Variants of PpuLcc, a multi-dye decolorizing laccase from Pleurotus pulmonarius expressed in Pichia pastoris

Production and characterization of homologous protoporphyrinogen IX oxidase (PPO) proteins: Evidence that small N-terminal amino acid changes do not impact protein function

Transgenic soybean, cotton, and maize tolerant to protoporphyrinogen IX oxidase (PPO)-inhibiting herbicides have been developed by introduction of a bacterial-derived PPO targeted into the chloroplast. PPO is a membrane-associated protein with an intrinsic tendency for aggregation, making expression, purification, and formulation at high concentrations difficult. In this study, transgenic PPO expressed in three crops was demonstrated to exhibit up to a 13 amino acid sequence difference in the N-terminus due to differential processing of the chloroplast transit peptide (CTP). Five PPO protein variants were produced in and purified from E. coli, each displaying equivalent immunoreactivity and functional activity, with values ranging from 193 to 266 nmol min-1 mg-1. Inclusion of an N-terminal 6xHis-tag or differential processing of the CTP peptide does not impact PPO functional activity. Additionally, structural modeling by Alphafold, ESMfold, and Openfold indicates that these short N-terminal extensions are disordered and predicted to not interfere with the mature PPO structure. These results support the view that safety studies on PPO from various crops can be performed from a single representative variant. Herein, we report a novel and robust method for large-scale production of PPO, enabling rapid production of more than 200 g of highly active PPO protein at 99% purity and low endotoxin contamination. We also present a formulation that allows for concentration of active PPO to > 75 mg/mL in a buffer suitable for mammalian toxicity studies.

Textile azo dyes discolouration using spent mushroom substrate: enzymatic degradation and adsorption mechanisms

This study evaluated the adsorption and enzymatic degradation of azo dyes when using SMS. The laccase present in the SMS was characterised, and the maximum activity was obtained at pH 2, a temperature of 45°C, a Michaelis-Menten constant (Km) of 0.264 mM, and a maximum reaction rate (Vmax) of 117.95 µmol L-1 min-1. The presence of NaCl at 5 mM inhibited enzyme activity while no inhibition was observed by Na2SO4, typically found in textile wastewater. The maximum dye adsorption (57.22%) was achieved at pH 8.0, 25°C, and 100 g L-1 of SMS while the maximum enzymatic degradation (14.18%) was obtained under the same conditions, except at pH 4.0. The enzymes laccase, lignin peroxidase, and manganese peroxidase trapped in the SMS resulted in higher dye discolouration when compared to that extracted with aqueous solution, meaning that SMS has strong adsorption capacity and is a natural immobilisation matrix, which improves the enzymatic degradation of the dyes. Thus, SMS can be used in the treatment of textile effluents for dye removal by simultaneous mechanisms of adsorption and enzymatic degradation, with reduction of environmental impacts for SMS disposal and reduction of the costs associated with commercial enzymes and adsorbents.

Artificial microbial consortium producing oxidases enhanced the biotransformation efficiencies of multi-antibiotics

Antibiotic mixtures in the environment result in the development of bacterial strains with resistance against multiple antibiotics. Oxidases are versatile that can bio-remove antibiotics. Various laccases (LACs), manganese peroxidases (MNPs), and versatile peroxidase (VP) were reconstructed in Pichia pastoris. For the single antibiotics, over 95.0% sulfamethoxazole within 48 h, tetracycline, oxytetracycline, and norfloxacin within 96 h were bio-removed by recombinant VP with α-signal peptide, respectively. In a mixture of the four antibiotics, 80.2% tetracycline and 95.6% oxytetracycline were bio-removed by recombinant MNP2 with native signal peptide (NSP) within 8 h, whereas < 80.0% sulfamethoxazole was bio-removed within 72 h, indicating that signal peptides significantly impacted removal efficiencies of antibiotic mixtures. Regarding mediators for LACs, 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) resulted in better removal efficiencies of multi-antibiotic mixtures than 1-hydroxybenzotriazole or syringaldehyde. Furthermore, artificial microbial consortia (AMC) producing LAC2 and MNP2 with NSP significantly improved bio-removal efficiency of sulfamethoxazole (95.5%) in four-antibiotic mixtures within 48 h. Tetracycline and oxytetracycline were completely bio-removed by AMC within 48 and 72 h, respectively, indicating that AMC accelerated sulfamethoxazole, tetracycline, and oxytetracycline bio-removals. Additionally, transformation pathways of each antibiotic by recombinant oxidases were proposed. Taken together, this work provides a new strategy to simultaneously remove antibiotic mixtures by AMC.

