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

Synthesis of Short-Chain Alkyl Butyrate through Esterification Reaction Using Immobilized Rhodococcus Cutinase and Analysis of Substrate Specificity through Molecular Docking

Alkyl butyrate with fruity flavor is known as an important additive in the food industry. We synthesized various alkyl butyrates from various fatty alcohol and butyric acid using immobilized Rhodococcus cutinase (Rcut). Esterification reaction was performed in a non-aqueous system including heptane, isooctane, hexane, and cyclohexane. As a result of performing the alkyl butyrate synthesis reaction using alcohols of various chain lengths, it was found that the preference for the alcohol substrate had the following order: C6 > C4 > C8 > C10 > C2. Through molecular docking analysis, it was found that the greater the hydrophobicity of alcohol, the higher the accessibility to the active site of the enzyme. However, since the number of torsions increased as the chain length increased, it became difficult for the hydroxyl oxygen of the alcohol to access the ^γO of serine at the enzyme active site. These molecular docking results were consistent with substrate preference results of the Rcut enzyme. The Rcut maintained the synthesis efficiency at least for 5 days in isooctane solvent. We synthesized as much as 452 mM butyl butyrate by adding 100 mM substrate daily for 5 days and performing the reaction. These results show that Rcut is an efficient enzyme for producing alkyl butyrate used in the food industry.

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.

Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes

Polyethylene terephthalate (PET) is one of the most commonly used polyester plastics worldwide but is extremely difficult to be hydrolyzed in a natural environment. PET plastic is an inexpensive, lightweight, and durable material, which can readily be molded into an assortment of products that are used in a broad range of applications. Most PET is used for single-use packaging materials, such as disposable consumer items and packaging. Although PET plastics are a valuable resource in many aspects, the proliferation of plastic products in the last several decades have resulted in a negative environmental footprint. The long-term risk of released PET waste in the environment poses a serious threat to ecosystems, food safety, and even human health in modern society. Recycling is one of the most important actions currently available to reduce these impacts. Current clean-up strategies have attempted to alleviate the adverse impacts of PET pollution but are unable to compete with the increasing quantities of PET waste exposed to the environment. In this review paper, current PET recycling methods to improve life cycle and waste management are discussed, which can be further implemented to reduce plastics pollution and its impacts on health and environment. Compared with conventional mechanical and chemical recycling processes, the biotechnological recycling of PET involves enzymatic degradation of the waste PET and the followed bioconversion of degraded PET monomers into value-added chemicals. This approach creates a circular PET economy by recycling waste PET or upcycling it into more valuable products with minimal environmental footprint.

Secretory production of an engineered cutinase in Bacillus subtilis for efficient biocatalytic depolymerization of polyethylene terephthalate

Polyethylene terephthalate (PET) waste has caused serious environmental pollution. Recently, PET depolymerization by enzymes with PET-depolymerizing activity has received attention as a solution to recycle PET. An engineered variant of leaf-branch compost cutinase (293 amino acid), ICCG (Phe243Ile/Asp238Cys/Ser283Cys/Tyr127Gly), showed excellent depolymerizing activity toward PET at 72 °C, which was the highest depolymerizing activity and thermo-stability ever reported in previous works. However, this enzyme was only produced by heterologous expression in the cytoplasm of Escherichia coli, which requires complex separation and purification steps. To simplify the purification steps of ICCG, we developed a secretory production system using Bacillus subtilis and its 174 types of N-terminal signal peptides. The recombinant strain expressing ICCG with the signal peptide of serine protease secreted the highest amount (9.4 U/mL) of ICCG. We improved the production of ICCG up to 22.6 U/mL (85 μg/mL) by performing batch fermentation of the selected strain in 2 L working volume using a 5-L fermenter, and prepared the crude ICCG solution by concentrating the culture supernatant. The recombinant ICCG successfully depolymerized a PET film with 37% crystallinity at 37 °C and 70 °C. In this study, we developed a secretory production system of the engineered cutinase with PET-depolymerizing activity to obtain high amounts of the enzyme by a relatively simple purification method. This system will contribute to the recycling of PET waste via a more efficient and environmentally friendly method based on enzymes with PET-depolymerizing activity.

Accessory enzymes of hypercellulolytic Penicillium funiculosum facilitate complete saccharification of sugarcane bagasse

BACKGROUND

Sugarcane bagasse (SCB) is an abundant feedstock for second-generation bioethanol production. This complex biomass requires an array of carbohydrate active enzymes (CAZymes), mostly from filamentous fungi, for its deconstruction to monomeric sugars for the production of value-added fuels and chemicals. In this study, we evaluated the repertoire of proteins in the secretome of a catabolite repressor-deficient strain of Penicillium funiculosum, PfMig1⁸⁸, in response to SCB induction and examined their role in the saccharification of SCB.

