Biochemical and molecular characterization of a novel dye-decolourizing peroxidase from Raoultella ornithinolytica OKOH-1

Biological oxidation methods for the removal of organic and inorganic contaminants from wastewater: A comprehensive review

Enzyme-based bioremediation is a simple, cost-effective, and environmentally friendly method for isolating and removing a wide range of environmental pollutants. This study is a comprehensive review of recent studies on the oxidation of pollutants by biological oxidation methods, performed individually or in combination with other methods. The main bio-oxidants capable of removing all types of pollutants, such as organic and inorganic molecules, from fungi, bacteria, algae, and plants, and different types of enzymes, as well as the removal mechanisms, were investigated. The use of mediators and modification methods to improve the performance of microorganisms and their resistance under harsh real wastewater conditions was discussed, and numerous case studies were presented and compared. The advantages and disadvantages of conventional and novel immobilization methods, and the development of enzyme engineering to adjust the content and properties of the desired enzymes, were also explained. The optimal operating parameters such as temperature and pH, which usually lead to the best performance, were presented. A detailed overview of the different combination processes was also given, including bio-oxidation in coincident or consecutive combination with adsorption, advanced oxidation processes, and membrane separation. One of the most important issues that this study has addressed is the removal of both organic and inorganic contaminants, taking into account the actual wastewaters and the economic aspect.

Efficient conversion of hemicellulose into 2, 3-butanediol by engineered psychrotrophic Raoultella terrigena: mechanism and efficiency

Low-temperature biorefineries inhibit the multiplication of undesired microorganisms, improve product purity and reduce economic costs. Herein, to improve the 2,3-butanediol (2,3-BD) bioconversion efficiency from hemicellulose, a psychrotrophic hemicellulose-degrading strain Raoultella terrigena HC6 with high β-xylosidase activity 1520 U/mL was isolated and genetically modified. Xylan (hemicellulose replacement) was depolymerized into xylooligosaccharides (XOS) and xylose by HC6, which were further converted into 2,3-BD. Transcriptomic analysis revealed that β-xylosidase gene (xynB) and xylose isomerase gene (xylA), which are beneficial for increasing the carbon flux from xylan to 2,3-BD, were significantly upregulated 56.9-fold and 234-fold, respectively. A recombinant strain was constructed by overexpressing xynB in HC6, which obtained 0.389 g/g yield of 2,3-BD from hemicellulose extracted from corn straw at 15 °C. This study proposed a promised strategy for the bioconversion of agricultural waste into 2,3-BD at low temperatures and provides a basis for future efforts in the achievement of carbon neutrality.

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.

An Integrative Approach to Study Bacterial Enzymatic Degradation of Toxic Dyes

Synthetic dyes pose a large threat to the environment and consequently to human health. Various dyes are used in textile, cosmetics, and pharmaceutical industries, and are released into the environment without any treatment, thus adversely affecting both the environment and neighboring human populations. Several existing physical and chemical methods for dye degradation are effective but have many drawbacks. Biological methods over the years have gained importance in the decolorization and degradation of dye and have also overcome the disadvantages of physiochemical methods. Furthermore, biological methods are eco-friendly and lead to complete decolorization. The mechanism of decolorization and degradation by several bacterial enzymes are discussed in detail. For the identification of ecologically sustainable strains and their application at the field level, we have focused on bioaugmentation aspects. Furthermore, in silico studies such as molecular docking of bacterial enzymes with dyes can give a new insight into biological studies and provide an easy way to understand the interaction at the molecular level. This review mainly focuses on an integrative approach and its importance for the effective treatment and decolorization of dyes.

