Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate

Upcycling of polyamides through chemical hydrolysis and engineered Pseudomonas putida

Aliphatic polyamides, or nylons, are widely used in the textile and automotive industry due to their high durability and tensile strength, but recycling rates are below 5%. Chemical recycling of polyamides is possible but typically yields mixtures of monomers and oligomers which hinders downstream purification. Here, Pseudomonas putida KT2440 was engineered to metabolize C6-polyamide monomers such as 6-aminohexanoic acid, ε-caprolactam and 1,6-hexamethylenediamine, guided by adaptive laboratory evolution. Heterologous expression of nylonases also enabled P. putida to metabolize linear and cyclic nylon oligomers derived from chemical polyamide hydrolysis. RNA sequencing and reverse engineering revealed the metabolic pathways for these non-natural substrates. To demonstrate microbial upcycling, the phaCAB operon from Cupriavidus necator was heterologously expressed to enable production of polyhydroxybutyrate (PHB) from PA6 hydrolysates. This study presents a microbial host for the biological conversion, in combination with chemical hydrolysis, of polyamide monomers and mixed polyamids hydrolysates to a value-added product.

The biochemical mechanisms of plastic biodegradation

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

Recycling and Degradation of Polyamides

As one of the five major engineering plastics, polyamide brings many benefits to humans in the fields of transportation, clothing, entertainment, health, and more. However, as the production of polyamide increases year by year, the pollution problems it causes are becoming increasingly severe. This article reviews the current recycling and treatment processes of polyamide, such as chemical, mechanical, and energy recovery, and degradation methods such as thermal oxidation, photooxidation, enzyme degradation, etc. Starting from the synthesis mechanism of polyamide, it discusses the advantages and disadvantages of different treatment methods of polyamide to obtain more environmentally friendly and economical treatment schemes. Finding enzymes that can degrade high-molecular-weight polyamides, exploring the recovery of polyamides under mild conditions, synthesizing environmentally degradable polyamides through copolymerization or molecular design, and finally preparing degradable bio-based polyamides may be the destination of polyamide.

Degradation and lifetime prediction of plastics in subsea and offshore infrastructures

Engineering and civil developments have relied on synthetic polymers and plastics (including polyethylene, polypropylene, polyamide, etc.) for decades, especially where their durability protects engineering structures against corrosion and other environmental stimuli. Offshore oil and gas infrastructure and renewable energy platforms are typical examples, where these plastics (100,000 s of metric tonnes worldwide) are used primarily as functional material to protect metallic flowlines and subsea equipment against seawater corrosion. Despite this, the current literature on polymers is limited to sea-surface environments, and a model for subsea degradation of plastics is needed. In this review, we collate relevant studies on the degradation of plastics and synthetic polymers in marine environments to gain insight into the fate of these materials when left in subsea conditions. We present a new mathematical model that accounts for various physicochemical changes in the oceanic environment as a function of depth to predict the lifespan of synthetic plastics and the possible formation of plastic debris, e.g., microplastics. We found that the degradation rate of the plastics decreases significantly as a function of water depth and can be estimated quantitatively by the mathematical model that accounts for the effect (and sensitivity) of geographical location, temperature, light intensity, hydrostatic pressure, and marine sediments. For instance, it takes a subsea polyethylene coating about 800 years to degrade on ocean floor (as opposed to <400 years in shallow coastal waters), generating 1000s of particles per g of degradation under certain conditions. Our results demonstrate how suspended sediments in the water column are likely to compensate for the decreasing depth-corrected degradation rates, resulting in surface abrasion and the formation of plastic debris such as microplastics. This review, and the complementing data, will be significant for the environmental impact assessment of plastics in subsea infrastructures. Moreover, as these infrastructures reach the end of their service life, the management of the plastic components becomes of great interest to environmental regulators, industry, and the community, considering the known sizeable impacts of plastics on global biogeochemical cycles.