RESULTS

A systematic approach was developed for the cultivation of the fungus with the aim of producing and understanding arrays of enzymes tailored for saccharification of SCB. To achieve this, the fungus was grown in media supplemented with different concentrations of pretreated SCB (0-45 g/L). The profile of secreted proteins was characterized by enzyme activity assays and liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 280 proteins were identified in the secretome of PfMig1⁸⁸, 46% of them being clearly identified as CAZymes. Modulation of the cultivation media with SCB up to 15 g/L led to sequential enhancement in the secretion of hemicellulases and cell wall-modifying enzymes, including endo-β-1,3(4)-glucanase (GH16), endo-α-1,3-glucanase (GH71), xylanase (GH30), β-xylosidase (GH5), β-1,3-galactosidase (GH43) and cutinase (CE5). There was ~ 122% and 60% increases in β-xylosidase and cutinase activities, respectively. There was also a 36% increase in activities towards mixed-linked glucans. Induction of these enzymes in the secretome improved the saccharification performance to 98% (~ 20% increase over control), suggesting their synergy with core cellulases in accessing the recalcitrant region of SCB.

CONCLUSION

Our findings provide an insight into the enzyme system of PfMig1⁸⁸ for degradation of complex biomass such as SCB and highlight the importance of adding SCB to the culture medium to optimize the secretion of enzymes specific for the saccharification of sugarcane bagasse.

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172

BACKGROUND

Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail.

RESULTS

We sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy.

CONCLUSIONS

Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.

Biodiesel and flavor compound production using a novel promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from the psychrophilic bacterium Halocynthiibacter arcticus

BACKGROUND

Biodiesel and flavor compound production using enzymatic transesterification by microbial lipases provides mild reaction conditions and low energy cost compared to the chemical process. SGNH-type lipases are very effective catalysts for enzymatic transesterification due to their high reaction rate, great stability, relatively small size for convenient genetic manipulations, and ease of immobilization. Hence, it is highly important to identify novel SGNH-type lipases with high catalytic efficiencies and good stabilities.

RESULTS

A promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from Halocynthiibacter arcticus was catalytically characterized and functionally explored. HaSGNH1 displayed broad substrate specificity that included tert-butyl acetate, glucose pentaacetate, and p-nitrophenyl esters with excellent stability and high efficiency. Important amino acids (N83, M86, R87, F131, and I173F) around the substrate-binding pocket were shown to be responsible for catalytic activity, substrate specificity, and reaction kinetics. Moreover, immobilized HaSGNH1 was used to produce high yields of butyl and oleic esters.

CONCLUSIONS

This work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from H. arcticus. This is the first analysis on biodiesel and flavor synthesis using a cold-adapted halophilic SGNH-type lipase from a Halocynthiibacter species.

Phylogenetic re-evaluation of Thielavia with the introduction of a new family Podosporaceae

The genus Thielavia is morphologically defined by having non-ostiolate ascomata with a thin peridium composed of textura epidermoidea, and smooth, single-celled, pigmented ascospores with one germ pore. Thielavia is typified with Th. basicola that grows in close association with a hyphomycete which was traditionally identified as Thielaviopsis basicola. Besides Th. basicola exhibiting the mycoparasitic nature, the majority of the described Thielavia species are from soil, and some have economic and ecological importance. Unfortunately, no living type material of Th. basicola exists, hindering a proper understanding of the classification of Thielavia. Therefore, Thielavia basicola was neotypified by material of a mycoparasite presenting the same ecology and morphology as described in the original description. We subsequently performed a multi-gene phylogenetic analyses (rpb2, tub2, ITS and LSU) to resolve the phylogenetic relationships of the species currently recognised in Thielavia. Our results demonstrate that Thielavia is highly polyphyletic, being related to three family-level lineages in two orders. The redefined genus Thielavia is restricted to its type species, Th. basicola, which belongs to the Ceratostomataceae (Melanosporales) and its host is demonstrated to be Berkeleyomyces rouxiae, one of the two species in the "Thielaviopsis basicola" species complex. The new family Podosporaceae is sister to the Chaetomiaceae in the Sordariales and accommodates the re-defined genera Podospora, Trangularia and Cladorrhinum, with the last genus including two former Thielavia species (Th. hyalocarpa and Th. intermedia). This family also includes the genetic model species Podospora anserina, which was combined in Triangularia (as Triangularia anserina). The remaining Thielavia species fall in ten unrelated clades in the Chaetomiaceae, leading to the proposal of nine new genera (Carteria, Chrysanthotrichum, Condenascus, Hyalosphaerella, Microthielavia, Parathielavia, Pseudothielavia, Stolonocarpus and Thermothielavioides). The genus Canariomyces is transferred from Microascaceae (Microascales) to Chaetomiaceae based on its type species Can. notabilis. Canariomyces is closely related to the human-pathogenic genus Madurella, and includes three thielavia-like species and one novel species. Three monotypic genera with a chaetomium-like morph (Brachychaeta, Chrysocorona and Floropilus) are introduced to better resolve the Chaetomiaceae and the thielavia-like species in the family. Chrysocorona lucknowensis and Brachychaeta variospora are closely related to Acrophialophora and three newly introduced genera containing thielavia-like species; Floropilus chiversii is closely related to the industrially important and thermophilic species Thermothielavioides terrestris (syn. Th. terrestris). This study shows that the thielavia-like morph is a homoplastic form that originates from several separate evolutionary events. Furthermore, our results provide new insights into the taxonomy of Sordariales and the polyphyletic Lasiosphaeriaceae.

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.

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.