Safety assessment of Mpp75Aa1.1, a new ETX_MTX2 protein from Brevibacillus laterosporus that controls western corn rootworm

The recently discovered insecticidal protein Mpp75Aa1.1 from Brevibacillus laterosporus is a member of the ETX_MTX family of beta-pore forming proteins (β-PFPs) expressed in genetically modified (GM) maize to control western corn rootworm (WCR; Diabrotica virgifera virgifera LeConte). In this manuscript, bioinformatic analysis establishes that although Mpp75Aa1.1 shares varying degrees of similarity to members of the ETX_MTX2 protein family, it is unlikely to have any allergenic, toxic, or otherwise adverse biological effects. The safety of Mpp75Aa1.1 is further supported by a weight of evidence approach including evaluation of the history of safe use (HOSU) of ETX_MTX2 proteins and Breviballus laterosporus. Comparisons between purified Mpp75Aa1.1 protein and a poly-histidine-tagged (His-tagged) variant of the Mpp75Aa1.1 protein demonstrate that both forms of the protein are heat labile at temperatures at or above 55°C, degraded by gastrointestinal proteases within 0.5 min, and have no adverse effects in acute mouse oral toxicity studies at a dose level of 1920 or 2120 mg/kg body weight. These results support the use of His-tagged proteins as suitable surrogates for assessing the safety of their non-tagged parent proteins. Taken together, we report that Mpp75Aa1.1 is the first ETX-MTX2 insecticidal protein from B. laterosporus and displays a similar safety profile as typical Cry proteins from Bacillus thuringiensis.

Improved Foods Using Enzymes from Basidiomycetes

Within the kingdom of fungi, the division Basidiomycota represents more than 30,000 species, some with huge genomes indicating great metabolic potential. The fruiting bodies of many basidiomycetes are appreciated as food (“mushrooms”). Solid-state and submerged cultivation processes have been established for many species. Specifically, xylophilic fungi secrete numerous enzymes but also form smaller metabolites along unique pathways; both groups of compounds may be of interest to the food processing industry. To stimulate further research and not aim at comprehensiveness in the broad field, this review describes some recent progress in fermentation processes and the knowledge of fungal genetics. Processes with potential for food applications based on lipases, esterases, glycosidases, peptidases and oxidoreductases are presented. The formation and degradation of colourants, the degradation of harmful food components, the formation of food ingredients and particularly of volatile and non-volatile flavours serve as examples. In summary, edible basidiomycetes are foods—and catalysts—for food applications and rich donors of genes to construct heterologous cell factories for fermentation processes. Options arise to support the worldwide trend toward greener, more eco-friendly and sustainable processes.

Alternative Routes for the Production of Natural 4-Vinylguaiacol from Sugar Beet Fiber Using Basidiomycetous Enzymes

Traditional smoking generates not only the impact flavor compound 4-vinylguaiacol, but concurrently many unwanted and potent toxic compounds such as polycyclic aromatic hydrocarbons. Enzyme technology provides a solution without any side-product formation. A feruloyl esterase from Rhizoctonia solani (RspCAE) liberated ferulic acid from low-priced sugar beet fiber. Decarboxylation of ferulic acid to 4-vinylguaiacol was achieved by a second enzyme from Schizophyllum commune (ScoFAD). Both enzymes were covalently immobilized on agarose to enable reusability in a fixed-bed approach. The two enzyme cascades showed high conversion rates with yields of 0.8 and 0.95, respectively, and retained activity for nearly 80 h of continuous operation. The overall productivity of the model process with bed volumes of 300 µL and a substrate flow rate of 0.25 mL min−1 was 3.98 mg 4-vinylguaiacol per hour. A cold online solid phase extraction using XAD4 was integrated into the bioprocess and provided high recovery rates during multiple elution steps. Attempting to facilitate the bioprocess, a fused gene coding for the two enzymes and a set of different linker lengths and properties was constructed and introduced into Komagataella phaffii. Longer and rigid linkers resulted in higher activity of the fusion protein with a maximum of 67 U L−1.

