Degradation potential of protocatechuate 3,4-dioxygenase from crude extract of Stenotrophomonas maltophilia strain KB2 immobilized in calcium alginate hydrogels and on glyoxyl agarose

Diclofenac, ibuprofen, and paracetamol biodegradation: overconsumed non-steroidal anti-inflammatories drugs at COVID-19 pandemic

The consumption of non-steroidal anti-inflammatory drugs (NSAIDs) have increased significantly in the last years (2020-2022), especially for patients in COVID-19 treatment. NSAIDs such as diclofenac, ibuprofen, and paracetamol are often available without restrictions, being employed without medical supervision for basic symptoms of inflammatory processes. Furthermore, these compounds are increasingly present in nature constituting complex mixtures discarded at domestic and hospital sewage/wastewater. Therefore, this review emphasizes the biodegradation of diclofenac, ibuprofen, and paracetamol by pure cultures or consortia of fungi and bacteria at in vitro, in situ, and ex situ processes. Considering the influence of different factors (inoculum dose, pH, temperature, co-factors, reaction time, and microbial isolation medium) relevant for the identification of highly efficient alternatives for pharmaceuticals decontamination, since biologically active micropollutants became a worldwide issue that should be carefully addressed. In addition, we present a quantitative bibliometric survey, which reinforces that the consumption of these drugs and consequently their impact on the environment goes beyond the epidemiological control of COVID-19.

Mechanism of Microbial Detoxification of Heavy Metals: A Review

Heavy metal contamination from anthropogenic activities has an adverse effect on the environment due to its cytotoxicity, carcinogenicity and mutagenicity. Environment harbours microorganisms, some of which have been found to modify physico-chemical conditions of their surrounding environment through certain processes such as detoxification, metal homeostasis, precipitation, redox transformations etc. Investigations in the past have shown that short term contact with metals of certain bacteria causes the selection of resistant bacteria within weeks, while a prolonged exposure showed selected strains able to thrive better. Hence biotic methods could assist removal of heavy metals based on biosorption or bioaccumulation by microorganisms, which are cost-effective and environmental friendly in the long run. Microbial remediation is influenced by biotic and environmental factors as also the contamination site characteristics. The aim of this paper is to highlight and review some of the mechanisms of microbial remediation through techniques such as biostimulation, bioaugmentation etc.

Characterization of Gentisate 1,2-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and Its Stabilization by Immobilization on Nickel-Functionalized Magnetic Nanoparticles

The aim of this study was the biochemical and kinetic characterization of the gentisate 1,2-dioxygenase (GDO) from Pseudarthrobacter phenanthrenivorans Sphe3 and the development of a nanobiocatalyst by its immobilization on Ni2+-functionalized Fe3O4-polydopamine magnetic nanoparticles (Ni2+-PDA-MNPs). This is the first GDO to be immobilized. The gene encoding the GDO was cloned with an N-terminal His-tag and overexpressed in E. coli. The nanoparticles showed a high purification efficiency of GDO from crude cell lysates with a maximum activity recovery of 97%. The immobilized enzyme was characterized by Fourier transform infrared spectroscopy (FTIR). The reaction product was identified by 1H NMR. Both free and immobilized GDO exhibited Michaelis–Menten kinetics with Km values of 25.9 ± 4.4 and 82.5 ± 14.2 μM and Vmax values of 1.2 ± 0.1 and 0.03 ± 0.002 mM*s−1, respectively. The thermal stability of the immobilized GDO was enhanced at 30 °C, 40 °C, and 50 °C, compared to the free GDO. Stored at −20 °C, immobilized GDO retained more than 60% of its initial activity after 30 d, while the free enzyme completely lost its activity after 10 d. Furthermore, the immobilized nanoparticle–enzyme conjugate retained more than 50% enzyme activity up to the fifth cycle.

