying the compounds themselves and as potential models for studying specific lignin-carbohydrate complexes. The primary DyP reaction products of salicin, arbutin, fraxin, naringin, rutin, and gossypin were oxidatively coupled oligomers. A cleavage of the glycone moiety upon radical polymerization was observed when using arbutin, fraxin, rutin, and gossypin as substrates. The amount of released glucose from arbutin and fraxin reached 23% and 3% of the total substrate, respectively. The proposed mechanism suggests a destabilization of the ether linkage due to the localization of the radical in the para position. In addition, DyP2 was tested on complex lignocellulosic materials such as wheat straw, spruce, willow, and purified water-soluble lignin fractions, but no remarkable changes in the carbohydrate profile were observed, despite obvious oxidative activity. The exact action of DyP2 on such lignin-carbohydrate complexes therefore remains elusive.

IMPORTANCE

Peroxidases require correct incorporation of the heme cofactor for activity. Heterologous overproduction of peroxidases often results in an inactive enzyme due to insufficient heme synthesis by the host organism. Therefore, peroxidases are incubated with excess heme during or after purification to reconstitute activity. S. lividans as a production host can produce fully active peroxidases both intracellularly and extracellularly without the need for heme supplementation. This reduces the number of downstream processing steps and is beneficial for more sustainable production of industrially relevant enzymes. Moreover, this research has extended the scope of dye-decolorizing peroxidase applications by studying naturally relevant plant secondary metabolites and analyzing the formed products. A previously overlooked artifact of radical polymerization leading to the release of the glycosyl moiety was revealed, shedding light on the mechanism of DyP peroxidases. The key aspect is the continuous addition, rather than the more common approach of a single addition, of the cosubstrate, hydrogen peroxide. This continuous addition allows the peroxidase to complete a high number of turnovers without self-oxidation.

Dye-decolorizing peroxidase of Thermobifida halotolerance displays complex kinetics with both substrate inhibition and apparent positive cooperativity

Dye-decolorizing peroxidases (DyPs) have been intensively investigated for the purpose of industrial dye decolourization and lignin degradation. Unfortunately, the characterization of these peroxidases is hampered by their non-Michaelis-Menten kinetics, exemplified by substrate inhibition and/or positive cooperativity. Although often observed, the underlying mechanisms behind the unusual kinetics of DyPs are poorly understood. Here we studied the kinetics of the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), hydroquinones, and anthraquinone dyes by DyP from the bacterium Thermobifida halotolerans (ThDyP) and solved its crystal structure. We also provide rate equations for different kinetic mechanisms explaining the complex kinetics of heme peroxidases. Kinetic studies along with the analysis of the structure of ThDyP suggest that the substrate inhibition is caused by the non-productive binding of ABTS to the enzyme resting state. Strong irreversible inactivation of ThDyP by H2O2 in the absence of ABTS suggests that the substrate inhibition by H2O2 may be caused by the non-productive binding of H2O2 to compound I. Positive cooperativity was observed only with the oxidation of ABTS but not with the two electron-donating substrates. Although the conventional mechanism of cooperativity cannot be excluded, we propose that the oxidation of ABTS assumes the simultaneous binding of two ABTS molecules to reduce compound I to the enzyme resting state, and this causes the apparent positive cooperativity.

pH-dependent and whole-cell catalytic decolorization of dyes using recombinant dye-decolorizing peroxidase from Rhodococcus jostii

Dyes in wastewater have adverse effects on the environment and human health. Dye-decolorizing peroxidase (DyP) is a promising biocatalyst to dyes degradation, but the decolorization rates varied greatly which influencing factors and mechanisms remain to be fully disclosed. To explore an effective decolorizing approach, we have studied a DyP from Rhodococcus jostii (RhDyPB) which was overexpressed in Escherichia coli to decolorize four kinds of dyes, Reactive blue 19, Eosin Y, Indigo carmine, and Malachite green. We found the decolorization rates of the dyes by purified RhDyPB were all pH-dependent and the highest one was 94.4% of Malachite green at pH 6.0. ESI-MS analysis of intermediates in the decolorization process of Reactive blue 19 proved the degradation was due to peroxidase catalysis. Molecular docking predicated the interaction of RhDyPB with dyes, and a radical transfer reaction. In addition, we performed decolorization of dyes with whole E. coli cell with and without expressing RhDyPB. It was found that decolorization of dyes by E. coli cell was due to both cell absorption and degradation, and RhDyPB expression improved the degradation rates towards Reactive blue 19, Indigo carmine and Malachite green. The effective decolorization of Malachite green and the successful application of whole DyP-overexpressed cells in dye decolorization is conducive to the bioremediation of dye-containing wastewaters by DyPs.

