Environmental role of aromatic carboxylesterases

Biodegradation of polyethylene terephthalate (PET) by Brucella intermedia IITR130 and its proposed metabolic pathway

Accumulation of polyethylene terephthalate (PET) polyester in ecosystems across the globe is a major pollution of concern. Microbial degradation recently generated novel insights into the biodegradation of varieties of plastics. In this study, a PET degrading bacterium Brucella intermedia IITR130 was isolated from a contaminated lake ecosystem at Pallikaranai, Chennai, India. Incubation of the bacterium along with the PET sheet (0.1 mm thickness) for 60 days resulted in 26.06% degradation, indicating a half-life of 137.8 days. Considerable changes in the surface morphology of the PET sheet were found as holes, pits, and cracks on incubation with strain IITR130, as revealed by scanning electron microscopy (SEM). After bacterial treatment of PET, the formation of new functional groups, most notably in the area of 3326 cm-1 suggestive of O-H stretch, leading to carboxylic acid and alcohol as products were suggested by fourier transform infrared (FTIR) analysis. Monomethyl terephthalate (MMT) and terephthalic acid (TPA) were identified by gas chromatography-mass spectrometry (GC-MS) analysis as PET degradation metabolites. Tributyrin clearance assay confirmed the presence of a lipase/esterase enzyme in the strain IITR130. In this study, a degradation pathway for PET by an isolated and identified bacterium Brucella intermedia IITR130 was characterized in detail.

Substrate Characterization for Hydrolysis of Multiple Types of Aromatic Esters by Promiscuous Aminopeptidases

Synthetic aromatic esters, widely employed in agriculture, food, and chemical industries, have become emerging environmental pollutants due to their strong hydrophobicity and poor bioavailability. This study attempted to address this issue by extracellularly expressing the promiscuous aminopeptidase (Aps) from Pseudomonas aeruginosa GF31 in B. subtilis, achieving an impressive enzyme activity of 13.7 U/mg. Notably, we have demonstrated, for the first time, the Aps-mediated degradation of diverse aromatic esters, including but not limited to pyrethroids, phthalates, and parabens. A biochemical characterization of Aps reveals its esterase properties and a broader spectrum of substrate profiles. The degradation rates of p-nitrobenzene esters (p-NB) with different side chain structures vary under the action of Aps, showing a preference for substrates with relatively longer alkyl side chains. The structure-dependent degradability aligns well with the binding energies between Aps and p-NB. Molecular docking and enzyme-substrate interaction elucidate that hydrogen bonding, hydrophobic interactions, and π-π stacking collectively stabilize the enzyme-substrate conformation, promoting substrate hydrolysis. These findings provide new insights into the enzymatic degradation of aromatic ester pollutants, laying a foundation for the further development and modification of promiscuous enzymes.

Review of nomenclature and methods of analysis of polyethylene terephthalic acid hydrolyzing enzymes activity

Enzymatic degradation of polyethylene terephthalic acid (PET) has been gaining increasing importance. This has resulted in a significant increase in the search for newer enzymes and the development of more efficient enzyme-based systems. Due to the lack of a standard screening process, screening new enzymes has relied on other assays to determine the presence of esterase activity. This, in turn, has led to various nomenclatures and methods used to describe them and measure their activity. Since all PET-hydrolyzing enzymes are α/β hydrolases, they catalyze a serine nucleophilic attack and cleave an ester bond. They are lipases, esterases, cutinases and hydrolases. This has been used interchangeably, leading to difficulties while comparing results and evaluating progress. This review discusses the varied enzyme nomenclature being adapted, the different assays and analysis methods reported, and the strategies used to increase PET-hydrolyzing enzyme efficiency. A section on the various ways to quantify PET hydrolysis is also covered.

Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability

Understanding the mechanisms influencing poly(ethylene terephthalate) (PET) biodegradation is crucial for developing innovative strategies to accelerate the breakdown of this persistent plastic. In this study, we employed all-atom molecular dynamics simulation to investigate the adsorption process of the LCC-ICCG cutinase enzyme onto the PET surface. Our results revealed that hydrophobic, π-π, and H bond interactions, specifically involving aliphatic, aromatic, and polar uncharged amino acids, were the primary driving forces for the adsorption of the cutinase enzyme onto PET. Additionally, we observed a negligible change in the enzyme's tertiary structure during the interaction with PET (RMSD = 1.35 Å), while its secondary structures remained remarkably stable. Quantitative analysis further demonstrated that there is about a 24% decrease in the number of enzyme-water hydrogen bonds upon adsorption onto the PET surface. The significance of this study lies in unraveling the molecular intricacies of the adsorption process, providing valuable insights into the initial steps of enzymatic PET degradation.

