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32 pages, 7600 KiB

Open AccessArticle

Functional Classification and Characterization of the Fungal Glycoside Hydrolase 28 Protein Family

by Fernando Villarreal, Nicolás Stocchi and Arjen ten Have

J. Fungi 2022, 8(3), 217; https://doi.org/10.3390/jof8030217 - 22 Feb 2022

Cited by 4 | Viewed by 2244

Pectin is a major constituent of the plant cell wall, comprising compounds with important industrial applications such as homogalacturonan, rhamnogalacturonan and xylogalacturonan. A large array of enzymes is involved in the degradation of this amorphous substrate. The Glycoside Hydrolase 28 (GH28) family includes [...] Read more.

Pectin is a major constituent of the plant cell wall, comprising compounds with important industrial applications such as homogalacturonan, rhamnogalacturonan and xylogalacturonan. A large array of enzymes is involved in the degradation of this amorphous substrate. The Glycoside Hydrolase 28 (GH28) family includes polygalacturonases (PG), rhamnogalacturonases (RG) and xylogalacturonases (XG) that share a structure of three to four pleated β-sheets that form a rod with the catalytic site amidst a long, narrow groove. Although these enzymes have been studied for many years, there has been no systematic analysis. We have collected a comprehensive set of GH28 encoding sequences to study their evolution in fungi, directed at obtaining a functional classification, as well as at the identification of substrate specificity as functional constraint. Computational tools such as Alphafold, Consurf and MEME were used to identify the subfamilies’ characteristics. A hierarchic classification defines the major classes of endoPG, endoRG and endoXG as well as three exoPG classes. Ascomycete endoPGs are further classified in two subclasses whereas we identify four exoRG subclasses. Diversification towards exomode is explained by loops that appear inserted in a number of turns. Substrate-driven diversification can be identified by various specificity determining positions that appear to surround the binding groove. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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20 pages, 3572 KiB

Open AccessArticle

Regulation of the Leucine Metabolism in Mortierella alpina

by Robin Sonnabend, Lucas Seiler and Markus Gressler

J. Fungi 2022, 8(2), 196; https://doi.org/10.3390/jof8020196 - 18 Feb 2022

Cited by 6 | Viewed by 2768

Abstract

The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely [...] Read more.

The oleaginous fungus Mortierella alpina is a safe source of polyunsaturated fatty acids (PUFA) in industrial food and feed production. Besides PUFA production, pharmaceutically relevant surface-active and antimicrobial oligopeptides were isolated from this basal fungus. Both production of fatty acids and oligopeptides rely on the biosynthesis and high turnover of branched-chain-amino acids (BCAA), especially l-leucine. However, the regulation of BCAA biosynthesis in basal fungi is largely unknown. Here, we report on the regulation of the leucine, isoleucine, and valine metabolism in M. alpina. In contrast to higher fungi, the biosynthetic genes for BCAA are hardly transcriptionally regulated, as shown by qRT-PCR analysis, which suggests a constant production of BCAAs. However, the enzymes of the leucine metabolism are tightly metabolically regulated. Three enzymes of the leucine metabolism were heterologously produced in Escherichia coli, one of which is inhibited by allosteric feedback loops: The key regulator is the α-isopropylmalate synthase LeuA1, which is strongly disabled by l-leucine, α-ketoisocaproate, and propionyl-CoA, the precursor of the odd-chain fatty acid catabolism. Its gene is not related to homologs from higher fungi, but it has been inherited from a phototrophic ancestor by horizontal gene transfer. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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26 pages, 3094 KiB

Open AccessArticle

In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi

by Małgorzata Orłowska and Anna Muszewska

J. Fungi 2022, 8(1), 67; https://doi.org/10.3390/jof8010067 - 09 Jan 2022

Cited by 2 | Viewed by 2640

Abstract

Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes [...] Read more.

Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes (carbohydrate-active enzymes), peptidases and transporters that serve multiple biological roles connected to, e.g., metabolism and nutrients intake. In order to study the link between ecology and its genomic underpinnings in a more comprehensive manner, we carried out a systematic in silico survey of protein family expansions and losses among EDF with diverse lifestyles. We found that 86 protein families are represented differently according to EDF ecological features (assessed by median count differences). Among these there are 19 families of proteases, 43 CAZymes and 24 transporters. Some of these protein families have been recognized before as serine and metallopeptidases, cellulases and other nutrition-related enzymes. Other clearly pronounced differences refer to cell wall remodelling and glycosylation. We hypothesize that these protein families altogether define the preliminary fungal adaptasome. However, our findings need experimental validation. Many of the protein families have never been characterized in fungi and are discussed in the light of fungal ecology for the first time. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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15 pages, 2108 KiB