Degradation of 2,4,6-Trinitrotoluene (TNT): Involvement of Protocatechuate 3,4-Dioxygenase (P34O) in Buttiauxella sp. S19-1

Extensive use and disposal of 2,4,6-trinitrotoluene (TNT), a primary constituent of explosives, pollutes the environment and causes severe damage to human health. Complete mineralization of TNT via bacterial degradation has recently gained research interest as an effective method for the restoration of contaminated sites. Here, screening for TNT degradation by six selected bacteria revealed that Buttiauxella sp. S19-1, possesses the strongest degrading ability. Moreover, BuP34O (a gene encoding for protocatechuate 3,4-dioxygenase—P34O, a key enzyme in the β-ketoadipate pathway) was upregulated during TNT degradation. A knockout of BuP34O in S19-1 to generate S-M1 mutant strain caused a marked reduction in TNT degradation efficiency compared to S19-1. Additionally, the EM1 mutant strain (Escherichia coli DH5α transfected with BuP34O) showed higher degradation efficiency than DH5α. Gas chromatography mass spectrometry (GC-MS) analysis of TNT degradation by S19-1 revealed 4-amino-2,6-dinitrotolune (ADNT) as the intermediate metabolite of TNT. Furthermore, the recombinant protein P34O (rP34O) expressed the activity of 2.46 µmol/min·mg. Our findings present the first report on the involvement of P34O in bacterial degradation of TNT and its metabolites, suggesting that P34O could catalyze downstream reactions in the TNT degradation pathway. In addition, the TNT-degrading ability of S19-1, a Gram-negative marine-derived bacterium, presents enormous potential for restoration of TNT-contaminated seas.

Construction of novel curdlan-based and Ca2+-chelated magnetic microspheres (CCMM) for efficient protein purification and oriented immobilization

In this study, curdlan-based and calcium ion (Ca²⁺)-chelated magnetic microspheres (CCMM) were prepared for protein purification and oriented immobilization. Additional purification steps before immobilization were not required. CCMM samples were produced by reverse embedding of Fe₃O₄ nanoparticles with curdlan and chelated with Ca²⁺ in the presence of iminodiacetic acid. The β-xylanase XynII from Trichoderma reesei QM6a was used to investigate the efficiency of CCMM preparation. The resulting CCMM-XynII was found to be very stable, showing 82 % and 60 % of initial activities after storage for 35 days and after being assayed ten times, respectively. In addition, the CCMM-XynII showed higher stabilities in the presence of organic solvents and multiple chemicals than the free XynII, suggesting that the CCMM-XynII could be efficient for applications requiring the presence of organic solvents. In addition, CCMM may be more suitable than commercially available Ni-NTA for purification of proteins intolerant of Ni²⁺.

Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach

The release of synthetic chemical pollutants in the environment is posing serious health risks. Enzymes, including oxygenases, play a crucial role in xenobiotic degradation. In the present study, we employed a functional metagenomics approach to overcome the limitation of cultivability of microbes under standard laboratory conditions in order to isolate novel dioxygenases capable of degrading recalcitrant pollutants. Fosmid clones possessing dioxygenase activity were further sequenced, and their genes were identified using bioinformatics tools. Two positive fosmid clones, SD3 and RW1, suggested the presence of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC-SD3) and catechol 2,3-dioxygenase (C23O-RW1), respectively. Recombinant versions of these enzymes were purified to examine their pollutant-degrading abilities. The crystal structure of BphC-SD3 was determined at 2.6-Å resolution, revealing a two-domain architecture, i.e., N-terminal and C-terminal domains, with the sequential arrangement of βαβββ in each domain, characteristic of Fe-dependent class II type I extradiol dioxygenases. The structure also reveals the presence of conserved amino acids lining the catalytic pocket and Fe³⁺ metal ion in the large funnel-shaped active site in the C-terminal domain. Further studies suggest that Fe³⁺ bound in the BphC-SD3 active site probably imparts aerobic stability. We further demonstrate the potential application of BphC-SD3 in biosensing of catecholic compounds. The halotolerant and oxygen-resistant properties of these enzymes reported in this study make them potential candidates for bioremediation and biosensing applications.IMPORTANCE The disposal and degradation of xenobiotic compounds have been serious issues due to their recalcitrant properties. Microbial oxygenases are the fundamental enzymes involved in biodegradation that oxidize the substrate by transferring oxygen from molecular oxygen. Among oxygenases, catechol dioxygenases are more versatile in biodegradation and are well studied among the bacterial world. The use of catechol dioxygenases in the field is currently not practical due to their aerobically unstable nature. The significance of our research lies in the discovery of aerobically stable and halotolerant catechol dioxygenases that are efficient in degrading the targeted environmental pollutants and, hence, could be used as cost-effective alternatives for the treatment of hypersaline industrial effluents. Moreover, the structural determination of novel catechol dioxygenases would greatly enhance our knowledge of the function of these enzymes and facilitate directed evolution to further enhance or engineer desired properties.

