A novel laccase, Lac3, was purified from Ganoderma lucidum fermentation broth by salting out, gel filtration chromatography, and Native-PAGE protein recovery. The molecular mass of Lac3 was 58.4 kDa as estimated by SDS-PAGE and exhibited catalytic properties with 2,2'-Biazobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) as substrate. The specific enzyme activity of Lac3 was determined to be 313.69 U/mg. The laccase was stable at temperatures < 65 °C and at pH of 2.5-4.5. The pH, temperature optima, Km and Vmax of the enzyme for ABTS oxidation were 3.0, 55 °C, 0.077 mM, and 2.98 mM/min, respectively. The metal ions and anions showed inhibitory effects on Lac3 activity except Cu2+ (1 mM). GC-MS analysis showed that various aroma products were generated by Lac3 treatment of alkaline lignin. The Lac3 and lignin model compounds had negative binding energy and hydrogen bonding. The analysis of docking suggested that Asp207, Asn256, and His459 play a key role in substrate binding and catalysis.

The microbiota within the guts of insects plays beneficial roles for their hosts, such as facilitating digestion and extracting energy from their diet. The African palm weevil (APW) lives within and feeds on the high lignin-containing trunk of palm trees; therefore, their guts could harbour a large community of lignin-degrading microbes. In this study, we aimed to explore the bacterial community within the gut of the APW larvae, specifically with respect to the potential for lignin degradation in various gut segments as a first step to determining the viability of mining bacterial lignin-degrading enzymes for the bioconversion of lignocellulosic biomass to biofuels and biomaterials. Bacterial metagenomic DNA was extracted from the foregut, midgut, and hindgut of larvae of the APW, and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. The generated data were analysed and taxonomically classified to identify the different bacterial phylotypes within the gut community cumulatively and per gut segment. We then determined the presence, diversity, and abundance of bacteria associated with lignin degradation within each larval gut compartment as a basis for suggesting the gut segment(s) where lignin degradation occurs the most. All sequences were classified and belonged to the bacterial kingdom. Firmicutes (54.3%) and Proteobacteria (42.5%) were the most dominant phyla within the gut, followed distantly by Bacteroidota (1.7%) and Actinobacteriota (1.4%). Enterococcus, Levilactobacillus, Lactococcus, Shimwellia, Megasphaera, Klebsiella, Pectinatus, Salmonella, Lelliotia, and Enterobacter constituted the most abundant genera found across all gut segments. The foregut and midgut had many similar genera, whilst the hindgut appeared unique. Overall, 29.5% of total gut bacteria comprising 21 genera were lignin degraders found predominantly in the Firmicutes and Proteobacteria phyla (56.8 and 39.5%, respectively), then moderately in Actinobacteriota (2.5%) and Bacteroidota (1.1%). The most abundant ligninolytic genera were Levilactobacillus (46.4%), Klebsiella (22.9%), Enterobacter (10.7%), Lactiplantibacillus (5.9%), Citrobacter (2.2%), Corynebacterium (1.8%), Paucilactobacillus (1.8%), Serratia (1.5%), Bacteroides (1.1%), and Leucobacter (1.0%) found in different amounts in different gut compartments. The foregut had the most diverse and highest abundance of lignin-degrading phylotypes, and we present reasons that point to the foregut as the main location for the depolymerization of lignin in the APW larval gut.

This study showcased the antibiotic degradation abilities of laccase and catalase-peroxidase from Bacillus ligniniphilus L1, an extremophile, against 18 common antibiotics using computationally guided approach. Molecular docking and simulation identified six enzyme-antibiotic complexes for laccase and four for catalase-peroxidase, demonstrating significant binding affinity and stability. Enzyme activity assays corroborated computational results, indicating both enzymes could degrade all tested antibiotics with varying efficiencies. L1 laccase outperformed commercial laccase against five antibiotics, notably vancomycin, levofloxacin, tobramycin, linezolid, and rifamycin, with enhanced degradation potential upon ABTS addition. Catalase-peroxidase from L1 exhibited superior degradation efficiency over commercial peroxidase against vancomycin, linezolid, tobramycin, and clindamycin. Overall, this study underscores the computational approach's utility in understanding enzyme-mediated antibiotic degradation, offering insights into environmental contaminant remediation.

While microbial technologies, which are considered to be environmentally friendly, have great potential for the recovery of rare earth elements (REEs) from mining wastewater, their applications have been restricted due to a lack of efficient biosorbents. In this study, a strain of Pseudomonas psychrotolerans isolated from yttrium-enriched mine soil was used to recover yttrium (Y(III)) from rare-earth mining wastewater. At an initial Y(III) dose of 50 mg L-1, the amount of Y(III) adsorbed by P. psychrotolerans reached 99.9 % after 24 h. Various characterization techniques revealed that P. psychrotolerans adsorbed Y(III) mainly through complexation of oxygen-containing functional groups and electrostatic interactions. A high level of adsorption efficiency (>99.9 %) was maintained after five consecutive adsorption/desorption cycles, indicating that P. psychrotolerans was highly reusable. While the efficiency of adsorbing Y(III) by P. psychrotolerans decreased (34.4 %) in actual rare earth mining wastewater, selectivity toward other REEs (≤ 18.4 %) was still observed. Consequently, this study provides a promising green, environmentally friendly and sustainable microbial approach for the selective recovery of REEs from rare earth wastewater.