Enzyme-assisted bioremediation approach for synthetic dyes and polycyclic aromatic hydrocarbons degradation

Environmental protection from emerging pollutants has become a significant challenge for mankind as an increasing number of contaminants, including synthetic dyes and polycyclic aromatic hydrocarbons (PAHs), represent a serious risk to ecological and environmental balance. Most synthetic dyes have complex aromatic structures and are resistant to degrade by classical approaches, such as physical and chemical processes, including adsorption, chemical coagulation, flocculation, ion exchange, membrane separation, froth flotation, and reverse osmosis. Enzymes-assisted catalytic transformation of pollutants has become a potential alternative to classical methods because of their ability to react with complex compounds, a quick degradation rate, and producing less harmful by-products. Plant peroxidases, and microbial laccase and lignin-degrading peroxidases (manganese and lignin peroxidase) have gained significant attention for treating aromatic waste due to their capability of oxidizing and detoxifying a wide range of recalcitrant xenobiotics, including PAHs and synthetic dyes. Peroxidases being efficient biocatalysts detoxify an array of toxic compounds by simple free-radical mechanism resulting in the formation of oxidized and depolymerized products of significantly reduced toxicity. Moreover, it is an ecofriendly and economically favorable approach towards the biodegradation of recalcitrant and toxic industrial waste. Among microbial and plant peroxidases, bacterial enzymes have broad substrate specificity and can transform a wide range of recalcitrant substrates. Ligninolytic enzymes oxidize the aromatic ring into quinones and acids by producing free hydroxyl radicals instead of dihydrodiols and mineralize aromatic hydrocarbon in combination with cytochrome P450, monooxygenases, and epoxide hydrolases. In the review, an attempt has been made to provide detailed knowledge about the availability of inexpensive peroxidases sources, their mechanism of action, and degradation potential. The present review summarizes the exploitation of peroxidases from plants, bacteria, and fungus (manganese peroxidase, lignin peroxidase, and laccases) for detoxification and degradation of textile dyes as well as PAHs. Conclusively, peroxidases have great potential to react with almost all classes of synthetic dyes and most PAHs due to broad substrate specificity and transformed them into less harmful metabolites.

Identification and Validation of Four Novel Promoters for Gene Engineering with Broad Suitability across Species

The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (P_k.rtufB, P_k.r1, P_k.r2, and P_k.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with P_k.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by P_k.r1 and P_k.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.

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.

Lignin peroxidase in focus for catalytic elimination of contaminants - A critical review on recent progress and perspectives

Lignin peroxidase (LiP) seems to be a catalyst for cleaving high-redox potential non-phenolic compounds with an oxidative cleavage of CC and COC bonds. LiP has been picked to seek a practical and cost-effective alternative to the sustainable mitigation of diverse environmental contaminants. LiP has been an outstanding tool for catalytic cleaning and efficient mitigation of environmental pollutants, including lignin, lignin derivatives, dyes, endocrine-disrupting compounds (EDCs), and persistent organic pollutants (POPs) for the past couple of decades. The extended deployment of LiP has proved to be a promising method for catalyzing these environmentally related hazardous pollutants of supreme interest. The advantageous potential and capabilities to act at different pH and thermostability offer its working tendencies in extended environmental engineering applications. Such advantages led to the emerging demand for LiP and increasing requirements in industrial and biotechnological sectors. The multitude of the ability attributed to LiP is triggered by its stability in xenobiotic and non-phenolic compound degradation. However, over the decades, the catalytic activity of LiP has been continuing in focus enormously towards catalytic functionalities over the available physiochemical, conventional, catalyst mediated technology for catalyzing such molecules. To cover this literature gap, this became much more evident to consider the catalytic attributes of LiP. In this review, the existing capabilities of LiP and other competencies have been described with recent updates. Furthermore, numerous recently emerged applications, such as textile effluent treatment, dye decolorization, catalytic elimination of pharmaceutical and EDCs compounds, have been discussed with suitable examples.

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.