Open AccessArticle

Enzymatic Bioprospecting of Fungi Isolated from a Tropical Rainforest in Mexico

by Karla Peraza-Jiménez, Susana De la Rosa-García, José Javier Huijara-Vasconselos, Manuela Reyes-Estebanez and Sergio Gómez-Cornelio

J. Fungi 2022, 8(1), 22; https://doi.org/10.3390/jof8010022 - 28 Dec 2021

Cited by 6 | Viewed by 2824

Abstract

The humid tropical environment provides an ideal place for developing a high diversity of plants; this is why it is an interesting site for the enzymatic bioprospecting of fungi that are responsible for the recycling of organic matter in an efficient and accelerated [...] Read more.

The humid tropical environment provides an ideal place for developing a high diversity of plants; this is why it is an interesting site for the enzymatic bioprospecting of fungi that are responsible for the recycling of organic matter in an efficient and accelerated way and whose enzymes could have multiple biotechnological applications. For this study, 1250 isolates of macroscopic and microscopic fungal morphotypes were collected from soil, leaf litter, and wood. One hundred and fifty strains (50 from each source) were selected for the enzymatic screening. From the first phase, 51 strains with positive activity for laccase, protease, amylase, xylanase, and lipase enzymes were evaluated, of which 20 were isolated from leaf litter, 18 from the soil, and 13 from wood. The 10 best strains were selected for the enzymatic quantification, considering the potency index and the production of at least two enzymes. High laccase activity was detected for Trametes villosa FE35 and Marasmius sp. CE25 (1179 and 710.66 U/mg, respectively), while Daedalea flavida PE47 showed laccase (521.85 U/mg) and protease activities (80.66 U/mg). Fusarium spp. PH79 and FS400 strains had amylase (14.0 U/mg, 49.23 U/mg) and xylanase activities (40.05 U/mg, 36.03 U/mg) respectively. These results confirm the enzymatic potential of fungi that inhabit little-explored tropical rainforests with applications in industry. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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18 pages, 3160 KiB

Open AccessArticle

Characterization of Fungal FAD-Dependent AA3_2 Glucose Oxidoreductases from Hitherto Unexplored Phylogenetic Clades

by Sudarma Dita Wijayanti, Leander Sützl, Adèle Duval and Dietmar Haltrich

J. Fungi 2021, 7(10), 873; https://doi.org/10.3390/jof7100873 - 17 Oct 2021

Cited by 6 | Viewed by 2346

Abstract

The CAZy auxiliary activity family 3 (AA3) comprises FAD-dependent enzymes belonging to the superfamily of glucose-methanol-choline (GMC) oxidoreductases. Glucose oxidase (GOx; EC 1.1.3.4) and glucose dehydrogenase (GDH; EC 1.1.5.9) are part of subfamily AA3_2 and catalyze the oxidation of β-D-glucose at its anomeric [...] Read more.

The CAZy auxiliary activity family 3 (AA3) comprises FAD-dependent enzymes belonging to the superfamily of glucose-methanol-choline (GMC) oxidoreductases. Glucose oxidase (GOx; EC 1.1.3.4) and glucose dehydrogenase (GDH; EC 1.1.5.9) are part of subfamily AA3_2 and catalyze the oxidation of β-D-glucose at its anomeric carbon to D-glucono-1,5-lactone. Recent phylogenetic analysis showed that AA3_2 glucose oxidoreductases can be grouped into four major clades, GOx I and GDH I–III, and in minor clades such as GOx II or distinct subclades. This wide sequence space of AA3_2 glucose oxidoreductases has, however, not been studied in detail, with mainly members of GOx I and GDH I studied biochemically or structurally. Here, we report the biochemical characterization of four fungal glucose oxidoreductases from distinct, hitherto unexplored clades or subclades. The enzyme from Aureobasidium subglaciale, belonging to the minor GOx II clade, showed a typical preference for oxygen and glucose, confirming the correct annotation of this clade. The other three enzymes exhibited strict dehydrogenase activity with different substrate specificities. GDH II from Trichoderma virens showed an almost six-fold higher catalytic efficiency for maltose compared to glucose. The preferred substrate for the two GDH III enzymes from Rhizoctonia solani and Ustilago maydis was gentiobiose, a β(1→6) disaccharide, as judged from the catalytic efficiency. Overall, the newly studied AA3_2 glucose oxidoreductases showed a much broader substrate spectrum than the archetypal GOx from Aspergillus niger, which belongs to clade GOx I. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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14 pages, 645 KiB

Open AccessArticle

Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica

by Felix Heeger, Elizabeth C. Bourne, Christian Wurzbacher, Elisabeth Funke, Anna Lipzen, Guifen He, Vivian Ng, Igor V. Grigoriev, Dietmar Schlosser and Michael T. Monaghan

J. Fungi 2021, 7(10), 854; https://doi.org/10.3390/jof7100854 - 12 Oct 2021

Cited by 7 | Viewed by 2392

Abstract

Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited [...] Read more.

Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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17 pages, 3421 KiB

Open AccessArticle

Immobilized Forms of the Ophiostoma piceae Lipase for Green Synthesis of Biodiesel. Comparison with Eversa Transform 2.0 and Cal A

by María Molina-Gutiérrez, Lorena Alcaraz, Félix A. López, Leonor Rodríguez-Sánchez, María Jesús Martínez and Alicia Prieto

J. Fungi 2021, 7(10), 822; https://doi.org/10.3390/jof7100822 - 30 Sep 2021

Cited by 8 | Viewed by 1663

Abstract

In this work, we analyzed the suitability of a versatile recombinant lipase, secreted by Ophiostoma piceae (OPEr) and produced in Pichia pastoris, as a catalyst of the synthesis of biodiesel. The enzyme was immobilized by five covalent procedures and by hydrophobicity [...] Read more.

In this work, we analyzed the suitability of a versatile recombinant lipase, secreted by Ophiostoma piceae (OPEr) and produced in Pichia pastoris, as a catalyst of the synthesis of biodiesel. The enzyme was immobilized by five covalent procedures and by hydrophobicity on functionalized nanoparticles of magnetite or of a novel Zn/Mn oxide named G1. Then, they were tested for green production of biodiesel by solventless enzymatic transesterification of discarded cooking oil and methanol (1:4) at 25 °C. The results were compared with those shown by free OPEr and the commercial lipases Eversa^® and Cal A^®. Several preparations with immobilized OPEr produced high synthesis yields (>90% transesterification), comparable to those obtained with Eversa^®, the commercial enzyme designed for this application. Three of the biocatalysts maintained their catalytic efficiency for nine cycles. The process catalyzed by AMNP-CH-OPEr was scaled from 500 µL to 25 mL (50 times), improving its efficiency. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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23 pages, 5685 KiB

Open AccessArticle

Structural Insight into a Yeast Maltase—The BaAG2 from Blastobotrys adeninivorans with Transglycosylating Activity

by Karin Ernits, Christian Kjeldsen, Karina Persson, Eliis Grigor, Tiina Alamäe and Triinu Visnapuu

J. Fungi 2021, 7(10), 816; https://doi.org/10.3390/jof7100816 - 29 Sep 2021

Cited by 4 | Viewed by 2866

Abstract

An early-diverged yeast, Blastobotrys (Arxula) adeninivorans (Ba), has biotechnological potential due to nutritional versatility, temperature tolerance, and production of technologically applicable enzymes. We have biochemically characterized from the Ba type strain (CBS 8244) the GH13-family maltase BaAG2 with [...] Read more.

An early-diverged yeast, Blastobotrys (Arxula) adeninivorans (Ba), has biotechnological potential due to nutritional versatility, temperature tolerance, and production of technologically applicable enzymes. We have biochemically characterized from the Ba type strain (CBS 8244) the GH13-family maltase BaAG2 with efficient transglycosylation activity on maltose. In the current study, transglycosylation of sucrose was studied in detail. The chemical entities of sucrose-derived oligosaccharides were determined using nuclear magnetic resonance. Several potentially prebiotic oligosaccharides with α-1,1, α-1,3, α-1,4, and α-1,6 linkages were disclosed among the products. Trisaccharides isomelezitose, erlose, and theanderose, and disaccharides maltulose and trehalulose were dominant transglycosylation products. To date no structure for yeast maltase has been determined. Structures of the BaAG2 with acarbose and glucose in the active center were solved at 2.12 and 2.13 Å resolution, respectively. BaAG2 exhibited a catalytic domain with a (β/α)₈-barrel fold and Asp216, Glu274, and Asp348 as the catalytic triad. The fairly wide active site cleft contained water channels mediating substrate hydrolysis. Next to the substrate-binding pocket an enlarged space for potential binding of transglycosylation acceptors was identified. The involvement of a Glu (Glu309) at subsite +2 and an Arg (Arg233) at subsite +3 in substrate binding was shown for the first time for α-glucosidases. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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17 pages, 1668 KiB

