Identification and characterization of a novel phthalate-degrading hydrolase from a soil metagenomic library

Bacterial Catabolism of Phthalates With Estrogenic Activity Used as Plasticisers in the Manufacture of Plastic Products

Phthalic acid esters (PAEs), the pervasive and ubiquitous endocrine-disrupting chemicals of environmental concern, generated annually on a million-ton scale, are primarily employed as plasticisers in the production of a variety of plastic products and as additives in a large number of commercial supplies. The increased awareness of various adverse effects on the ecosystem and human health including reproductive and developmental disorders has led to a striking increase in research interest aimed at managing these man-made oestrogenic chemicals. In these circumstances, microbial metabolism appeared as the major realistic process to neutralise the toxic burdens of PAEs in an ecologically accepted manner. Among a wide variety of microbial species capable of degrading/transforming PAEs reported so far, bacteria-mediated degradation has been studied most extensively. The main purpose of this review is to provide current knowledge of metabolic imprints of microbial degradation/transformation of PAEs, a co-contaminant of plastic pollution. In addition, this communication illustrates the recent advancement of the structure-functional aspects of the key metabolic enzyme phthalate hydrolase, their inducible regulation of gene expression and evolutionary relatedness, besides prioritising future research needs to facilitate the development of new insights into the bioremediation of PAE in the environment.

Improved microbial-plant soil bioremediation of PAHs and heavy metal through in silico methods

The combined pollution of polycyclic aromatic hydrocarbons (PAHs) and organic cadmium (Cd) in farmland soils, and the field controlling strategy need to be studied urgently. In this study, 5 PAHs, 5 Cd and 11 soil conditioners were selected to explore the co-exposure risk and remediation efficiency. Firstly, a significant combination Fl-alkylalkoxy cadmium was obtained using forward and reverse methods coupling variation coefficient methods (the combined pollution value was 0.173). Secondly, the interaction energy of microbial degradation / plant absorption of Fl under Cd stress, and microbial mineralization / plant absorption of alkylalkoxy cadmium under PAHs stress were characterized using factorial experimental design, molecular docking and molecular dynamics simulation. The combined pollution of alkylalkoxy cadmium and dialkyl cadmium, phenanthrene and Benzo [a] pyrene was significant (synergistic contribution rates were 17.58 % and 19.22 %, respectively). In addition, 6 soil conditioners with significant efficiency were selected to design Taguchi orthogonal experimental schemes, indicating the microbial degradation / mineralization and plant absorption were significantly effective (the maximum increase of remediation efficiency was 93.81 %) under the combinations (i.e., trratone, coumarol, fulvamic acid, potassium fertilizer and others, etc.). Finally, it was found that the soil conditioners affected the hydrophobic groups and forces, and the efficiency was proportional to the highest peak value and minimum distance in the RDF curve. This study identifies the risk characteristics of co-exposure of PAHs and Cd and screens effective soil conditioners, providing theoretical guidance for risk controlling.

Engineering bacterial biocatalysts for the degradation of phthalic acid esters

Phthalic acid esters (PAEs) are synthetic diesters derived from o-phthalic acid, commonly used as plasticizers. These compounds pose significant environmental and health risks due to their ability to leach into the environment and act as endocrine disruptors, carcinogens, and mutagens. Consequently, PAEs are now considered major emerging contaminants and priority pollutants. Microbial degradation, primarily by bacteria and fungi, offers a promising method for PAEs bioremediation. This article highlights the current state of microbial PAEs degradation, focusing on the major bottlenecks and associated challenges. These include the identification of novel and more efficient PAE hydrolases to address the complexity of PAE mixtures in the environment, understanding PAEs uptake mechanisms, characterizing novel o-phthalate degradation pathways, and studying the regulatory network that controls the expression of PAE degradation genes. Future research directions include mitigating the impact of PAEs on health and ecosystems, developing biosensors for monitoring and measuring bioavailable PAEs concentrations, and valorizing these residues into other products of industrial interest, among others.

