Cloning and characterization of a novel acidic cutinase from Sirococcus conigenus

Current Understanding on the Heterogenous Expression of Plastic Depolymerising Enzymes in Pichia pastoris

Enzymatic depolymerisation is increasingly recognised as a reliable and environmentally friendly method. The development of this technology hinges on the availability of high-quality enzymes and associated bioreaction systems for upscaling biodegradation. Microbial heterologous expression systems have been studied for meeting this demand. Among these systems, the Pichia pastoris expression system has emerged as a widely used platform for producing secreted heterologous proteins. This article provides an overview of studies involving the recombinant expression of polymer-degrading enzymes using the P. pastoris expression system. Research on P. pastoris expression of interested enzymes with depolymerising ability, including cutinase, lipase, and laccase, are highlighted in the review. The key factors influencing the heterologous expression of polymer-degrading enzymes in P. pastoris are discussed, shedding light on the challenges and opportunities in the development of depolymerising biocatalysts through the P. pastoris expression system.

Enzymes' Power for Plastics Degradation

Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.

A Review of the Fungi That Degrade Plastic

Plastic has become established over the world as an essential basic need for our daily life. Current global plastic production exceeds 300 million tons annually. Plastics have many characteristics such as low production costs, inertness, relatively low weight, and durability. The primary disadvantage of plastics is their extremely slow natural degradation. The latter results in an accumulation of plastic waste in nature. The amount of plastic waste as of 2015 was 6300 million tons worldwide, and 79% of this was placed in landfills or left in the natural environment. Moreover, recent estimates report that 12,000 million tons of plastic waste will have been accumulated on the earth by 2050. Therefore, it is necessary to develop an effective plastic biodegradation process to accelerate the natural degradation rate of plastics. More than 400 microbes have been identified as capable of plastic degradation. This is the first paper of the series on plastic-degrading fungi. This paper provides a summary of the current global production of plastic and plastic waste accumulation in nature. A list is given of all the plastic-degrading fungi recorded thus far, based on the available literature, and comments are made relating to the major fungal groups. In addition, the phylogenetic relationships of plastic-degrading fungi were analyzed using a combined ITS, LSU, SSU, TEF, RPB1, and RPB2 dataset consisting of 395 strains. Our results confirm that plastic-degrading fungi are found in eleven classes in the fungal phyla Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes, Saccharomycetes, and Sordariomycetes), Basidiomycota (Agaricomycetes, Microbotryomycetes, Tremellomycetes, Tritirachiomycetes, and Ustilaginomy-cetes), and Mucoromycota (Mucoromycetes). The taxonomic placement of plastic-degrading fungal taxa is briefly discussed. The Eurotiomycetes include the largest number of plastic degraders in the kingdom Fungi. The results presented herein are expected to influence the direction of future research on similar topics in order to find effective plastic-degrading fungi that can eliminate plastic wastes. The next publication of the series on plastic-degrading fungi will be focused on major metabolites, degradation pathways, and enzyme production in plastic degradation by fungi.

Phylogenetic analysis and in-depth characterization of functionally and structurally diverse CE5 cutinases

Cutinases are esterases that release fatty acids from the apoplastic layer in plants. As they accept bulky and hydrophobic substrates, cutinases could be used in many applications, ranging from valorization of bark-rich side streams to plastic recycling. Advancement of these applications, however, requires deeper knowledge of cutinases' biodiversity and structure-function relationships. Here, we mined over 3000 members from carbohydrate esterase family 5 for putative cutinases and condensed it to 151 genes from known or putative lignocellulose-targeting organisms. The 151 genes were subjected to a phylogenetic analysis, which showed that cutinases with available crystal structures were phylogenetically closely related. We then selected nine phylogenic diverse cutinases for recombinant production and characterized their kinetic activity against para-nitrophenol substrates esterified with consecutively longer alkyl chains (pNP-C2 to C16). Each investigated cutinase had a unique activity fingerprint against the tested pNP substrates. The five enzymes with the highest activity on pNP-C12 and C16, indicative of activity on bulky hydrophobic compounds, were selected for in-depth kinetic and structure-function analysis. All five enzymes showed a decrease in kcat values with increasing substrate chain length, whereas KM values and binding energies (calculated from in silico docking analysis) improved. Two cutinases from Fusarium solani and Cryptococcus sp. exhibited outstandingly low KM values, resulting in high catalytic efficiencies toward pNP-C16. Docking analysis suggested that different clades of the phylogenetic tree may harbor enzymes with different modes of substrate interaction, involving a solvent-exposed catalytic triad, a lipase-like lid, or a clamshell-like active site possibly formed by flexible loops.