Bacterial transformation of lignin: key enzymes and high-value products

Lignin, a natural organic polymer that is recyclable and inexpensive, serves as one of the most abundant green resources in nature. With the increasing consumption of fossil fuels and the deterioration of the environment, the development and utilization of renewable resources have attracted considerable attention. Therefore, the effective and comprehensive utilization of lignin has become an important global research topic, with the goal of environmental protection and economic development. This review focused on the bacteria and enzymes that can bio-transform lignin, focusing on the main ways that lignin can be utilized to produce high-value chemical products. Bacillus has demonstrated the most prominent effect on lignin degradation, with 89% lignin degradation by Bacillus cereus. Furthermore, several bacterial enzymes were discussed that can act on lignin, with the main enzymes consisting of dye-decolorizing peroxidases and laccase. Finally, low-molecular-weight lignin compounds were converted into value-added products through specific reaction pathways. These bacteria and enzymes may become potential candidates for efficient lignin degradation in the future, providing a method for lignin high-value conversion. In addition, the bacterial metabolic pathways convert lignin-derived aromatics into intermediates through the "biological funnel", achieving the biosynthesis of value-added products. The utilization of this "biological funnel" of aromatic compounds may address the heterogeneous issue of the aromatic products obtained via lignin depolymerization. This may also simplify the separation of downstream target products and provide avenues for the commercial application of lignin conversion into high-value products.

Dye Decolorization by a Miniaturized Peroxidase Fe-MimochromeVI*a

Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless, their widespread use is somehow hindered because of their cost, availability, and batch-to-batch reproducibility. Here, we report the catalytic proficiency of a miniaturized synthetic peroxidase, Fe-Mimochrome VI*a, in the decolorization of four organic dyes, as representatives of either the heterocyclic or triarylmethane class of dyes. Fe-Mimochrome VI*a performed over 130 turnovers in less than five minutes in an aqueous buffer at a neutral pH under mild conditions.

Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases

Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H₂O₂ to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H₂O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.

Bacterial Peroxidase on Electrochemically Reduced Graphene Oxide for Highly Sensitive H2 O2 Detection

Peroxidase enzymes enable the construction of electrochemical sensors for highly sensitive and selective quantitative detection of various molecules, pathogens and diseases. Herein, we describe the immobilization of a peroxidase from Bacillus s. (BsDyP) on electrochemically reduced graphene oxide (ERGO) deposited on indium tin oxide (ITO) and polyethylene terephthalate (PET) layers. XRD, SEM, AFM, FT-IR and Raman characterization of the sensor confirmed its structural integrity and a higher enzyme surface occupancy. The BsDyP-ERGO/ITO/PET electrode performed better than other horseradish peroxidase-based electrodes, as evinced by an improved electrochemical response in the nanomolar range (linearity 0.05-280 μM of H2 O2 , LOD 32 nM). The bioelectrode was mechanically robust, active in the 3.5-6 pH range and exhibited no loss of activity upon storage for 8 weeks at 4 °C.