In-silico characterization of a hypothetical protein of Sulfobacillus sp. hq2 for degradation of phthalate diesters

Phthalate plasticizers are hazardous compounds capable of causing endocrine disruption, cancers, and developmental disorders. Phthalate diesters are commonly used plasticizers in plastic products (PVC pipes) that leach out into the environment due to changes in temperature, pressure, and pH, posing harmful effects on different life forms. Bioremediation of phthalate diesters utilizing bacterial esterase has been recognized as an efficient approach but few effective esterases capable of degrading a wide range of phthalate diesters have been identified. Further, the thermostability of these esterases is a highly desirable property for their applications in diverse in-situ conditions. In this present in-silico study a hypothetical protein (POB10642.1) as a high-potential esterase from a thermostable strain of Sulfobacillus sp. hq2 has been characterized. Analysis revealed a significant sequence identity of 42.67 % and structural similarity (RMSD 0.557) with known phthalate diester degrading EstS1 esterase and a high Tm range of 55-66 °C. Structural analysis revealed the presence of two cavities on the surface mediating toward the catalytic site forming a catalytic tunnel. The enzyme POB10642.1 has significant molecular docking binding energies in the range of -5.4 to -7.5 kcal/mol with several phthalate diesters, including Diethyl phthalate, Dipropyl phthalate, Dibutyl phthalate, Dipentyl phthalate, Dihexyl phthalate, Benzyl butyl phthalate, Dicyclohexyl phthalate, and Bis(2-ethylhexyl) phthalate. High stability of binding during 100 ns molecular dynamics simulations revealed efficient and stable binding of the enzyme with a wide range of phthalate diesters at its active site, demonstrating the ability of the identified esterase to interact with and degrade diverse phthalate diesters. Therefore, POB10642.1 esterase can be an efficient candidate to be utilized in the development of enzyme-based bioremediation technologies to reduce the toxic levels of phthalate diesters.

Molecular insights into the catalytic mechanism of a phthalate ester hydrolase

Phthalate esters (PAEs) are emerging hazardous and toxic chemicals that are extensively used as plasticizers or additives. Diethyl phthalate (DEP) and dimethyl phthalate (DMP), two kinds of PAEs, have been listed as the priority pollutants by many countries. PAE hydrolases are the most effective enzymes in PAE degradation, among which family IV esterases are predominate. However, only a few PAE hydrolases have been characterized, and as far as we know, no crystal structure of any PAE hydrolases of the family IV esterases is available to date. HylD1 is a PAE hydrolase of the family IV esterases, which can degrade DMP and DEP. Here, the recombinant HylD1 was characterized. HylD1 maintained a dimer in solution, and functioned under a relatively wide pH range. The crystal structures of HylD1 and its complex with monoethyl phthalate were solved. Residues involved in substrate binding were identified. The catalytic mechanism of HylD1 mediated by the catalytic triad Ser140-Asp231-His261 was further proposed. The hylD1 gene is widely distributed in different environments, suggesting its important role in PAEs degradation. This study provides a better understanding of PAEs hydrolysis, and lays out favorable bases for the rational design of highly-efficient PAEs degradation enzymes for industrial applications in future.

Molecular docking and metagenomics assisted mitigation of microplastic pollution

Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.

Mechanistic understanding on the uptake of micro-nano plastics by plants and its phytoremediation

Contaminated soil is one of today's most difficult environmental issues, posing serious hazards to human health and the environment. Contaminants, particularly micro-nano plastics, have become more prevalent around the world, eventually ending up in the soil. Numerous studies have been conducted to investigate the interactions of micro-nano plastics in plants and agroecosystems. However, viable remediation of micro-nano plastics in soil remains limited. In this review, a powerful in situ soil remediation technology known as phytoremediation is emphasized for addressing micro-nano-plastic contamination in soil and plants. It is based on the synergistic effects of plants and the microorganisms that live in their rhizosphere. As a result, the purpose of this review is to investigate the mechanism of micro-nano plastic (MNP) uptake by plants as well as the limitations of existing MNP removal methods. Different phytoremediation options for removing micro-nano plastics from soil are also described. Phytoremediation improvements (endophytic-bacteria, hyperaccumulator species, omics investigations, and CRISPR-Cas9) have been proposed to enhance MNP degradation in agroecosystems. Finally, the limitations and future prospects of phytoremediation strategies have been highlighted in order to provide a better understanding for effective MNP decontamination from soil.

