Characterization of a Dye-Decolorizing Peroxidase from Irpex lacteus Expressed in Escherichia coli: An Enzyme with Wide Substrate Specificity Able to Transform Lignosulfonates

Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste

Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.

Synergistic degradation of Azure B and sulfanilamide antibiotics by the white-rot fungus Trametes versicolor with an activated ligninolytic enzyme system

The treatment of complex polluted wastewater has become an increasingly critical concern for the various types of hazardous organic compounds, including synthetic dyes and pharmaceuticals. Due to their efficient and eco-friendly advantages, the white-rot fungi (WRF) have been applied to degrade environmental pollutants. This study aimed to investigate the removal ability of WRF (i.e., Trametes versicolor WH21) in the co-contamination system composed of Azure B dye and sulfacetamide (SCT). Our study discovered that the decolorization of Azure B (300 mg/L) by strain WH21 was significantly improved (from 30.5% to 86.5%) by the addition of SCT (30 mg/L), while the degradation of SCT was also increased from 76.4% to 96.2% in the co-contamination system. Transcriptomic and biochemical analyses indicated that the ligninolytic enzyme system was activated by the enhanced enzymatic activities of MnPs and laccases, generating higher concentration of extracellular H₂O₂ and organic acids in strain WH21 in response to SCT stress. Purified MnP and laccase of strain WH21 were revealed with remarkable degradation effect on both Azure B and SCT. These findings significantly expanded the existing knowledge on the biological treatment of organic pollutants, indicating the strong promise of WRF in the treatment of complex polluted wastewater.

Creative biological lignin conversion routes toward lignin valorization

Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a 'biological funnel' offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy.

Endophytes in Lignin Valorization: A Novel Approach

Lignin, one of the essential components of lignocellulosic biomass, comprises an abundant renewable aromatic resource on the planet earth. Although 15%––40% of lignocellulose pertains to lignin, its annual valorization rate is less than 2% which raises the concern to harness and/or develop effective technologies for its valorization. The basic hindrance lies in the structural heterogeneity, complexity, and stability of lignin that collectively makes it difficult to depolymerize and yield common products. Recently, microbial delignification, an eco-friendly and cheaper technique, has attracted the attention due to the diverse metabolisms of microbes that can channelize multiple lignin-based products into specific target compounds. Also, endophytes, a fascinating group of microbes residing asymptomatically within the plant tissues, exhibit marvellous lignin deconstruction potential. Apart from novel sources for potent and stable ligninases, endophytes share immense ability of depolymerizing lignin into desired valuable products. Despite their efficacy, ligninolytic studies on endophytes are meagre with incomplete understanding of the pathways involved at the molecular level. In the recent years, improvement of thermochemical methods has received much attention, however, we lagged in exploring the novel microbial groups for their delignification efficiency and optimization of this ability. This review summarizes the currently available knowledge about endophytic delignification potential with special emphasis on underlying mechanism of biological funnelling for the production of valuable products. It also highlights the recent advancements in developing the most intriguing methods to depolymerize lignin. Comparative account of thermochemical and biological techniques is accentuated with special emphasis on biological/microbial degradation. Exploring potent biological agents for delignification and focussing on the basic challenges in enhancing lignin valorization and overcoming them could make this renewable resource a promising tool to accomplish Sustainable Development Goals (SDG’s) which are supposed to be achieved by 2030.

Modelling and Environmental Profile Associated with the Valorization of Wheat Straw as Carbon Source in the Biotechnological Production of Manganese Peroxidase

Interest in the development of biorefineries and biotechnological processes based on renewable resources has multiplied in recent years. This driving force is the result of the availability of lignocellulosic biomass and the range of applications that arise from its use and valorization. The approach of second-generation sugars from lignocellulosic biomass opens up the possibility of producing biotechnological products such as enzymes as a feasible alternative in the framework of biorefineries. It is in this context that this manuscript is framed, focusing on the modelling of a large-scale fermentative biotechnological process to produce the enzyme manganese peroxidase (MnP) by the fungus Irpex lacteus using wheat straw as a carbon source. The production scheme is based on the sequence of four stages: pretreatment of wheat straw, seed fermenters, enzyme production and downstream processes. For its environmental assessment, the Life Cycle Assessment methodology, which allows the identification and quantification of environmental impacts associated with the process, was utilized. As the main finding, the stages of the process with the highest environmental burdens are those of pretreatment and fermentation, mainly due to energy requirements. With the aim of proposing improvement scenarios, sensitivity analyses were developed around the identified hotspots. An improvement in the efficiency of steam consumption leads to a reduction of environmental damage of up to 30%.

Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes

Abstract

Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162 fully sequenced fungal species, we defined seven distinct fungal DyP clades on basis of a sequence similarity network. Sequences from one of these clades clearly diverged from all others, having on average the lower isoelectric points and hydropathy indices, the highest number of N-glycosylation sites, and N-terminal sequence peptides for secretion. Putative proteins from this clade are absent from brown-rot and ectomycorrhizal species that have lost the capability of degrading lignin enzymatically. They are almost exclusively present in white-rot and other saprotrophic Basidiomycota that digest lignin enzymatically, thus lending support for a specific role of DyPs from this clade in biochemical lignin modification. Additional nearly full-length fungal DyP genes were isolated from the environment by sequence capture by hybridization; they all belonged to the clade of the presumably secreted DyPs and to another related clade. We suggest focusing our attention on the presumably intracellular DyPs from the other clades, which have not been characterized thus far and could represent enzyme proteins with novel catalytic properties.

Key points

• A fungal DyP phylogeny delineates seven main sequence clades.