Mycoremediation of PCBs by Pleurotus ostreatus: Possibilities and Prospects

With the rising awareness on environmental issues and the increasing risks through industrial development, clean up remediation measures have become the need of the hour. Bioremediation has become increasingly popular owing to its environmentally friendly approaches and cost effectiveness. Polychlorinated biphenyls (PCBs) are an alarming threat to human welfare as well as the environment. They top the list of hazardous xenobiotics. The multiple effects these compounds render to the niche is not unassessed. Bioremediation does appear promising, with myco remediation having a clear edge over bacterial remediation. In the following review, the inputs of white-rot fungi in PCB remediation are examined and the lacunae in the practical application of this versatile technology highlighted. The unique abilities of Pleurotus ostreatus and its deliverables with respect to removal of PCBs are presented. The need for improvising P. ostreatus-mediated remediation is emphasized.

Metabolism of diethyl phthalate (DEP) and identification of degradation intermediates by Pseudomonas sp. DNE-S1

A Pseudomonas sp. DNE-S1 (GenBank accession number MF803832), able to degrade DEP in a wide range of acid-base conditions, was isolated from landfill soil. The growth kinetics of DNE-S1 on DEP followed the inhibition model. Fe³⁺ could promote the degradation ability of DNE-S1 to DEP probably by over-expression of the gene phthalate dihydrodiol dehydrogenase (ophB) and phthalate dioxygenase ferredoxin reductase (ophA4). The degradation rate of DEP (500 mg L^-1 at 12 h) increased by 14.5% in the presence of Fe³⁺. Cu²⁺, Zn²⁺, and Mn²⁺ showed an inhibiting effect on the degradation performance of the strain and could alter the cellular morphology, surface area and volume of DNE-S1. Three degradation intermediates, namely ethyl methyl phthalate (EMP), dimethyl phthalate (DMP), and phthalic acid (PA), were detected in the biodegradation of DEP, and the biochemical pathway of DEP degradation was proposed. This study provides new information on the biochemical pathways and the responsible genes involved in DEP degradation.

Paracetamol - toxicity and microbial utilization. Pseudomonas moorei KB4 as a case study for exploring degradation pathway

Paracetamol, a widely used analgesic and antipyretic drug, is currently one of the most emerging pollutants worldwide. Besides its wide prevalence in the literature only several bacterial strains able to degrade this compound have been described. In this study, we isolated six new bacterial strains able to remove paracetamol. The isolated strains were identified as the members of Pseudomonas, Bacillus, Acinetobacter and Sphingomonas genera and characterized phenotypically and biochemically using standard methods. From the isolated strains, Pseudomonas moorei KB4 was able to utilize 50 mg L^-1 of paracetamol. As the main degradation products, p-aminophenol and hydroquinone were identified. Based on the measurements of specific activity of acyl amidohydrolase, deaminase and hydroquinone 1,2-dioxygenase and the results of liquid chromatography analyses, we proposed a mechanism of paracetamol degradation by KB4 strain under co-metabolic conditions with glucose. Additionally, toxicity bioassays and the influence of various environmental factors, including pH, temperature, heavy metals at no-observed-effective-concentrations, and the presence of aromatic compounds on the efficiency and mechanism of paracetamol degradation by KB4 strain were determined. This comprehensive study about paracetamol biodegradation will be helpful in designing a treatment systems of wastewaters contaminated with paracetamol.

Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil

Burkholderia gladioli Coa14 is a bacterium isolated from water collected from Coari Lake (Amazonas, Brazil) that shows a capacity for survival in a medium containing only oil as a carbon source. Here, we report its draft genome sequence, highlighting some genes involved with petroleum derivative degradation.

Improvement of the Stabilization and Activity of Protocatechuate 3,4-Dioxygenase Isolated from Rhizobium sp. LMB-1 and Immobilized on Fe3O4 Nanoparticles

Protocatechuate 3,4-dioxygenase (P34O), which is isolated from Rhizobium sp. LMB-1, catalyzes the ring cleavage step in the metabolism of aromatic compounds, and has great potential for environmental bioremediation. However, its structure is very sensitive to different environmental factors, which weaken its activity. Immobilization of the enzyme can improve its stability, allow reusability, and reduce operation costs. In this work, the relative molecular mass of the native P34O enzyme was determined to be 500 kDa by gel filtration chromatography on Sephadex G-200, and the enzyme was immobilized onto (3-aminopropyl) triethoxysilane-modified Fe₃O₄ nanoparticles (NPs) by the glutaraldehyde method. The optimum pH of immobilized and free P34O was unaffected, but the optimum temperature of immobilized P34O increased from 60 to 70 °C, and the thermal stability of immobilized P34O was better than that of the free enzyme and showed higher enzymatic activity at 60 and 70 °C. In addition, with the exception of Fe³⁺, most metal ions and organic chemicals could not improve the activity of free and immobilized P34O. The kinetic parameters of the immobilized P34O were higher than those of the free enzyme, and immobilized P34O on Fe₃O₄ NPs could be reused ten times without a remarkable decrease in enzymatic activity.