Complete genome sequence of Acinetobacter indicus and identification of the hydrolases provides direct insights into phthalate ester degradation

A strain designated Acinetobacter indicus WMB-7 with the ability to hydrolyze phthalate esters (PAEs) was isolated from the fermented grains of Baijiu. The genome of the strain was sequenced with a length of 3,256,420 bp and annotated with 3183 genes, of which 36 hydrolases encoding genes were identified. The hydrolases were analyzed by protein structure modeling and molecular docking, and 14 enzymes were docked to the ligand di-butyl phthalate with the catalytic active regions, and showed binding affinity. The 14 enzymes were expressed in E. coli and 5 of them showed the ability for PAEs hydrolysis. Enzyme GK020_RS15665 showed high efficiency for PAEs hydrolysis and could efficiently hydrolyze di-butyl phthalate under an initial concentration of 1000 mg/L with a half-life of 4.24 h. This work combined a series of methods for identifying PAEs hydrolases and offered a molecular basis for PAEs degradation of A. indicus strains from Baijiu.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01334-w.

A comprehensive review on enzymatic biodegradation of polyethylene terephthalate

Polyethylene terephthalate (PET) is a polymer synthesized via the dehydration and condensation reaction between ethylene glycol and terephthalic acid. PET has emerged as one of the most extensively employed plastic materials due to its exceptional plasticity and durability. Nevertheless, PET has a complex structure and is extremely difficult to degrade in nature, causing severe pollution to the global ecological environment and posing a threat to human health. Currently, the methods for PET processing mainly include physical, chemical, and biological methods. Biological enzyme degradation is considered the most promising PET degradation method. In recent years, an increasing number of enzymes that can degrade PET have been identified, and they primarily target the ester bond of PET. This review comprehensively introduced the latest research progress in PET enzymatic degradation from the aspects of PET-degrading enzymes, PET biodegradation pathways, the catalytic mechanism of PET-degrading enzymes, and biotechnological strategies for enhancing PET-degrading enzymes. On this basis, the current challenges within the enzymatic PET degradation process were summarized, and the directions that need to be worked on in the future were pointed out. This review provides a reference and basis for the subsequent effective research on PET biodegradation.

A Novel and Efficient Phthalate Hydrolase from Acinetobacter sp. LUNF3: Molecular Cloning, Characterization and Catalytic Mechanism

Phthalic acid esters (PAEs), which are widespread environmental contaminants, can be efficiently biodegraded, mediated by enzymes such as hydrolases. Despite great advances in the characterization of PAE hydrolases, which are the most important enzymes in the process of PAE degradation, their molecular catalytic mechanism has rarely been systematically investigated. Acinetobacter sp. LUNF3, which was isolated from contaminated soil in this study, demonstrated excellent PAE degradation at 30 °C and pH 5.0-11.0. After sequencing and annotating the complete genome, the gene dphAN1, encoding a novel putative PAE hydrolase, was identified with the conserved motifs catalytic triad (Ser201-Asp295-His325) and oxyanion hole (H127GGG130). DphAN1 can hydrolyze DEP (diethyl phthalate), DBP (dibutyl phthalate) and BBP (benzyl butyl phthalate). The high activity of DphAN1 was observed under a wide range of temperature (10-40 °C) and pH (6.0-9.0). Moreover, the metal ions (Fe2+, Mn2+, Cr2+ and Fe3+) and surfactant TritonX-100 significantly activated DphAN1, indicating a high adaptability and tolerance of DphAN1 to these chemicals. Molecular docking revealed the catalytic triad, oxyanion hole and other residues involved in binding DBP. The mutation of these residues reduced the activity of DphAN1, confirming their interaction with DBP. These results shed light on the catalytic mechanism of DphAN1 and may contribute to protein structural modification to improve catalytic efficiency in environment remediation.

Human Endocrine-Disrupting Effects of Phthalate Esters through Adverse Outcome Pathways: A Comprehensive Mechanism Analysis