• Putative extracellular DyPs form a single clade of Basidiomycota sequences.

• Extracellular DyPs are associated to white-rot fungi.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11923-0.

Efficient degradation of various emerging pollutants by wild type and evolved fungal DyP4 peroxidases

The accumulation of emerging pollutants in the environment remains a major concern as evidenced by the increasing number of reports citing their potential risk on environment and health. Hence, removal strategies of such pollutants remain an active area of investigation. One way through which emerging pollutants can be eliminated from the environment is by enzyme-mediated bioremediation. Enzyme-based degradation can be further enhanced via advanced protein engineering approaches. In the present study a sensitive and robust bioanalytical liquid chromatography-tandem mass spectrometry (LCMSMS)-based approach was used to investigate the ability of a fungal dye decolorizing peroxidase 4 (DyP4) and two of its evolved variants—that were previously shown to be H₂O₂ tolerant—to degrade a panel of 15 different emerging pollutants. Additionally, the role of a redox mediator was examined in these enzymatic degradation reactions. Our results show that three emerging pollutants (2-mercaptobenzothiazole (MBT), paracetamol, and furosemide) were efficiently degraded by DyP4. Addition of the redox mediator had a synergistic effect as it enabled complete degradation of three more emerging pollutants (methyl paraben, sulfamethoxazole and salicylic acid) and dramatically reduced the time needed for the complete degradation of MBT, paracetamol, and furosemide. Further investigation was carried out using pure MBT to study its degradation by DyP4. Five potential transformation products were generated during the enzymatic degradation of MBT, which were previously reported to be produced during different bioremediation approaches. The current study provides the first instance of the application of fungal DyP4 peroxidases in bioremediation of emerging pollutants.

Direct Electrochemical Generation of Catalytically Competent Oxyferryl Species of Classes I and P Dye Decolorizing Peroxidases

This work introduces a novel way to obtain catalytically competent oxyferryl species for two different dye-decolorizing peroxidases (DyPs) in the absence of H2O2 or any other peroxide by simply applying a reductive electrochemical potential under aerobic conditions. UV-vis and resonance Raman spectroscopies show that this method yields long-lived compounds II and I for the DyPs from Bacillus subtilis (BsDyP; Class I) and Pseudomonas putida (PpDyP; Class P), respectively. Both electrochemically generated high valent intermediates are able to oxidize ABTS at both acidic and alkaline pH. Interestingly, the electrocatalytic efficiencies obtained at pH 7.6 are very similar to the values recorded for regular catalytic ABTS/H2O2 assays at the optimal pH of the enzymes, ca. 3.7. These findings pave the way for the design of DyP-based electrocatalytic reactors operable in an extended pH range without the need of harmful reagents such as H2O2.

Efficient Degradation of Zearalenone by Dye-Decolorizing Peroxidase from Streptomyces thermocarboxydus Combining Catalytic Properties of Manganese Peroxidase and Laccase

Ligninolytic enzymes, including laccase, manganese peroxidase, and dye-decolorizing peroxidase (DyP), have attracted much attention in the degradation of mycotoxins. Among these enzymes, the possible degradation pathway of mycotoxins catalyzed by DyP is not yet clear. Herein, a DyP-encoding gene, StDyP, from Streptomyces thermocarboxydus 41291 was identified, cloned, and expressed in Escherichia coli BL21/pG-Tf2. The recombinant StDyP was capable of catalyzing the oxidation of the peroxidase substrate 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), phenolic lignin compounds 2,6-dimethylphenol, and guaiacol, non-phenolic lignin compound veratryl alcohol, Mn²⁺, as well as anthraquinone dye reactive blue 19. Moreover, StDyP was able to slightly degrade zearalenone (ZEN). Most importantly, we found that StDyP combined the catalytic properties of manganese peroxidase and laccase, and could significantly accelerate the enzymatic degradation of ZEN in the presence of their corresponding substrates Mn²⁺ and 1-hydroxybenzotriazole. Furthermore, the biological toxicities of the main degradation products 15-OH-ZEN and 13-OH-ZEN-quinone might be remarkably removed. These findings suggested that DyP might be a promising candidate for the efficient degradation of mycotoxins in food and feed.

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.

Enzymatic Degradation of Multiple Major Mycotoxins by Dye-Decolorizing Peroxidase from Bacillus subtilis

The co-occurrence of multiple mycotoxins, including aflatoxin B₁ (AFB₁), zearalenone (ZEN) and deoxynivalenol (DON), widely exists in cereal-based animal feed and food. At present, most reported mycotoxins degrading enzymes target only a certain type of mycotoxins. Therefore, it is of great significance for mining enzymes involved in the simultaneous degradation of different types of mycotoxins. In this study, a dye-decolorizing peroxidase-encoding gene BsDyP from Bacillus subtilis SCK6 was cloned and expressed in Escherichia coli BL21/pG-Tf2. The purified recombinant BsDyP was capable of oxidizing various substrates, including lignin phenolic model compounds 2,6-dimethylphenol and guaiacol, the substrate 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid), anthraquinone dye reactive blue 19 and azo dye reactive black 5, as well as Mn²⁺. In addition, BsDyP could efficiently degrade different types of mycotoxins, including AFB₁, ZEN and DON, in presence of Mn²⁺. More important, the toxicities of their corresponding enzymatic degradation products AFB₁-diol, 15-OH-ZEN and C₁₅H₁₈O₈ were significantly lower than AFB₁, ZEN and DON. In summary, these results proved that BsDyP was a promising candidate for the simultaneous degradation of multiple mycotoxins in animal feed and food.