Open AccessArticle

Biocatalytic Syntheses of Antiplatelet Metabolites of the Thienopyridines Clopidogrel and Prasugrel Using Fungal Peroxygenases

by Jan Kiebist, Kai-Uwe Schmidtke, Marina Schramm, Rosalie König, Stephan Quint, Johannes Kohlmann, Ralf Zuhse, René Ullrich, Martin Hofrichter and Katrin Scheibner

J. Fungi 2021, 7(9), 752; https://doi.org/10.3390/jof7090752 - 13 Sep 2021

Cited by 4 | Viewed by 2492

Abstract

Antithrombotic thienopyridines, such as clopidogrel and prasugrel, are prodrugs that undergo a metabolic two-step bioactivation for their pharmacological efficacy. In the first step, a thiolactone is formed, which is then converted by cytochrome P450-dependent oxidation via sulfenic acids to the active thiol metabolites. [...] Read more.

Antithrombotic thienopyridines, such as clopidogrel and prasugrel, are prodrugs that undergo a metabolic two-step bioactivation for their pharmacological efficacy. In the first step, a thiolactone is formed, which is then converted by cytochrome P450-dependent oxidation via sulfenic acids to the active thiol metabolites. These metabolites are the active compounds that inhibit the platelet P2Y₁₂ receptor and thereby prevent atherothrombotic events. Thus far, described biocatalytic and chemical synthesis approaches to obtain active thienopyridine metabolites are rather complex and suffer from low yields. In the present study, several unspecific peroxygenases (UPOs, EC 1.11.2.1) known to efficiently mimic P450 reactions in vitro—but requiring only hydroperoxide as oxidant—were tested for biocatalytic one-pot syntheses. In the course of the reaction optimization, various parameters such as pH and reductant, as well as organic solvent and amount were varied. The best results for the conversion of 1 mM thienopyridine were achieved using 2 U mL⁻¹ of a UPO from agaric fungus Marasmius rotula (MroUPO) in a phosphate-buffered system (pH 7) containing 5 mM ascorbate, 2 mM h⁻¹ H₂O₂ and 20% acetone. The preparation of the active metabolite of clopidogrel was successful via a two-step oxidation with an overall yield of 25%. In the case of prasugrel, a cascade of porcine liver esterase (PLE) and MroUPO was applied, resulting in a yield of 44%. The two metabolites were isolated with high purity, and their structures were confirmed by MS and MS² spectrometry as well as NMR spectroscopy. The findings broaden the scope of UPO applications again and demonstrate that they can be effectively used for the selective synthesis of metabolites and late-state diversification of organic molecules, circumventing complex multistage chemical syntheses and providing sufficient material for structural elucidation, reference material, or cellular assays. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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15 pages, 10884 KiB

Open AccessArticle

Proline-Specific Fungal Peptidases: Genomic Analysis and Identification of Secreted DPP4 in Alkaliphilic and Alkalitolerant Fungi

by Nikita Alkin, Yakov Dunaevsky, Elena Elpidina, Galina Beljakova, Valeria Tereshchenkova, Irina Filippova and Mikhail Belozersky

J. Fungi 2021, 7(9), 744; https://doi.org/10.3390/jof7090744 - 10 Sep 2021

Cited by 3 | Viewed by 1888

Abstract

Proline-specific peptidases (PSP) play a crucial role in the processing of fungal toxins, pheromones, and intracellular signaling. They are of particular interest to biotechnology, as they are able to hydrolyze proline-rich oligopeptides that give a bitter taste to food and can also cause [...] Read more.

Proline-specific peptidases (PSP) play a crucial role in the processing of fungal toxins, pheromones, and intracellular signaling. They are of particular interest to biotechnology, as they are able to hydrolyze proline-rich oligopeptides that give a bitter taste to food and can also cause an autoimmune celiac disease. We performed in silico analysis of PSP homologs in the genomes of 42 species of higher fungi which showed the presence of PSP homologs characteristic of various kingdoms of living organisms and belonging to different families of peptidases, including homologs of dipeptidyl peptidase 4 (DPP4) and prolyl aminopeptidase 1 found in almost all the studied fungal species. Homologs of proliniminopeptidases from the S33 family absent in humans were also found. Several studied homologs are characteristic of certain taxonomic groups of fungi. Phylogenetic analysis suggests a duplication of ancestral DPP4 into transmembrane and secreted versions, which predate the split of ascomycete and basidiomycete lineages. Comparative biochemical analysis of DPP4 in alkaliphilic and alkali-tolerant strains of fungi showed that, notwithstanding some individual features of these enzymes, in both cases, the studied DPP4 are active and stable under alkaline conditions and at high salt concentrations, which makes them viable candidates for biotechnology and bioengineering. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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17 pages, 4493 KiB