Phthalate esters (PAEs) are widely exposed in the environment as plasticizers in plastics, and they have been found to cause significant environmental and health hazards, especially in terms of endocrine disruption in humans. In order to investigate the processes underlying the endocrine disruption effects of PAEs, three machine learning techniques were used in this study to build an adverse outcome pathway (AOP) for those effects on people. According to the results of the three machine learning techniques, the random forest and XGBoost models performed well in terms of prediction. Subsequently, sensitivity analysis was conducted to identify the initial events, key events, and key features influencing the endocrine disruption effects of PAEs on humans. Key features, such as Mol.Wt, Q+, QH+, ELUMO, minHCsats, MEDC-33, and EG, were found to be closely related to the molecular structure. Therefore, a 3D-QSAR model for PAEs was constructed, and, based on the three-dimensional potential energy surface information, it was discovered that the hydrophobic, steric, and electrostatic fields of PAEs significantly influence their endocrine disruption effects on humans. Lastly, an analysis of the contributions of amino acid residues and binding energy (BE) was performed, identifying and confirming that hydrogen bonding, hydrophobic interactions, and van der Waals forces are important factors affecting the AOP of PAEs' molecular endocrine disruption effects. This study defined and constructed a comprehensive AOP for the endocrine disruption effects of PAEs on humans and developed a method based on theoretical simulation to characterize the AOP, providing theoretical guidance for studying the mechanisms of toxicity caused by other pollutants.

Substrate-enzyme interactions and catalytic mechanism in a novel family VI esterase with dibutyl phthalate-hydrolyzing activity

Microbial degradation has been confirmed as effective and environmentally friendly approach to remediate phthalates from the environment, and hydrolase is an effective element for contaminant degradation. In the present study, a novel dibutyl phthalate (DBP)-hydrolyzing carboxylesterase (named PS06828) from Pseudomonas sp. PS1 was heterogeneously expressed in E. coli, which was identified as a new member of the lipolytic family VI. Purified PS06828 could efficiently degrade DBP with a wide range of temperature (25-37 °C) and pH (6.5-9.0). Multi-spectroscopy methods combined with molecular docking were employed to study the interaction of PS06828 with DBP. Fluorescence and UV-visible absorption spectra revealed the simultaneous presence of static and dynamic component in the fluorescence quenching of PS06828 by DBP. Synchronous fluorescence and circular dichroism spectra showed inconspicuous alteration in micro-environmental polarity around amino acid residues but obvious increasing of α-helix and reducing of β-sheet and random coil in protein conformation. Based on the information on exact binding sites of DBP on PS06828 provided by molecular docking, the catalytic mechanism mediated by key residues (Ser113, Asp166, and His197) was proposed and subsequently confirmed by site-directed mutagenesis. The results can strengthen our mechanistic understanding of family VI esterase involved in hydrolysis of phthalic acid esters, and provide a solid foundation for further enzymatic modification.

Molecular insights into the catalytic mechanism of plasticizer degradation by a monoalkyl phthalate hydrolase

Phthalate acid esters (PAEs), a group of xenobiotic compounds used extensively as plasticizers, have attracted increasing concern for adverse effects to human health and the environment. Microbial degradation relying on PAE hydrolases is a promising treatment. However, only a limited number of PAE hydrolases were characterized to date. Here we report the structures of MehpH, a monoalkyl phthalate (MBP) hydrolase that catalyzes the reaction of MBP to phthalic acid and the corresponding alcohol, in apo and ligand-bound form. The structures reveal a positively-charged catalytic center, complementary to the negatively-charged carboxyl group on MBP, and a penetrating tunnel that serves as exit of alcohol. The study provides a first glimpse into the enzyme-substrate binding model for PAE hydrolases, leading strong support to the development of better enzymes in the future.

Improving the activity and expression level of a phthalate-degrading enzyme by a combination of mutagenesis strategies and strong promoter replacement

Phthalic acid esters (PAEs) are widely used plasticizers found in consumer products, which enter the environment and pose severe threats to human health. Here, a new PAE-degrading enzyme EstJ6 was modified by combining mutagenesis strategies and a strong promoter replacement to improve its catalytic activity and expression level. Four mutants with enhanced activity were obtained by random mutation, among which EstJ6M1.1 exhibited the highest catalytic activity with an increase in catalytic activity by 2.9-fold toward dibutyl phthalate (DBP) than that of the wild-type (WT) enzyme. With these mutants as a template, a variant EstJ6M2 with 3.1-fold higher catalytic activity and 4.61 times higher catalytic efficiency (Kcat/Km) was identified by staggered extension PCR. Targeting four mutation sites of EstJ6M2, a variant EstJ6M3.1 was gained by site-directed saturation mutagenesis and displayed 4.3-fold higher activity and 5.97 times higher Kcat/Km than WT. The expression level of three mutants EstJ6M1.1, EstJ6M2, and EstJ6M3.1, as well as the WT, increased nearly threefold after a strong promoter replacement. These results provide a proof-theoretical basis and practicable pipeline for applying PAE-degrading enzymes.

Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G

Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.

Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics

Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to α/β-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the α/β hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.

Multi-omics approaches for remediation of bisphenol A: Toxicity, risk analysis, road blocks and research perspectives

In this "plastic era" with the increased use of plastic in day today's life the accumulation of its degraded products like microplastics or plastic additives such as Bisphenol A(BPA) is also increasing. BPA is an endocrine-disrupting chemical used as a plasticizing agent in clear plastic, building materials, coatings, and epoxy resin. Several enzymes including laccases and lipases have been studied for the reduction of BPA toxicity. Over the decades of encountering these toxicants, microorganisms have evolved to degrade different classes of plastic additives. Since the degradation of BPA is a long process thus meta-omics approaches have been employed to identify the active microbiota and microbial dynamics involved in the mitigation of BPA. It is also necessary to investigate the impact of processing activities on transit of BPA in food items and to limit its entrance in food world. This review summarizes a comprehensive overview on BPA sources, toxicity, bio-based mitigation approaches along with a deeper understanding of multi-omics approaches for its reduction and risk analysis. Knowledge gaps and opportunities have been comprehensively compiled that would aid the state-of-the-art information in the available literature for the researchers to further address this issue.

Phthalate hydrolase: distribution, diversity and molecular evolution

The alpha/beta-fold superfamily of hydrolases is rapidly becoming one of the largest groups of structurally related enzymes with diverse catalytic functions. In this superfamily of enzymes, esterase deserves special attention because of their wide distribution in biological systems and importance towards environmental and industrial applications. Among various esterases, phthalate hydrolases are the key alpha/beta enzymes involved in the metabolism of structurally diverse estrogenic phthalic acid esters, ubiquitously distributed synthetic chemicals, used as plasticizer in plastic manufacturing processes. Although they vary both at the sequence and functional levels, these hydrolases use a similar acid-base-nucleophile catalytic mechanism to catalyse reactions on structurally different substrates. The current review attempts to present insights on phthalate hydrolases, describing their sources, structural diversities, phylogenetic affiliations and catalytically different types or classes of enzymes, categorized as diesterase, monoesterase and diesterase-monoesterase, capable of hydrolysing phthalate diester, phthalate monoester and both respectively. Furthermore, available information on in silico analyses and site-directed mutagenesis studies revealing structure-function integrity and altered enzyme kinetics have been highlighted along with the possible scenario of their evolution at the molecular level.

Phthalate's multiple hormonal effects and their supplementary dietary regulation scheme of health risks for children

Four common phthalic acid esters (PAEs), namely, butylbenzyl phthalate (BBzP), dibutyl phthalate (DBP), di(2-ethylhexyl) phthalate (DEHP), and di-n-octyl phthalate (DNOP) that are known to affect children upon exposure, were selected, and the hormone effects were explored during different supplementary food intakes by using methods such as factorial design experiment, molecular docking, and dynamics simulation techniques. A supplementary diet regulation scheme to prevent health risks of PAEs was constructed to avoid or mitigate the hormonal effects in children exposed to PAEs. Firstly, the MM/PBSA binding energy of PAEs with single hormone receptors and multiple hormone receptor complexes was calculated. In addition, 10 foods were selected as external interference conditions to carry out dynamic simulation, which showed that kiwi fruit and broccoli can effectively alleviate the PAEs' hormone effects. Furthermore, inference of the metabolic process of DEHP found that the supplementary diets could effectively promote the metabolism of PAEs. Finally, based on the mechanism analysis, it was confirmed that the selected supplementary diets could inhibit the binding process. This study aims to explore the role of supplementary diets in regulating various PAEs' hormone effects and thereby provide theoretical support for slowing down hormonal effects in children.