Genome-based engineering of ligninolytic enzymes in fungi

Background

Many fungi grow as saprobic organisms and obtain nutrients from a wide range of dead organic materials. Among saprobes, fungal species that grow on wood or in polluted environments have evolved prolific mechanisms for the production of degrading compounds, such as ligninolytic enzymes. These enzymes include arrays of intense redox-potential oxidoreductase, such as laccase, catalase, and peroxidases. The ability to produce ligninolytic enzymes makes a variety of fungal species suitable for application in many industries, including the production of biofuels and antibiotics, bioremediation, and biomedical application as biosensors. However, fungal ligninolytic enzymes are produced naturally in small quantities that may not meet the industrial or market demands. Over the last decade, combined synthetic biology and computational designs have yielded significant results in enhancing the synthesis of natural compounds in fungi.

Main body of the abstract

In this review, we gave insights into different protein engineering methods, including rational, semi-rational, and directed evolution approaches that have been employed to enhance the production of some important ligninolytic enzymes in fungi. We described the role of metabolic pathway engineering to optimize the synthesis of chemical compounds of interest in various fields. We highlighted synthetic biology novel techniques for biosynthetic gene cluster (BGC) activation in fungo and heterologous reconstruction of BGC in microbial cells. We also discussed in detail some recombinant ligninolytic enzymes that have been successfully enhanced and expressed in different heterologous hosts. Finally, we described recent advance in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR associated) protein systems as the most promising biotechnology for large-scale production of ligninolytic enzymes.

Short conclusion

Aggregation, expression, and regulation of ligninolytic enzymes in fungi require very complex procedures with many interfering factors. Synthetic and computational biology strategies, as explained in this review, are powerful tools that can be combined to solve these puzzles. These integrated strategies can lead to the production of enzymes with special abilities, such as wide substrate specifications, thermo-stability, tolerance to long time storage, and stability in different substrate conditions, such as pH and nutrients.

Generation of 4-vinylguaiacol through a novel high-affinity ferulic acid decarboxylase to obtain smoke flavours without carcinogenic contaminants

Traditional smoke flavours bear the risk of containing a multitude of contaminating carcinogenic side-products. Enzymatic decarboxylation of ferulic acid released from agro-industrial side-streams by ferulic acid esterases (FAE) enables the sustainable generation of pure, food grade 4-vinylguaiacol (4-VG), the impact compound of smoke flavour. The first basidiomycetous ferulic acid decarboxylase (FAD) was isolated from Schizophyllum commune (ScoFAD) and heterologously produced by Komagataella phaffii. It showed a molecular mass of 21 kDa, catalytic optima at pH 5.5 and 35°C, and a sequence identity of 63.6% to its next relative, a FAD from the ascomycete Cordyceps farinosa. The ScoFAD exhibited a high affinity to its only known substrate ferulic acid (FA) of 0.16 mmol L^-1 and a turnover number of 750 s^-1. The resulting catalytic efficiency k_cat K_M^-1 of 4,779 L s^-1 mmol^-1 exceeded the next best known enzyme by more than a factor of 50. Immobilised on AminoLink Plus Agarose, ScoFAD maintained its activity for several days. The combination with FAEs and agro-industrial side-streams paves the way for a new generation of sustainable, clean, and safe smoke flavours.

Expression of Pleurotus ostreatus Laccase Gene in Pichia pastoris and Its Degradation of Corn Stover Lignin

Pleurotus ostreatus is a species of white-rot fungi that effectively degrades lignin. In this study, we aimed to efficiently express the lac-2 gene of Pleurotus ostreatus in the Pichia pastoris X33 yeast strain. The enzymatic properties of recombinant yeast were determined, and its ability to degrade corn stover lignin was determined. The results showed the optimum pH values of recombinant laccase for 2,2’-Azinobis-3-ethylbenzothiazoline-6-sulfonic acid, 2,6-dimethoxyphenol, and 2-methoxyphenol were 3.0, 3.0, and 3.5, respectively. The optimum reaction temperature was 50 °C, and it had good thermal stability and acid and alkali resistance. The degradation rate of lignin in corn stover by recombinant laccase was 18.36%, and the native Pleurotus ostreatus degradation rate was 14.05%, the difference between them is significant (p < 0.05). This experiment lays a foundation for the study of the degradation mechanism of lignin by laccase.