Open AccessArticle

Enhanced Lignocellulolytic Enzyme Activities on Hardwood and Softwood during Interspecific Interactions of White- and Brown-Rot Fungi

by Junko Sugano, Ndegwa Maina, Janne Wallenius and Kristiina Hildén

J. Fungi 2021, 7(4), 265; https://doi.org/10.3390/jof7040265 - 31 Mar 2021

Cited by 12 | Viewed by 2934

Abstract

Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying [...] Read more.

Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying fungal species have traditionally been classified as white-rot and brown-rot fungi, which differ in their decay mechanism and enzyme repertoire. To mimic the species interaction during wood decomposition, we have cultivated the white-rot fungus, Bjerkandera adusta, and two brown-rot fungi, Gloeophyllum sepiarium and Antrodia sinuosa, in single and co-cultivations on softwood and hardwood. We compared their extracellular hydrolytic carbohydrate-active and oxidative lignin-degrading enzyme activities and production profiles. The interaction of white-rot and brown-rot species showed enhanced (hemi)cellulase activities on birch and spruce-supplemented cultivations. Based on the enzyme activity profiles, the combination of B. adusta and G. sepiarium facilitated birch wood degradation, whereas B. adusta and A. sinuosa is a promising combination for efficient degradation of spruce wood, showing synergy in β-glucosidase (BGL) and α-galactosidase (AGL) activity. Synergistic BGL and AGL activity was also detected on birch during the interaction of brown-rot species. Our findings indicate that fungal interaction on different woody substrates have an impact on both simultaneous and sequential biocatalytic activities. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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Review

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17 pages, 5405 KiB

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Fungal Enzymes as Catalytic Tools for Polyethylene Terephthalate (PET) Degradation

by Seyedehazita Ahmaditabatabaei, Godfrey Kyazze, Hafiz M. N. Iqbal and Tajalli Keshavarz

J. Fungi 2021, 7(11), 931; https://doi.org/10.3390/jof7110931 - 02 Nov 2021

Cited by 22 | Viewed by 6877

Abstract

The ubiquitous persistence of plastic waste in diverse forms and different environmental matrices is one of the main challenges that modern societies are facing at present. The exponential utilization and recalcitrance of synthetic plastics, including polyethylene terephthalate (PET), results in their extensive accumulation, [...] Read more.

The ubiquitous persistence of plastic waste in diverse forms and different environmental matrices is one of the main challenges that modern societies are facing at present. The exponential utilization and recalcitrance of synthetic plastics, including polyethylene terephthalate (PET), results in their extensive accumulation, which is a significant threat to the ecosystem. The growing amount of plastic waste ending up in landfills and oceans is alarming due to its possible adverse effects on biota. Thus, there is an urgent need to mitigate plastic waste to tackle the environmental crisis of plastic pollution. With regards to PET, there is a plethora of literature on the transportation route, ingestion, environmental fate, amount, and the adverse ecological and human health effects. Several studies have described the deployment of various microbial enzymes with much focus on bacterial-enzyme mediated removal and remediation of PET. However, there is a lack of consolidated studies on the exploitation of fungal enzymes for PET degradation. Herein, an effort has been made to cover this literature gap by spotlighting the fungi and their unique enzymes, e.g., esterases, lipases, and cutinases. These fungal enzymes have emerged as candidates for the development of biocatalytic PET degradation processes. The first half of this review is focused on fungal biocatalysts involved in the degradation of PET. The latter half explains three main aspects: (1) catalytic mechanism of PET hydrolysis in the presence of cutinases as a model fungal enzyme, (2) limitations hindering enzymatic PET biodegradation, and (3) strategies for enhancement of enzymatic PET biodegradation. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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24 pages, 808 KiB

Open AccessReview

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi

by Grace N. Ijoma, Sylvie M. Heri, Tonderayi S. Matambo and Memory Tekere

J. Fungi 2021, 7(9), 700; https://doi.org/10.3390/jof7090700 - 27 Aug 2021

Cited by 3 | Viewed by 3823

Abstract

Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. [...] Read more.

Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation. Full article

(This article belongs to the Special Issue Fungal Enzymes 2021)

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