Microbiology and Biochemistry of Pesticides Biodegradation

Pesticides are chemicals used in agriculture, forestry, and, to some extent, public health. As effective as they can be, due to the limited biodegradability and toxicity of some of them, they can also have negative environmental and health impacts. Pesticide biodegradation is important because it can help mitigate the negative effects of pesticides. Many types of microorganisms, including bacteria, fungi, and algae, can degrade pesticides; microorganisms are able to bioremediate pesticides using diverse metabolic pathways where enzymatic degradation plays a crucial role in achieving chemical transformation of the pesticides. The growing concern about the environmental and health impacts of pesticides is pushing the industry of these products to develop more sustainable alternatives, such as high biodegradable chemicals. The degradative properties of microorganisms could be fully exploited using the advances in genetic engineering and biotechnology, paving the way for more effective bioremediation strategies, new technologies, and novel applications. The purpose of the current review is to discuss the microorganisms that have demonstrated their capacity to degrade pesticides and those categorized by the World Health Organization as important for the impact they may have on human health. A comprehensive list of microorganisms is presented, and some metabolic pathways and enzymes for pesticide degradation and the genetics behind this process are discussed. Due to the high number of microorganisms known to be capable of degrading pesticides and the low number of metabolic pathways that are fully described for this purpose, more research must be conducted in this field, and more enzymes and genes are yet to be discovered with the possibility of finding more efficient metabolic pathways for pesticide biodegradation.

Computational analysis of carboxylesterase genes and proteins in non-pathogenic food bacterium Alicyclobacillus acidocaldarius: insights from proteogenomics

Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å2) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.

Concurrent production of ferulic acid and glucose from wheat bran by catalysis of a putative bifunctional enzyme

The aim of this work is to study a bifunctional endoglucanase/carboxylesterase in Sphingobacterium soilsilvae Em02 and express it in soluble form in engineered Escherichia coli. The molecular weight of the recombinant protein of the bifunctional enzyme was 41 KDa. This research also determined the enzymatic activities of the bifunctional enzymes using microcrystalline cellulose and p-nitrophenyl butyrate as substrates and found 40 °C as the optimum temperature for their enzymatic activities. The optimal pH in dual function was 6.0 for endoglucanase and 7.0 for carboxylesterase. The bifunctional enzyme also exhibited enzymatic activities on the natural biomass by generating up to 3.94 mg of glucose and 49.4 μg of ferulic acid from 20 mg of destarched wheat bran. This indicates the broad application prospects of the bifunctional enzyme in agriculture and industry.

Application of Milk Permeate as an Inducer for the Production of Microbial Recombinant Lipolytic Enzymes

Recombinantly produced enzymes are applied in many fields, ranging from medicine to food and nutrition, production of detergents, textile, leather, paper, pulp, and plastics. Thus, the cost-effectiveness of recombinant enzyme synthesis is an important issue in biotechnological industry. Isopropyl-β-D-thiogalactoside (IPTG), an analog of lactose, is currently the most widely used chemical agent for the induction of recombinant enzyme synthesis. However, the use of IPTG can lead to production of toxic elements and can introduce physiological stress to cells. Thus, this study aims to find a simpler, cheaper, and safer way to produce recombinant enzymes. In this study, production of several previously designed recombinant lipolytic enzymes (GDEst-95 esterase, GD-95RM lipase, fused GDEst-lip lipolytic enzyme, and putative cutinase Cut+SP from Streptomyces scabiei 87.22) is induced in E. coli BL21 (DE3) using 4 mM milk permeate, a type of waste of the milk manufacturing process possessing >82% lactose. The SDS-PAGE analysis clearly indicates synthesis of all target enzymes during a 2–12 h post-induction timeframe. Further investigation of GDEst-95, GD-95RM, GDEst-lip, and Cut+SP biocatalysts was carried out spectrophotometrically and using zymography method, confirming production of fully active enzymes.