A DyP-Type Peroxidase of Pleurotus sapidus with Alkene Cleaving Activity

Alkene cleavage is a possibility to generate aldehydes with olfactory properties for the fragrance and flavor industry. A dye-decolorizing peroxidase (DyP) of the basidiomycete Pleurotus sapidus (PsaPOX) cleaved the aryl alkene trans-anethole. The PsaPOX was semi-purified from the mycelium via FPLC, and the corresponding gene was identified. The amino acid sequence as well as the predicted tertiary structure showed typical characteristics of DyPs as well as a non-canonical Mn²⁺-oxidation site on its surface. The gene was expressed in Komagataella pfaffii GS115 yielding activities up to 142 U/L using 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) as substrate. PsaPOX exhibited optima at pH 3.5 and 40 °C and showed highest peroxidase activity in the presence of 100 µM H₂O₂ and 25 mM Mn²⁺. PsaPOX lacked the typical activity of DyPs towards anthraquinone dyes, but oxidized Mn²⁺ to Mn³⁺. In addition, bleaching of β-carotene and annatto was observed. Biotransformation experiments verified the alkene cleavage activity towards the aryl alkenes (E)-methyl isoeugenol, α-methylstyrene, and trans-anethole, which was increased almost twofold in the presence of Mn²⁺. The resultant aldehydes are olfactants used in the fragrance and flavor industry. PsaPOX is the first described DyP with alkene cleavage activity towards aryl alkenes and showed potential as biocatalyst for flavor production.

Cross-Linking of Wheat Bran Arabinoxylan by Fungal Laccases Yields Firm Gels

The native extractable arabinoxylans (AX) from wheat bran were cross-linked by the commercial laccase C (LccC) and self-produced laccases from Funalia trogii (LccFtr) and Pleurotus pulmonarius (LccPpu) (0.04 U/µg FA, each). Dynamic oscillation measurements of the 6% AX gels demonstrated a storage modulus of 9.4 kPa for LccC, 9.8 kPa for LccFtr, and 10.0 kPa for LccPpu. A loss factor ≤ 0.6 was recorded in the range from 20 to 80 Hz for all three laccases, and remained constant for four weeks of storage, when LccFtr and LccPpu were used. Arabinoxylan gel characteristics, including high water holding capacity, swelling ratio in saliva, and heat resistance indicated a covalently cross-linked network. Neither the mediator compounds caffeic acid and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid (ABTS), nor citrus pectin, enhanced the elastic properties of the gels. Using laccases as an oxidant provided gels with a solid and stable texture, comparable in firmness to traditional gelatin gels. Thus, AX gels can be presented in the vegan, halal, and kosher food markets. They may also find use in pharmaceutical and other industrial applications.

Long-Term Monokaryotic Cultures of Pleurotus ostreatus var. florida Produce High and Stable Laccase Activity Capable to Degrade ß-Carotene

An extracellular laccase (Lacc10) was discovered in submerged cultures of Pleurotus ostreatus var. florida bleaching ß-carotene effectively without the addition of a mediator (650 mU/L, pH 4). Heterologous expression in P. pastoris confirmed the activity and structural analyses revealed a carotenoid-binding domain, which formed the substrate-binding pocket and is reported here for the first time. In order to increase activity, 106 basidiospore-derived monokaryons and crosses of compatible progenies were generated. These showed high intraspecific variability in growth rate and enzyme formation. Seventy-two homokaryons exhibited a higher activity-to-growth-rate-relation than the parental dikaryon, and one isolate produced a very high activity (1800 mU/L), while most of the dikaryotic hybrids showed lower activity. The analysis of the laccase gene of the monokaryons revealed two sequences differing in three amino acids, but the primary sequences gave no clue for the diversity of activity. The enzyme production in submerged cultures of monokaryons was stable over seven sub-cultivation cycles.