A Middle-Aged Enzyme Still in Its Prime: Recent Advances in the Field of Cutinases

Cutinases are α/β hydrolases, and their role in nature is the degradation of cutin. Such enzymes are usually produced by phytopathogenic microorganisms in order to penetrate their hosts. The first focused studies on cutinases started around 50 years ago. Since then, numerous cutinases have been isolated and characterized, aiming at the elucidation of their structure–function relations. Our deeper understanding of cutinases determines the applications by which they could be utilized; from food processing and detergents, to ester synthesis and polymerizations. However, cutinases are mainly efficient in the degradation of polyesters, a natural function. Therefore, these enzymes have been successfully applied for the biodegradation of plastics, as well as for the delicate superficial hydrolysis of polymeric materials prior to their functionalization. Even though research on this family of enzymes essentially began five decades ago, they are still involved in many reports; novel enzymes are being discovered, and new fields of applications arise, leading to numerous related publications per year. Perhaps the future of cutinases lies in their evolved descendants, such as polyesterases, and particularly PETases. The present article reviews the biochemical and structural characteristics of cutinases and cutinase-like hydrolases, and their applications in the field of bioremediation and biocatalysis.

High-level expression and characterization of a novel cutinase from Malbranchea cinnamomea suitable for butyl butyrate production

BACKGROUND

Butyl butyrate has been considered as a promising fuel source because it is a kind of natural ester which can be converted from renewable and sustainable lignocellulosic biomass. Compared with the conventional chemical methods for butyl butyrate production, the enzymatic approach has been demonstrated to be more attractive, mainly owing to the mild reaction conditions, high specificity, low energy consumption, and environmental friendliness. Cutinases play an important role in the butyl butyrate production process. However, the production level of cutinases is still relatively low. Thus, to identify novel cutinases suitable for butyl butyrate synthesis and enhance their yields is of great value in biofuel industry.

RESULTS

A novel cutinase gene (McCut) was cloned from a thermophilic fungus Malbranchea cinnamomea and expressed in Pichia pastoris. The highest cutinase activity of 12, 536 U/mL was achieved in 5-L fermentor, which is by far the highest production for a cutinase. McCut was optimally active at pH 8.0 and 45 °C. It exhibited excellent stability within the pH range of 3.0-10.5 and up to 75 °C. The cutinase displayed broad substrate specificity with the highest activity towards p-nitrophenyl butyrate and tributyrin. It was capable of hydrolyzing cutin, polycaprolactone, and poly(butylene succinate). Moreover, McCut efficiently synthesized butyl butyrate with a maximum esterification efficiency of 96.9% at 4 h. The overall structure of McCut was resolved as a typical α/β-hydrolase fold. The structural differences between McCut and Aspergillus oryzae cutinase in groove and loop provide valuable information for redesign of McCut. These excellent features make it useful in biosynthesis and biodegradation fields.

CONCLUSIONS

A novel cutinase from M. cinnamomea was identified and characterized for the first time. High-level expression by P. pastoris is by far the highest for a cutinase. The enzyme exhibited excellent stability and high esterification efficiency for butyl butyrate production, which may make it a good candidate in biofuel and chemical industries.

Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics

Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding.

Expression and characterization of a cutinase (AnCUT2) from Aspergillus niger

Cutin hydrolase (EC 3.1.1.74), an extracellular polyesterase found in pollens, bacteria and fungi, is an efficient catalyst that exhibits hydrolytic activity on a variety of water-soluble esters, synthetic fibers, plastics and triglycerides. Thus, cutinase can be used in various applications such as ester synthesis, bio-scouring, food and detergent industries. Ancut2 is one of five genes encoding cutinases present in the Aspergillus niger ATCC 10574 genome. The cDNA of Ancut2 comprising of an open reading frame of 816 bp encoding a protein of 271 amino acid residues, was isolated and expressed in Pichia pastoris. The partially purified recombinant cutinase exhibited a molecular mass of approximately 40 kDa. The enzyme showed highest activity at 40°C with a preference for acidic pH (5.0-6.0). AnCUT2 showed hydrolytic activity towards various p-nitrophenyl esters with preference towards shorter chain esters such as p-nitrophenyl butyrate (C4). Scanning Electron Microscopy demonstrated that AnCUT2 was capable of modifying surfaces of synthetic polycaprolactone and polyethylene terephthalate plastics. The properties of this enzyme suggest that it may be applied in synthetic fiber modification and fruit processing industries.