Dual functional roles of a novel bifunctional β-lactamase/esterase from Lactococcus garvieae

A novel bifunctional β-lactamase/esterase (LgLacI), which is capable of hydrolyzing β-lactam-containing antibiotics including ampicillin, oxacillin, and cefotaxime as well as synthesizing biodiesels, was cloned from Lactococcus garvieae. Unlike most bacterial esterases/lipases that have G-x-S-x-G motif, LgLacI, which contains S-x-x-K catalytic motif, has sequence similarities to bacterial family VIII esterase as well as β-lactamases. The catalytic properties of LgLacI were explored using a wide range of biochemical methods including spectroscopy, assays, structural modeling, mutagenesis, and chromatography. We confirmed the bifunctional property of LgLacI hydrolyzing both esters and β-lactam antibiotics. This study provides novel perspectives into a bifunctional enzyme from L. garvieae, which can degrade β-lactam antibiotics with high esterase activity.

Environmental role of aromatic carboxylesterases

The carboxylesterases (EC 3.1.1.x) are widely distributed and form an important yet diverse group of hydrolases catalysing the ester bond cleavage in a variety of substrates. Besides acting on plant cell wall components like cutin, tannin and feruloyl esters, they are often the first line of defence to metabolize drugs, xenobiotics, pesticides, insecticides and plastic. But for the promiscuity of some carboxylesterases and cutinases, very few enzymes act exclusively on aromatic carboxylic acid esters. Infrequent occurrence of aromatic carboxylesterases suggests that aromatic carboxylesters are inherently more difficult to hydrolyse than the regular carboxylesters because of both steric and polar effects. Naturally occurring aromatic carboxylesters were rare before the anthropogenic activity augmented their environmental presence and diversity. An appraisal of the literature shows that the hydrolysis of aromatic carboxylic esters is a uniquely difficult endeavour and hence deserves special attention. Enzymes to hydrolyse such esters are evolving rapidly in nature. Very few such enzymes are known and they often display much lower catalytic efficiencies. Obviously, the esters of aromatic carboxylic acids, including polyethylene terephthalate waste, pose an environmental challenge. In this review, we highlight the uniqueness of aromatic carboxylesters and then underscore the importance of relevant carboxylesterases.

Characterization of a novel carboxylesterase with catalytic activity toward di(2-ethylhexyl) phthalate from a soil metagenomic library

A novel carboxylesterase gene estyz5 was isolated from a soil metagenomic library. The recombinant enzyme EstYZ5 is 298 amino acids in length with a predicted molecular weight of 32 kDa. Sequence alignment and phylogenetic analysis revealed that EstYZ5 belongs to the hormone-sensitive lipase (HSL) family with a deduced catalytic triad of Ser144-Glu238-His268. EstYZ5 contains two conserved motifs, a pentapeptide motif GDSAG and a HGGG motif, which are typically found in members of the HSL family. Esterolytic activity of the recombinant enzyme was optimal at 30 °C and pH 8.0, and the kcat/Km value of the enzyme for the optimum substrate p-nitrophenyl butyrate was as high as 1272 mM^-1·s^-1. Importantly, EstYZ5 showed activity toward di(2-ethylhexyl) phthalate with complex side chains, which is rare for HSLs. Molecular docking simulations revealed that the catalytic triad and an oxyanion hole likely play vital roles in enzymatic activity and specificity. The phthalate-degrading activity of EstYZ5, combined with its high levels of esterolytic activity, render this new enzyme a candidate for biotechnological applications.

Characterization of a Novel Family IV Esterase Containing a Predicted CzcO Domain and a Family V Esterase with Broad Substrate Specificity from an Oil-Polluted Mud Flat Metagenomic Library

Two novel esterase genes, est2L and est4L, were identified from a previously constructed metagenomic library derived from an oil-polluted mud flat sample. The encoded Est2L and Est4L were composed of 839 and 267 amino acids, respectively, without signal peptides. Est2L was a unique fusion type of protein composed of two domains: a domain of the CzcO superfamily, associated with a cationic diffusion promoter with CzcD, and a domain of the acetylesterase superfamily, belonging to family IV with conserved motifs, such as HGG, GXSAG, and GXPP. Est2L was the first fused esterase with a CzcO domain. Est4L belonged to family V with GXS, GXSMGG, and PTL motifs. Native Est2L and Est4L were found to be in dimeric and tetrameric forms, respectively. Est2L and Est4L showed the highest activities at 60 °C and 50 °C, respectively, and at a pH of 10.0. Est2L preferred short length substrates, especially p-nitrophenyl (pNP)-acetate, with moderate butyrylcholinesterase activity, whereas Est4L showed the highest activity with pNP-decanoate and had broad specificity. Significant effects were not observed in Est2L from Co2+ and Zn2+, although Est2L contains the domain CzcD. Est2L and Est4L showed high stabilities in 30% methanol and 1% Triton X-100. These enzymes could be used for a variety of applications, such as detergent and mining processing under alkaline conditions.