X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase

Nylon hydrolase (NylC), a member of the N-terminal nucleophile (Ntn) hydrolase superfamily, is responsible for the degradation of various aliphatic nylons, including nylon-6 and nylon-66. NylC is initially expressed as an inactive precursor (36 kDa), but the precursor is autocatalytically cleaved at Asn266/Thr267 to generate an active enzyme composed of 27 and 9 kDa subunits. We isolated various mutants with amino acid changes at the catalytic centre. X-ray crystallographic analysis revealed that the NylC precursor forms a doughnut-shaped quaternary structure composed of four monomers (molecules A-D) with D2 symmetry. Catalytic residues in the precursor are covered by loop regions at the A/B interface (equivalent to the C/D interface). However, the catalytic residues are exposed to the solvent environment through autocleavage followed by movements of the loop regions. T267A, D306A and D308A mutations resulted in a complete loss of autocleavage. By contrast, in the T267S mutant, autocleavage proceeded slowly at a constant reaction rate (k = 2.8 × 10^-5  s^-1 ) until complete conversion, but the reaction was inhibited by K189A and N219A mutations. Based on the crystallographic and molecular dynamic simulation analyses, we concluded that the Asp308-Asp306-Thr267 triad, resembling the Glu-Ser-Ser triad conserved in Ntn-hydrolase family enzymes, is responsible for autocleavage and that hydrogen-bonding networks connecting Thr267 with Lys189 and Asn219 are required for increasing the nucleophilicity of Thr267-OH in both the water accessible and water inaccessible systems. Furthermore, we determined that NylC employs the Asp308-Asp306-Thr267 triad as catalytic residues for substrate hydrolysis, but the reaction requires Lys189 and Tyr146 as additional catalytic/substrate-binding residues specific for nylon hydrolysis.

In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T

Gulosibacter molinativorax ON4^T is the only known organism to produce molinate hydrolase (MolA), which catalyses the breakdown of the thiocarbamate herbicide into azepane-1-carboxylic acid (ACA) and ethanethiol. A combined genomic and transcriptomic strategy was used to fully characterize the strain ON4^T genome, particularly the molA genetic environment, to identify the potential genes encoding ACA degradation enzymes. Genomic data revealed that molA is the only catabolic gene of a novel composite transposon (Tn6311), located in a novel low copy number plasmid (pARLON1) harbouring a putative T4SS of the class FATA. pARLON1 had an ANI value of 88.2% with contig 18 from Agrococcus casei LMG 22410^T draft genome. Such results suggest that pARLON1 is related to genomic elements of other Actinobacteria, although Tn6311 was observed only in strain ON4^T. Furthermore, genomic and transcriptomic data demonstrated that the genes involved in ACA degradation are chromosomal. Based on their overexpression when growing in the presence of molinate, the enzymes potentially involved in the heterocyclic ring breakdown were predicted. Among these, the activity of a protein related to caprolactone hydrolase was demonstrated using heterologous expression. However, further studies are needed to confirm the role of the other putative enzymes.

The metabolic potential of plastics as biotechnological carbon sources - Review and targets for the future

The plastic crisis requires drastic measures, especially for the plastics' end-of-life. Mixed plastic fractions are currently difficult to recycle, but microbial metabolism might open new pathways. With new technologies for degradation of plastics to oligo- and monomers, these carbon sources can be used in biotechnology for the upcycling of plastic waste to valuable products, such as bioplastics and biosurfactants. We briefly summarize well-known monomer degradation pathways and computed their theoretical yields for industrially interesting products. With this information in hand, we calculated replacement scenarios of existing fossil-based synthesis routes for the same products. Thereby, we highlight fossil-based products for which plastic monomers might be attractive alternative carbon sources. Notably, not the highest yield of product on substrate of the biochemical route, but rather the (in-)efficiency of the petrochemical routes (i.e., carbon, energy use) determines the potential of biochemical plastic upcycling. Our results might serve as a guide for future metabolic engineering efforts towards a sustainable plastic economy.

Recent endeavors in microbial remediation of micro- and nanoplastics

Petrochemical plastics are frequently utilized in our daily lives for various purposes such as packaging and transportation, but their burden on the environment is considered one of the most man-made pollution crises. These pollutants are slowly fragmented in the environment into microplastics and nanoplastics by consolidated actions of abiotic and biotic factors. Microplastics and nanoplastics can easily be dispersed in the atmosphere and be harmful to all kinds of life. As a result, the remediation of micro- and nanoplastics has recently received a tremendous research impetus in the realm of an ecologically benign approach, notably microbial-based remediation. Thus, the current article looks at the formation, properties, analysis, and biological effects of micro- and nanoplastics. The content is then streamlined towards a comprehensive discussion on microbial-mediated degradation of microplastics and nanoplastics, with an emphasis on front-line bacteria and enzymes, as well as remediation mechanisms. Further, technologies for the removal of microplastics and nanoplastics from the environment are presented for possible remedial considerations. An attempt is also made to highlight the practical snags of microbial plastic degradation while aiming to alleviate the environmental burden of plastic waste.