Three New Cutinases from the Yeast Arxula adeninivorans That Are Suitable for Biotechnological Applications

The genes ACUT1, ACUT2, and ACUT3, encoding cutinases, were selected from the genomic DNA of Arxula adeninivorans LS3. The alignment of the amino acid sequences of these cutinases with those of other cutinases or cutinase-like enzymes from different fungi showed that they all had a catalytic S-D-H triad with a conserved G-Y-S-Q-G domain. All three genes were overexpressed in A. adeninivorans using the strong constitutive TEF1 promoter. Recombinant 6× His (6h)-tagged cutinase 1 protein (p) from A. adeninivorans LS3 (Acut1-6hp), Acut2-6hp, and Acut3-6hp were produced and purified by immobilized-metal ion affinity chromatography and biochemically characterized using p-nitrophenyl butyrate as the substrate for standard activity tests. All three enzymes from A. adeninivorans were active from pH 4.5 to 6.5 and from 20 to 30°C. They were shown to be unstable under optimal reaction conditions but could be stabilized using organic solvents, such as polyethylene glycol 200 (PEG 200), isopropanol, ethanol, or acetone. PEG 200 (50%, vol/vol) was found to be the best stabilizing agent for all of the cutinases, and acetone greatly increased the half-life and enzyme activity (up to 300% for Acut3-6hp). The substrate spectra for Acut1-6hp, Acut2-6hp, and Acut3-6hp were quite similar, with the highest activity being for short-chain fatty acid esters of p-nitrophenol and glycerol. Additionally, they were found to have polycaprolactone degradation activity and cutinolytic activity against cutin from apple peel. The activity was compared with that of the 6× His-tagged cutinase from Fusarium solani f. sp. pisi (FsCut-6hp), also expressed in A. adeninivorans, as a positive control. A fed-batch cultivation of the best Acut2-6hp-producing strain, A. adeninivorans G1212/YRC102-ACUT2-6H, was performed and showed that very high activities of 1,064 U ml(-1) could be achieved even with a nonoptimized cultivation procedure.

Characterization of an acidic cold-adapted cutinase from Thielavia terrestris and its application in flavor ester synthesis

An acidic cutinase (TtcutB) from Thielavia terrestris CAU709 was purified to apparent homogeneity with 983 Um g(-1) specific activity. The molecular mass of the enzyme was estimated to be 27.3 and 27.9 kDa by SDS-PAGE and gel filtration, respectively. A peptide sequence homology search revealed no homologous cutinases from T. terrestris, except for one putative cutinase gene (XP003656017.1), indicating that TtcutB is a novel enzyme. TtcutB exhibited an acidic pH optimum of 4.0, and stability at pH 2.5-10.5. Optimal activity was at 55 °C, it was stable up to 65 °C, and retained over 30% activity at 0 °C. Km values toward p-nitrophenyl (pNP) acetate, pNP-butyrate and pNP-caproate were 8.3, 1.1 and 0.88 mM, respectively. The cutinase exhibited strong synthetic activity on flavor ester butyl butyrate under non-aqueous environment, and the highest esterification efficiency of 95% was observed under the optimized reaction conditions. The enzyme's unique biochemical properties suggest great potential in flavor esters-producing industries.

pH effects on the structural dynamics of cutinase from Trichoderma reesei: insights from molecular dynamics simulations

The influence of different pH conditions on conformational changes of Tr cutinase was investigated using molecular dynamics simulations.

A Cutinase from Trichoderma reesei with a lid-covered active site and kinetic properties of true lipases

Cutinases belong to the α/β-hydrolase fold family of enzymes and degrade cutin and various esters, including triglycerides, phospholipids and galactolipids. Cutinases are able to degrade aggregated and soluble substrates because, in contrast with true lipases, they do not have a lid covering their catalytic machinery. We report here the structure of a cutinase from the fungus Trichoderma reesei (Tr) in native and inhibitor-bound conformations, along with its enzymatic characterization. A rare characteristic of Tr cutinase is its optimal activity at acidic pH. Furthermore, Tr cutinase, in contrast with classical cutinases, possesses a lid covering its active site and requires the presence of detergents for activity. In addition to the presence of the lid, the core of the Tr enzyme is very similar to other cutinase cores, with a central five-stranded β-sheet covered by helices on either side. The catalytic residues form a catalytic triad involving Ser164, His229 and Asp216 that is covered by the two N-terminal helices, which form the lid. This lid opens in the presence of surfactants, such as β-octylglucoside, and uncovers the catalytic crevice, allowing a C11Y4 phosphonate inhibitor to bind to the catalytic serine. Taken together, these results reveal Tr cutinase to be a member of a new group of lipolytic enzymes resembling cutinases but with kinetic and structural features of true lipases and a heightened specificity for long-chain triglycerides.