Highly Efficient and Stable Novel NanoBiohybrid Catalyst to Avert 3,4-Dihydroxybenzoic Acid Pollutant in Water

The present study reported for the first time covalent immobilization of protocatechuate 3,4-dioxygenase (3,4-POD) onto functionalized multi-walled carbon nanotubes (F-MWCNT) for degrading the toxic 3,4-dihydroxybenzoic acid (3,4-DHBA) pollutant in water. The F-MWCNTs had a maximum 3,4-POD loading of 1060 μg/mg. Immobilized 3,4 POD had 44% of relative structural changes to its free configurations. Nevertheless, >90% of relative activity and about 50% of catalytic efficiency were retained to the free enzyme. Immobilized 3,4-POD demonstrated higher alkaline stability and thermostability than the free 3,4-POD. The free and immobilized 3,4-POD lost 82% and 66% of relative activities, respectively after 180 min of incubations at 90 °C. Excellent shelf-life was observed for the immobilized 3,4-POD with residual activity of 56% compared with 41% and 39% of the free 3,4-POD at 4 °C and 25 °C over 30 days storage. Immobilized 3,4-POD showed >60% of catalytic activity retention even after ten-cycle uses, defraying the expenses of free 3,4-POD productions for long term uses. Finally, the immobilized 3,4-POD removed 71% of 3,4-DHBA from water in <4 h, paving its future application for water purification with reduced costs and time.

Isolation and identification of Bacillus megaterium YB3 from an effluent contaminated site efficiently degrades pyrene

Industrial effluents contaminated sites may serve as repositories of ecologically adapted efficient pyrene degrading bacteria. In the present study, six bacterial isolates from industrial effluents were purified using serial enrichment technique and their pyrene degrading potential on pyrene supplemented mineral salt medium was assessed. 16S rRNA sequence analysis showed that they belong to four bacterial genera, namely Acinetobacter, Bacillus, Microbacterium, and Ochrobactrum. Among these isolates, Bacillus megaterium YB3 showed considerably good growth and was further evaluated for its pyrene-degrading efficiency. B. megaterium YB3 could degrade 72.44% of 500 mg L(-1) pyrene within 7 days. GC-MS analysis of ethyl acetate extracted fractions detected two relatively less toxic metabolic intermediates of the pyrene degradation pathway. B. megaterium YB3 also tested positive for catechol 1, 2-dioxygenase and aromatic-ring-hydroxylating dioxygenase indole-indigo conversion assays. Considering the ability and efficiency of B. megaterium YB3 to degrade high pyrene content, the strain can be used as a tool to develop bioremediation technologies for the effective biodegradation of pyrene and possibly other PAHs in the environment.

Draft Genome of the Arthrobacter sp. Strain Edens01

We report the draft genome sequence of Arthrobacter sp. strain Edens01, isolated from a leaf surface of a Rosa hybrid plant as part of the Howard Hughes Medical Institute-funded Student Initiated Microbial Discovery (SIMD) project. The genome has a total size of 3,639,179 bp and contig N₅₀ of 454,897 bp.

Immobilization as a strategy for improving enzyme properties-application to oxidoreductases

The main objective of the immobilization of enzymes is to enhance the economics of biocatalytic processes. Immobilization allows one to re-use the enzyme for an extended period of time and enables easier separation of the catalyst from the product. Additionally, immobilization improves many properties of enzymes such as performance in organic solvents, pH tolerance, heat stability or the functional stability. Increasing the structural rigidity of the protein and stabilization of multimeric enzymes which prevents dissociation-related inactivation. In the last decade, several papers about immobilization methods have been published. In our work, we present a relation between the influence of immobilization on the improvement of the properties of selected oxidoreductases and their commercial value. We also present our view on the role that different immobilization methods play in the reduction of enzyme inhibition during biotechnological processes.