A model for phthalic acid esters' biodegradability and biotoxicity multi-effect pharmacophore and its application in molecular modification

The objective of this study was to investigate 13 phthalic acid esters (PAEs) with medium or long straight-alkyl-chain, branching or unsaturated side chains, because their structural characteristics make them difficult to biodegrade or highly toxic. A biodegradability and biotoxicity multi-effect pharmacophore model was built using comprehensive evaluation method. The results suggested that introducing hydrophobic groups to the side chains of the PAEs could improve the molecules' biodegradability and biotoxicity effects simultaneously. Thus, 40 target PAE (HEHP, DNOP, DUP) derivatives were designed. Two environmentally friendly PAE derivatives (HEHP-Anthryl and HEHP-Naphthyl) were screened via the test of environmental friendliness and functionality. In addition, the biodegradation and biotoxicity of derivatives were found to have improved as a result of the change in van der Waals forces between molecules and their corresponding proteins. Moreover, the environmental safety of the screened PAE derivatives was confirmed by predicting the toxicity of their intermediates and calculating the energy barrier values for biodegradation and metabolic pathways. This study could provide theoretical guidance for the practical development of environmentally friendly plasticizer.

Enhancing the activity and thermal stability of a phthalate-degrading hydrolase by random mutagenesis

Our previous work has reported that EstJ6 was a phthalate-degrading hydrolase. In the study, a random mutant library was constructed by two rounds of error-prone PCR, three mutants (ET1.1, ET2.1, and ET2.2) with enhanced hydrolytic activity against dibutyl phthalate (DBP) were obtained. The best mutant ET2.2, accumulated three amino acid substitutions (Thr91Met, Ala67Val, and Val249Ile) and exhibited 2.8-fold increase enzyme activity and 2.3-fold higher expression level. Meanwhile, compared with EstJ6, ET2.2 showed over 50% improvement in thermostability (at 50 °C for 1 h) and 1.2-fold increase in 50% methanol tolerance. Kinetic parameters analysis revealed that the Km value for ET2.2 decreased by 60% and the kcat/Km value increased by 166%. The molecular docking indicated that the shortening of hydrogen bond between Ser146-OH and DBP-CO, which may led to an increase in enzyme activity and catalytic efficiency, the enhancement of hydrophobicity of hydrophobic pocket was related to the improvement of organic solvents tolerance, and three hydrophobic amino acid substitutions Thr91Met, Ala67Val, and Val249Ile facilitated to improve the thermal stability and organic solvents tolerance. These results confirmed that random mutagenesis was an effective tool for improving enzyme properties and lay a foundation for practical applications of phthalate-degrading hydrolase in biotechnology and industrial fields.

Characterization of XtjR8: A novel esterase with phthalate-hydrolyzing activity from a metagenomic library of lotus pond sludge

A fosmid metagenomic library containing 9.7 × 104 clones was constructed. A novel esterase, XtjR8, was isolated through functional screening. XtjR8 shared the maximum amino acid identity (44%) with acetyl-hydrolase from Streptomyces hygroscopicus, and was classified into family IV esterase. XtjR8 exhibited the highest hydrolytic activity for p-nitrophenyl acetate at 40 °C and pH 8.0, and presented more than 40% activity from 20 °C to 80 °C. More importantly, XtjR8 displayed the ability to hydrolyze both phthalate monoesters and diesters, this feature is extremely rare among previously reported esterases. Site-directed mutagenesis experiments revealed that the catalytic triad residues were Ser152, Glu246, and His276. Among them, Ser152 formed a hydrogen bond with dibutyl phthalate (DBP) by molecular docking, Gly84, Gly85, and Leu248 of conserved motifs formed hydrophobic interactions with DBP, respectively, which were important for the catalytic activity. Considering its wide range of temperature and hydrolytic potential toward phthalate esters, XtjR8 will be served as an interesting candidate for biodegradation and industrial applications.