Genome Functional Analysis of the Psychrotrophic Lignin-Degrading Bacterium Arthrobacter sp. C2 and the Role of DyP in Catalyzing Lignin Degradation

In the cold regions of China, lignin-rich corn straw accumulates at high levels due to low temperatures. The application of psychrotrophic lignin-degrading bacteria should be an effective means of overcoming the low-temperature limit for lignin degradation and promoting the utilization of corn straw. However, this application is limited by the lack of suitable strains for decomposition of lignin; furthermore, the metabolic mechanism of psychrotrophic lignin-degrading bacteria is unclear. Here, the whole genome of the psychrotrophic lignin-degrading bacterium Arthrobacter sp. C2, isolated in our previous work, was sequenced. Comparative genomics revealed that C2 contained unique genes related to lignin degradation and low-temperature adaptability. DyP may participate in lignin degradation and may be a cold-adapted enzyme. Moreover, DyP was proven to catalyze lignin Cα-Cβ bond cleavage. Deletion and complementation of the DyP gene verified its ability to catalyze the first-step reaction of lignin degradation. Comparative transcriptomic analysis revealed that the transcriptional expression of the DyP gene was upregulated, and the genetic compensation mechanism allowed C2ΔDyP to degrade lignin, which provided novel insights into the survival strategy of the psychrotrophic mutant strain C2ΔdyP. This study improved our understanding of the metabolic mechanism of psychrotrophic lignin-degrading bacteria and provided potential application options for energy-saving production using cold-adapted lignin-degrading enzymes.

Hydrophilic magnetic molecularly imprinted resin in PVDF membrane for efficient selective removal of dye

Selective removal of contaminants from water by membranes is of practical importance for water purification and environmental protection. In the present study, through an in-situ polymerization process, a novel composite of Fe₃O₄/molecularly imprinted resorcinol -formaldehyde-melamine resin (Fe₃O₄/MIRFMR) was synthesized. Then, the novel membrane was prepared from a tea filter bag (TFB) as a base substrate which was subsequently coated by a casting solution containing polyvinylidene fluoride (PVDF) matrix, Prunus scoparia gum as a hydrophilic agent and Fe₃O₄/MIRFMR as selective filler by phase inversion technique. Resorcinol as functional monomers with multiple hydrophilic groups such as -OH, -NH₂ and -NH-, were used for selective removal of Rhodamine B (RhB) as target molecule. The Fe₃O₄/MIRFMR/PVDF/TFB membranes were characterized by FE-SEM, XRD, FTIR, BET, VSM, water contact angle (WCA) and mechanical analysis. The filtration and adsorption of RhB on the prepared membrane was investigated parameters in a cross-module filtration setup. Casting solution containing 0.01 g of Fe₃O₄/MIRFMR as optimum value showed good wettability, high water flux (42.5 L/m² h), flux recovery ratio (88.9%), RhB removal efficiency (95.8%). The selectivity of 4.9, 3.3, 2.1 and 2.5 was found to be for RhB compared to AB, MG, EB, and TB dye. It seems that the fabricated membrane could be an effective and selective option for wastewater containing pollutants. The high removal efficiency, fouling resistance, good wettability and stability of the fabricated membrane are promising for use in practical water filtration, especially for selective removal of dyes.

Characterization of Two Hydrogen Peroxide Resistant Peroxidases from Rhodococcus opacus 1CP

The dye-decolorizing peroxidases (DyP) are a family of heme-dependent enzymes present on a broad spectrum of microorganisms. While the natural function of these enzymes is not fully understood, their capacity to degrade highly contaminant pigments such as azo dyes or anthraquinones make them excellent candidates for applications in bioremediation and organic synthesis. In this work, two novel DyP peroxidases from the organism Rhodococcus opacus 1CP (DypA and DypB) were cloned and expressed in Escherichia coli. The enzymes were purified and biochemically characterized. The activities of the two DyPs via 2,2′-azino-bis [3-ethylbenzthiazoline-6-sulphonic acid] (ABTS) assay and against Reactive Blue 5 were assessed and optimized. Results showed varying trends for DypA and DypB. Remarkably, these enzymes presented a particularly high tolerance towards H2O2, retaining its activities at about 10 mM H2O2 for DypA and about 4.9 mM H2O2 for DypB.

Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase

Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.

Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering

Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.