Faced with the escalating challenge of global plastic pollution, this study specifically addresses the research gap in the biodegradation of polystyrene (PS). A PS-degrading bacterial strain was isolated from the gut of Tenebrio molitor, and genomics, molecular docking, and proteomics were employed to thoroughly investigate the biodegradation mechanisms of Pseudomonas putida H-01 against PS. Using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (ATR-FTIR), and contact angle analysis, significant morphological and structural changes in the PS films under the influence of the H-01 strain were observed. The study revealed several potential degradation genes and ten enzymes that were specifically upregulated in the PS degradation environment. Additionally, a novel protein with laccase-like activity, LacQ1, was purified from this strain for the first time, and its crucial role in the PS degradation process was confirmed. Through molecular docking and molecular dynamics (MD) simulations, the interactions between the enzymes and PS were detailed, elucidating the binding and catalytic mechanisms of the degradative enzymes with the substrate. These findings have deepened our understanding of PS degradation.

A multicopper oxidase Lac-W from Weizmannia coagulans 36D1 was identified and characterized as a laccase (Lac-W) with a robust enzymatic activity, which was used in various mycotoxins degradation. We demonstrated that Lac-W could directly degrade six major mycotoxins in the absence of redox mediators in pH 9.0, 24h static incubation at room temperature, including aflatoxin B1 (AFB1, 88%), zearalenone (60%), deoxynivalenol (34%), T-2 toxin (19%), fumonisin B1 (18%), and ochratoxin A (12%). The optimal condition for Lac-W to degrade AFB1 was 30 °C, pH 9.0, enzyme-substrate ratio 3U/μg in 24h static condition. Furthermore, we characterized aflatoxin Q1 as a Lac-W-mediated degradation product of AFB1 using UHPLC-MS/MS. Interestingly, degradation products of AFB1 failed to generate cell death and apoptosis of intestinal porcine epithelial cells. Finally, our molecular docking simulation results revealed that the substrate-binding pocket of Lac-W was large enough to allow the entry of six mycotoxins with different structures, and their degradation rates were positively correlated to their interacting affinity with Lac-W. In summary, the unique properties of the Lac-W make it a great candidate for detoxifying multiple mycotoxins contaminated food and feed cost-effectively and eco-friendly. Our study provides new insights into development of versatile enzymes which could simultaneously degrade multiple mycotoxins.

While laccase oxidation is a novel and promising method for treating arsenite-containing wastewater, the high cost and unsustainability of commercially available enzymes indicate a need to investigate more cost-effective viable alternatives. Here, a microorganism sustained secrete laccase-straw oxidation system (MLOS) was established and subsequently evaluated for the removal of As(III). MLOS showed efficient biological As(III) oxidation, with an As(III) removal efficiency reaching 99.9% at an initial As(III) concentration of 1.0 mg·L^-1. IC-AFS and XPS analysis showed that As(III) was partially oxidized to As(V), and partially As(III) adsorbed on the surface of rice straw. FTIR analysis revealed that hydroxyl, amine and amide groups were all involved in the As(III) removal process. SEM-EDS demonstrated that the surface structure of rice straw was destroyed following Comamonas testosteroni FJ17 (C. testosteroni FJ17) treatment, and the metal ions binding sites of rice straw were increased resulting in elemental arsenic being detected on the material surface. Molecular docking revealed the interaction between key residues of laccase and As(III). Laccase activity was negatively correlated with Cu(II) concentration in the As(III) oxidation. EEM showed that humic-like acids were also involved in the interaction with As(III). Overall, a MLOS derived from biomass waste has a significant potential to be developed as a green and sustainable technology for the treatment of wastewater containing As(III).

Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry.

Machine learning (ML) applications have become ubiquitous in all fields of research including protein science and engineering. Apart from protein structure and mutation prediction, scientists are focusing on knowledge gaps with respect to the molecular mechanisms involved in protein binding and interactions with other components in the experimental setups or the human body. Researchers are working on several wet-lab techniques and generating data for a better understanding of concepts and mechanics involved. The information like biomolecular structure, binding affinities, structure fluctuations and movements are enormous which can be handled and analyzed by ML. Therefore, this review highlights the significance of ML in understanding the biomolecular interactions while assisting in various fields of research such as drug discovery, nanomedicine, nanotoxicity and material science. Hence, the way ahead would be to force hand-in hand of laboratory work and computational techniques.