Research on the coagulant aid effects of modified diatomite on coal microbial flocculation

Diatomite was modified by chitosan to prepare modified diatomite, and the modified diatomite in an optimized ratio was utilized in coal bio-flocculation. The interaction behavior and flocculation mechanism of modified diatomite on coal slurry water were investigated by single factor experiments, infrared spectroscopy, Brunauer-Emmett-Teller (BET) measurements, and zeta potential measurements. The single factor experiments showed that when the amount of microbial flocculant added was 1.5 ml, the temperature of coal slurry water was 39 °C, the pH was 5, and the amount of modified diatomite was 0.2 g, after 30 min of sedimentation, the flocculation transmittance of the coal slurry water reached 84.3%. The infrared spectra showed that the -NH₂ and -OH of the chitosan molecule had a polar interaction with the Si-OH bond in diatomite. The BET measurements showed that the specific surface area of diatomite was not a decisive factor affecting the flocculation effect. Zeta potential measurements indicated that the amino protonation of chitosan increased the isoelectric point (IEP) of modified diatomite. These results showed that modified diatomite has a good effect on coal bio-flocculation.

Exoproduction and Molecular Characterization of Peroxidase from Ensifer adhaerens

The increased industrial application potentials of peroxidase have led to high market demand, which has outweighed the commercially available peroxidases. Hence, the need for alternative and efficient peroxidase-producers is imperative. This study reported the process parameters for enhanced exoperoxidase production by Ensifer adhaerens NWODO-2 (accession number: KX640918) for the first time, and characterized the enzyme using molecular methods. Peroxidase production by the bacteria was optimal at 48 h, with specific productivity of 12.76 U mg−1 at pH 7, 30 °C and 100 rpm in an alkali lignin fermentation medium supplemented with guaiacol as the most effective inducer and ammonium sulphate as the best inorganic nitrogen source. Upon assessment of some agricultural residues as sources of carbon for the enzyme production, sawdust gave the highest peroxidase productivity (37.50 U mg−1) under solid-state fermentation. A search of the polymerase chain reaction (PCR)-amplified peroxidase gene in UniProtKB using blastx showed 70.5% similarity to an uncharacterized protein in Ensifer adhaerens but phylogenetic analysis suggests that the gene may encode a catalase-peroxidase with an estimated molecular weight of approximately 31 kDa and isoelectric point of about 11. The nucleotide sequence of the detected gene was deposited in the GenBank under the accession number MF374336. In conclusion, the ability of the strain to utilize lignocellulosic materials for peroxidase production augurs well for biotechnological application as this would greatly reduce cost, which is a major challenge in industrial enzyme production.

Dye-decolorizing peroxidases in Irpex lacteus combining the catalytic properties of heme peroxidases and laccase play important roles in ligninolytic system

BACKGROUND

The white rot fungus Irpex lacteus exhibits a great potential in biopretreatment of lignocellulose as well as in biodegradation of xenobiotic compounds by extracellular ligninolytic enzymes. Among these enzymes, the possible involvement of dye-decolorizing peroxidase (DyP) in lignin degradation is not clear yet.

RESULTS

Based on the extracellular enzyme activities and secretome analysis, I. lacteus CD2 produced DyPs as the main ligninolytic enzymes when grown in Kirk's medium supplemented with lignin. Further transcriptome analysis revealed that induced transcription of genes encoding DyPs was accompanied by the increased expression of transcripts for H₂O₂-generating enzymes such as alcohol oxidase, pyranose 2-oxidase, and glyoxal oxidases. Meanwhile, accumulation of transcripts for glycoside hydrolase and protease was observed, in agreement with abundant proteins. Moreover, the biochemical analysis of IlDyP2 and IlDyP1 confirmed that DyPs were able to catalyze the oxidation of typical peroxidases substrates ABTS, phenolic lignin compounds DMP, and guaiacol as well as non-phenolic lignin compound, veratryl alcohol. More importantly, IlDyP1 enhanced catalytic activity for veratryl alcohol oxidation in the presence of mediator 1-hydroxybenzotriazole, which was similar to the laccase/1-hydroxybenzotriazole system.

CONCLUSIONS

The results proved for the first time that DyPs depolymerized lignin individually, combining catalytic features of different peroxidases on the functional level. Therefore, DyPs may be considered an important part of ligninolytic system in wood-decaying fungi.