Comparing Ligninolytic Capabilities of Bacterial and Fungal Dye-Decolorizing Peroxidases and Class-II Peroxidase-Catalases

We aim to clarify the ligninolytic capabilities of dye-decolorizing peroxidases (DyPs) from bacteria and fungi, compared to fungal lignin peroxidase (LiP) and versatile peroxidase (VP). With this purpose, DyPs from Amycolatopsis sp., Thermomonospora curvata, and Auricularia auricula-judae, VP from Pleurotus eryngii, and LiP from Phanerochaete chrysosporium were produced, and their kinetic constants and reduction potentials determined. Sharp differences were found in the oxidation of nonphenolic simple (veratryl alcohol, VA) and dimeric (veratrylglycerol-β- guaiacyl ether, VGE) lignin model compounds, with LiP showing the highest catalytic efficiencies (around 15 and 200 s⁻¹·mM⁻¹ for VGE and VA, respectively), while the efficiency of the A. auricula-judae DyP was 1–3 orders of magnitude lower, and no activity was detected with the bacterial DyPs. VP and LiP also showed the highest reduction potential (1.28–1.33 V) in the rate-limiting step of the catalytic cycle (i.e., compound-II reduction to resting enzyme), estimated by stopped-flow measurements at the equilibrium, while the T. curvata DyP showed the lowest value (1.23 V). We conclude that, when using realistic enzyme doses, only fungal LiP and VP, and in much lower extent fungal DyP, oxidize nonphenolic aromatics and, therefore, have the capability to act on the main moiety of the native lignin macromolecule.

Breakthroughs in the discovery and use of different peroxidase isoforms of microbial origin

Peroxidases are classified as oxidoreductases and are the second largest class of enzymes applied in biotechnological processes. These enzymes are used to catalyze various oxidative reactions using hydrogen peroxide and other substrates as electron donors. They are isolated from various sources such as plants, animals and microbes. Peroxidase enzymes have versatile applications in bioenergy, bioremediation, dye decolorization, humic acid degradation, paper and pulp, and textile industries. Besides, peroxidases from different sources have unique abilities to degrade a broad range of environmental pollutants such as petroleum hydrocarbons, dioxins, industrial dye effluents, herbicides and pesticides. Ironically, unlike most biological catalysts, the function of peroxidases varies according to their source. For instance, manganese peroxidase (MnP) of fungal origin is widely used for depolymerization and demethylation of lignin and bleaching of pulp. While, horseradish peroxidase of plant origin is used for removal of phenols and aromatic amines from waste waters. Microbial enzymes are believed to be more stable than enzymes of plant or animal origin. Thus, making microbially-derived peroxidases a well-sought-after biocatalysts for versatile industrial and environmental applications. Therefore, the current review article highlights on the recent breakthroughs in the discovery and use of peroxidase isoforms of microbial origin at a possible depth.

Emerging biotechnological potentials of DyP-type peroxidases in remediation of lignin wastes and phenolic pollutants: a global assessment (2007-2019)

Dye decolourizing peroxidase (DyP) is an emerging biocatalyst with enormous bioremediation and biotechnological potentials. This study examined the global trend of research related to DyP through a bibliometric analysis. The search term 'dye decolourizing peroxidase' or 'DyP-type peroxidase' was used to retrieve published articles between 2007 and 2019 from the Web of Science (WoS) and Scopus databases. A total of 62 articles were published within the period, with an annual growth rate of 17·6%. The highest research output was observed in 2015, which accounted for about 13% of the total output in 12 years. Germany published the highest number of articles (n = 10, 16·1%) with a total citation of 478. However, the lowest number of published articles among the top 10 countries was observed in India and Korea (n = 2, 3·2%). Research collaboration was low (collaboration index = 4·08). In addition to dye decolourizing peroxidase(s) and DyP-type peroxidase(s) (n = 33, 53·23%), the top authors keywords and research focus included lignin and lignin degradation (n = 10, 16·1 %). More so, peroxidase (n = 59, 95·2%), amino acid sequence (n = 27, 46·8%), lignin (n = 24, 38·7%) and metabolism (n = 23, 37·1%) were highly represented in keywords-plus. The most common conceptual framework from this study include characterization, lignin degradation and environmental proteomics. Apart from the inherent efficient dye-decolourizing properties, this study showed that DyP has emerging biotechnological potentials in lignin degradation and remediation of phenolic environmental pollutants, which at the moment are under explored globally.

