strain NyZ500 with deacetylation activity for acetylated polymer polyvinyl alcohol

A Novel Estrone Degradation Gene Cluster and Catabolic Mechanism in Microbacterium oxydans ML-6

Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.

Molecular Mechanism of Chloramphenicol and Thiamphenicol Resistance Mediated by a Novel Oxidase, CmO, in Sphingomonadaceae

Antibiotic resistance mediated by bacterial enzyme inactivation plays a crucial role in the degradation of antibiotics in the environment. Chloramphenicol (CAP) resistance by enzymatic inactivation comprises nitro reduction, amide bond hydrolysis, and acetylation modification. However, the molecular mechanism of enzymatic oxidation of CAP remains unknown. Here, a novel oxidase gene, cmO, was identified and confirmed biochemically. The encoded CmO oxidase could catalyze the oxidation at the C-1' and C-3' positions of CAP and thiamphenicol (TAP) in Sphingobium sp. strain CAP-1. CmO is highly conserved in members of the family Sphingomonadaceae and shares the highest amino acid similarity of 41.05% with the biochemically identified glucose methanol choline (GMC) oxidoreductases. Molecular docking and site-directed mutagenesis analyses demonstrated that CAP was anchored inside the protein pocket of CmO with the hydrogen bonding of key residues glycine (G) 99, asparagine (N) 518, methionine (M) 474, and tyrosine (Y) 380. CAP sensitivity tests demonstrated that the acetyltransferase and CmO could enable a higher level of resistance to CAP than the amide bond-hydrolyzing esterase and nitroreductase. This study provides a better theoretical basis and a novel diagnostic gene for understanding and assessing the fate and resistance risk of CAP and TAP in the environment. IMPORTANCE Rising levels of antibiotic resistance are undermining ecological and human health as a result of the indiscriminate usage of antibiotics. Various resistance mechanisms have been characterized-for example, genes encoding proteins that degrade antibiotics-and yet, this requires further exploration. In this study, we report a novel gene encoding an oxidase involved in the inactivation of typical amphenicol antibiotics (chloramphenicol and thiamphenicol), and the molecular mechanism is elucidated. The findings provide novel data with which to understand the capabilities of bacteria to tackle antibiotic stress, as well as the complex function of enzymes in the contexts of antibiotic resistance development and antibiotic removal. The reported gene can be further employed as an indicator to monitor amphenicol's fate in the environment, thus benefiting risk assessment in this era of antibiotic resistance.

Biodegradation of Biodegradable Polymers in Mesophilic Aerobic Environments

Finding alternatives to diminish plastic pollution has become one of the main challenges of modern life. A few alternatives have gained potential for a shift toward a more circular and sustainable relationship with plastics. Biodegradable polymers derived from bio- and fossil-based sources have emerged as one feasible alternative to overcome inconveniences associated with the use and disposal of non-biodegradable polymers. The biodegradation process depends on the environment's factors, microorganisms and associated enzymes, and the polymer properties, resulting in a plethora of parameters that create a complex process whereby biodegradation times and rates can vary immensely. This review aims to provide a background and a comprehensive, systematic, and critical overview of this complex process with a special focus on the mesophilic range. Activity toward depolymerization by extracellular enzymes, biofilm effect on the dynamic of the degradation process, CO2 evolution evaluating the extent of biodegradation, and metabolic pathways are discussed. Remarks and perspectives for potential future research are provided with a focus on the current knowledge gaps if the goal is to minimize the persistence of plastics across environments. Innovative approaches such as the addition of specific compounds to trigger depolymerization under particular conditions, biostimulation, bioaugmentation, and the addition of natural and/or modified enzymes are state-of-the-art methods that need faster development. Furthermore, methods must be connected to standards and techniques that fully track the biodegradation process. More transdisciplinary research within areas of polymer chemistry/processing and microbiology/biochemistry is needed.

Characterisation of a Novel Acetyl Xylan Esterase (BaAXE) Screened from the Gut Microbiota of the Common Black Slug (Arion ater)

Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from Buttiauxella agrestis, hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments.

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.