Anchor peptides promote degradation of mixed plastics for recycling

Resource stewardship and sustainable use of natural resources is mandatory for a circular plastic economy. The discovery of microbes and enzymes that can selectively degrade mixed-plastic waste enables to recycle plastics. Knowledge on how to achieve efficient and selective enzymatic plastic degradation is a key prerequisite for biocatalytic recycling of plastics. Wild-type natural polymer degrading enzymes such as cellulases pose often selective non-catalytic binding domains that facilitate a targeting and efficient degradation of polymeric substrates. Recently identified polyester hydrolases with synthetic polymer degrading activities, however, lack in general such selective domains. Inspired by nature, we herein report a protocol for the identification and engineering of anchor peptides which serve as non-catalytic binding domains specifically toward synthetic plastics. The identified anchor peptides hold the promise to be fused to known plastic degrading enzymes and thereby enhance the efficiency of biocatalytic plastic recycling processes.

Structural and functional characterization of nylon hydrolases

Biodegradation of synthetic polymers is recognized as a useful way to reduce their environmental load and pollution, loss of natural resources, extensive energy consumption, and generation of greenhouse gases. The potential use of enzymes responsible for the degradation of the targeted polymers is an effective approach which enables the conversion of the used polymers to original monomers and/or other useful compounds. In addition, the enzymes are expected to be applicable in industrial processes such as improving the surface structures of the polymers. Especially, conversion of the solid polymers to soluble oligomers/monomers is a key step for the biodegradation of the polymers. Regarding the hydrolysis of polyamides, three enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (NylA), 6-aminohexanoate-dimer hydrolase (NylB), and 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC), are found in several bacterial strains. In this chapter, we describe our approach for the screening of microorganisms which degrade nylons and related compounds; preparation of substrates; assay of hydrolytic activity for soluble and insoluble substrates; and X-ray crystallographic and computational approaches for analysis of structure and catalytic mechanisms of the nylon-degrading enzymes.

Isolation and genomic analysis of 11-aminoundecanoic acid-degrading bacterium Pseudomonas sp. JG-B from nylon 11 enrichment culture

Nylon 11 is a polymer synthesized from 11-aminoundecanoic acid, and widely used in commercial manufacturing. In this study, we describe the isolation of the first organism capable of metabolizing 11-aminoundecanoic acid from nylon 11 enrichment culture. The strain shows rapid growth on 11-aminoundecanoic acid as a sole source of carbon, nitrogen, and energy. Furthermore, the genome sequence of strain JG-B was deciphered and shown to belong to genus Pseudomonas. Many genes encoding putative extracellular hydrolases, as well as homologues of nylon 6 hydrolases (NylB and NylA) were identified, suggesting the metabolic versatility and possibility that this organism could also depolymerase nylon 11 polymers.

Plastics: Environmental and Biotechnological Perspectives on Microbial Degradation

Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.

Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism

The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest K_M values (highest affinity) and highest specificity constant (k_cat /K_M ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).

Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics

Some bacterial cultures are capable of growth on caprolactam as sole carbon and nitrogen source, but the enzymes of the catabolic pathway have not been described. We isolated a caprolactam-degrading strain of Pseudomonas jessenii from soil and identified proteins and genes putatively involved in caprolactam metabolism using quantitative mass spectrometry-based proteomics. This led to the discovery of a caprolactamase and an aminotransferase that are involved in the initial steps of caprolactam conversion. Additionally, various proteins were identified that likely are involved in later steps of the pathway. The caprolactamase consists of two subunits and demonstrated high sequence identity to the 5-oxoprolinases. Escherichia coli cells expressing this caprolactamase did not convert 5-oxoproline but were able to hydrolyze caprolactam to form 6-aminocaproic acid in an ATP-dependent manner. Characterization of the aminotransferase revealed that the enzyme deaminates 6-aminocaproic acid to produce 6-oxohexanoate with pyruvate as amino acceptor. The amino acid sequence of the aminotransferase showed high similarity to subgroup II ω-aminotransferases of the PLP-fold type I proteins. Finally, analyses of the genome sequence revealed the presence of a caprolactam catabolism gene cluster comprising a set of genes involved in the conversion of caprolactam to adipate.