Production and characterisation of a novel actinobacterial DyP-type peroxidase and its application in coupling of phenolic monomers

The extracellular peroxidase from Streptomyces albidoflavus BSII#1 was purified to near homogeneity using sequential steps of acid and acetone precipitation, followed by ultrafiltration. The purified peroxidase was characterised and tested for the ability to catalyse coupling reactions between selected phenolic monomer pairs. A 46-fold purification of the peroxidase was achieved, and it was shown to be a 46 kDa haem peroxidase. Unlike other actinobacteria-derived peroxidases, it was only inhibited (27 % inhibition) by relatively high concentrations of sodium azide (5 mM) and was capable of oxidising eleven (2,4-dichlorophenol, 2,6-dimethoxyphenol, 4-tert-butylcatechol, ABTS, caffeic acid, catechol, guaiacol, l-DOPA, o-aminophenol, phenol, pyrogallol) of the seventeen substrates tested. The peroxidase remained stable at temperatures of up to 80 °C for 60 min and retained >50 % activity after 24 h between pH 5.0-9.0, but was most sensitive to incubation with hydrogen peroxide (H₂O₂; 0.01 mM), l-cysteine (0.02 mM) and ascorbate (0.05 mM) for one hour. It was significantly inhibited by all organic solvents tested (p ≤ 0.05). The K_m and V_max values of the partially purified peroxidase with the substrate 2,4-DCP were 0.95 mM and 0.12 mmol min^-1, respectively. The dyes reactive blue 4, reactive black 5, and Azure B, were all decolourised to a certain extent: approximately 30 % decolourisation was observed after 24 h (1 μM dye). The peroxidase successfully catalysed coupling reactions between several phenolic monomer pairs including catechin-caffeic acid, catechin-catechol, catechin-guaiacol and guaiacol-syringaldazine under the non-optimised conditions used in this study. Genome sequencing confirmed the identity of strain BSII#1 as a S. albidoflavus strain. In addition, the genome sequence revealed the presence of one peroxidase gene that includes the twin arginine translocation signal sequence of extracellular proteins. Functional studies confirmed that the peroxidase produced by S. albidoflavus BSII#1 is part of the dye-decolourising peroxidase (DyP-type) family.

Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives

Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.

Expression and Characterization of a Dye-Decolorizing Peroxidase from Pseudomonas Fluorescens Pf0-1

The consumption of dyes is increasing worldwide in line with the increase of population and demand for clothes and other colored products. However, the efficiency of dyeing processes is still poor and results in large amounts of colored effluents. It is desired to develop a portfolio of enzymes which can be used for the treatment of colored wastewaters. Herein, we used genome sequence information to discover a dye-decolorizing peroxidase (DyP) from Pseudomonas fluorescens Pf-01. Two genes putatively encoding for DyPs were identified in the respective genome and cloned for expression in Escherichia coli, of which one (PfDyP B2) could be overexpressed as a soluble protein. PfDyP B2 shows some typical features known for DyPs which includes the ability to convert dyes at the expense of hydrogen peroxide. Interestingly, t-butyl hydroperoxide could be used as an alternative substrate to hydrogen peroxide. Immobilization of PfDyP B2 in calcium-alginate beads resulted in a significant increase in stability: PfDyP B2 retains 80% of its initial activity after 2 h incubation at 50 °C, while the soluble enzyme is inactivated within minutes. PfDyP B2 was also tested with aniline and ethyl diazoacetate as substrates. Based on GC-MS analyses, 30% conversion of the starting material was achieved after 65 h at 30 °C. Importantly, this is the first report of a DyP-catalyzed insertion of a carbene into an N-H bond.

Characterization of a New DyP-Peroxidase from the Alkaliphilic Cellulomonad, Cellulomonas bogoriensis

DyP-type peroxidases are heme-containing enzymes that have received increasing attention over recent years with regards to their potential as biocatalysts. A novel DyP-type peroxidase (CboDyP) was discovered from the alkaliphilic cellulomonad, Cellulomonas bogoriensis, which could be overexpressed in Escherichia coli. The biochemical characterization of the recombinant enzyme showed that it is a heme-containing enzyme capable to act as a peroxidase on several dyes. With the tested substrates, the enzyme is most active at acidic pH values and is quite tolerant towards solvents. The crystal structure of CboDyP was solved which revealed atomic details of the dimeric heme-containing enzyme. A peculiar feature of CboDyP is the presence of a glutamate in the active site which in most other DyPs is an aspartate, being part of the DyP-typifying sequence motif GXXDG. The E201D CboDyP mutant was prepared and analyzed which revealed that the mutant enzyme shows a significantly higher activity on several dyes when compared with the wild-type enzyme.

Comprehensive investigation of a dye-decolorizing peroxidase and a manganese peroxidase from Irpex lacteus F17, a lignin-degrading basidiomycete

Irpex lacteus F17 is well-known for its ability to degrade recalcitrant aromatic pollutants, which mainly results from the action of the manganese peroxidase (MnP) that it is able to produce. Recently, the genome sequencing and annotation of this strain provided comprehensive picture of the ligninolytic peroxidase gene family. In addition to revealing the presence of 13 MnPs, genes for five dye-decolorizing peroxidases (DyPs) were also discovered in the I. lacteus F17 genome, which are unrelated to the fungal class II peroxidases. In the present study, amino acid sequences of five DyPs and 13 MnPs, representing two different families of heme peroxidases, were analyzed. Of these, two enzymes, a DyP (Il-DyP4) and a MnP (Il-MnP6) were expressed respectively in Escherichia coli, and were characterized by comparing their molecular models, substrate specificities, and catalytic features. The results showed that Il-DyP4 possessed a higher catalytic efficiency for some representative substrates, and a stronger decolorizing ability to a wide range of synthetic dyes in acidic conditions. Based on electrochemical measurements, Il-DyP4 was found to have a high redox potential of 27 mV at pH 3.5, which was superior to that of Il-MnP6 (− 75 mV), thereby contributing to its ability to oxidize high redox potential substrates, such as veratryl alcohol and polymeric dye Poly R-478. The results highlighted the potential of Il-DyP4 for use in industrial and environmental applications.

Multienzyme immobilized polymeric membrane reactor for transformation of lignin model compound

We have developed a multienzyme functionalized membrane reactor for bioconversion of lignin model compound involving enzymatic catalysis. Layer-by-layer approach was used to immobilize three different enzymes (glucose oxidase, peroxidase and laccase) into pH-responsive membranes. This novel membrane reactor couples the in situ generation of hydrogen peroxide (by glucose oxidase) to oxidative conversion of a lignin model compound, guaiacylglycerol-B-guaiacylether (GGE). Preliminary investigation of the efficacy of these functional membranes towards GGE degradation is demonstrated under convective flow mode. Over 90% of the initial feed could be degraded with the multienzyme immobilized membranes at a residence time of approximately 22 seconds. GGE conversion product analysis revealed formation of oligomeric oxidation products with peroxidase, which might be potential hazard to membrane bioreactors. These oxidation products could be further degraded by laccase enzymes in the multienzymatic membranes explaining the potential of multienzyme membrane reactors. The multienzyme incorporated membrane reactors were active for about a month time of storage at 4 °C, and retention of activity was demonstrated after repetitive use.

Creating Oxidase-Peroxidase Fusion Enzymes as a Toolbox for Cascade Reactions

A set of bifunctional oxidase-peroxidases has been prepared by fusing four distinct oxidases to a peroxidase. Although such fusion enzymes have not been observed in nature, they could be expressed and purified in good yields. Characterization revealed that the artificial enzymes retained the capability to bind the two required cofactors and were catalytically active as oxidase and peroxidase. Peroxidase fusions of alditol oxidase and chitooligosaccharide oxidase could be used for the selective detection of xylitol and cellobiose with a detection limit in the low-micromolar range. The peroxidase fusions of eugenol oxidase and 5-hydroxymethylfurfural oxidase could be used for dioxygen-driven, one-pot, two-step cascade reactions to convert vanillyl alcohol into divanillin and eugenol into lignin oligomers. The designed oxidase-peroxidase fusions represent attractive biocatalysts that allow efficient biocatalytic cascade oxidations that only require molecular oxygen as an oxidant.