The nature and mode of action of the cellulolytic component C1 of Trichoderma koningii on native cellulose

Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma

Introduction

Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns.

Methods

The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes.

Results

T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers.

Discussion

The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

Economically viable production of cellulosic biofuels requires operation at high solids loadings—on the order of 15 wt%. To this end we characterize Nature’s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes—all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.

Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications

Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various "omics" technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields.

Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives

Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.

An alkaline and surfactant-tolerant lipase from Trichoderma lentiforme ACCC30425 with high application potential in the detergent industry

Alkaline lipases with adaptability to low temperatures and strong surfactant tolerance are favorable for application in the detergent industry. In the present study, a lipase-encoding gene, TllipA, was cloned from Trichoderma lentiforme ACCC30425 and expressed in Pichia pastoris GS115. The purified recombinant TlLipA was found to have optimal activities at 50 °C and pH 9.5 and retain stable over the pH range of 6.0–10.0 and 40 °C and below. When using esters of different lengths as substrates, TlLipA showed preference for the medium length p-nitrophenyl octanoate. In comparison to commercial lipases, TlLipA demonstrated higher tolerance to various surfactants (SDS, Tween 20, and Triton X100) and retained more activities after incubation with Triton X100 for up to 24 h. These favorable characteristics make TlLipA prospective as an additive in the detergent industry.

Strong cellulase inhibition by Mannan polysaccharides in cellulose conversion to sugars

Cellulase enzymes contribute a major fraction of the total cost for biological conversion of lignocellulosic biomass to fuels and chemicals. Although a several fold reduction in cellulase production costs and enhancement of cellulase activity and stability have been reported in recent years, sugar yields are still lower at low enzyme doses than desired commercially. We recently reported that hemicellulose xylan and its oligomers strongly inhibit cellulase and that supplementation of cellulase with xylanase and β-xylosidase would significantly reduce such inhibition. In this study, mannan polysaccharides and their enzymatically prepared hydrolyzates were discovered to be strongly inhibitory to fungal cellulase in cellulose conversion (>50% drop in % relative conversion), even at a small concentration of 0.1 g/L, and inhibition was much greater than experienced by other known inhibitors such as cellobiose, xylooligomers, and furfural. Furthermore, cellulase inhibition dramatically increased with heteromannan loading and mannan substitution with galactose side units. In general, enzymatically prepared hydrolyzates were less inhibitory than their respective mannan polysaccharides except highly substituted ones. Supplementation of cellulase with commercial accessory enzymes such as xylanase, pectinase, and β-glucosidase was effective in greatly relieving inhibition but only for less substituted heteromannans. However, cellulase supplementation with purified heteromannan specific enzymes relieved inhibition by these more substituted heteromannans as well, suggesting that commercial preparations need to have higher amounts of such activities to realize high sugar yields at the low enzyme protein loadings needed for low cost fuels production.

Production of cellulases and saccharification of lignocellulosics by A. Micromonospora sp

A locally isolated strain of Micromonospora sp. when grown on different natural cellulosic substrates gave the highest activity of carboxymethylcellulase (34 U/ml) and Avicelase (0.9 U/ml) on rice straw. Sugar cane bagasse was also a good substrate for growth and cellulase production. With commercial cellulosic substrates, highest carboxymethylcellulase (90 U/ml) and Avicelase (2.8 U/ml) activities were when the organism grew on xylan. Saccharification of sugar cane bagasse and rice straw by enzyme preparations of the organism grown on the respective substrates released 5.6 and 5.8 mg reducing sugar/ml. With all enzyme preparations, bagasse was more easily saccharified than rice straw.

Kinetics of the enzymatic hydrolysis of cellulose

Enzymatic hydrolysis of cellulose for sugar production offers advantages of higher conversion, minimal by-product formation, low energy requirements, and mild operating conditions over other chemical conversions. The development of a kinetic model, based on observable, macroscopic properties of the overall system, is helpful in design and economic evaluation of processes for sugar conversion and ethanol production. A kinetic model is presented, incorporating enzyme adsorption, product inhibition, and considers a multiple enzyme and substrate system. This model was capable of simulating saccharification of a lignocellulosic material, rice straw, at high substrate (up to 333 g/L) and enzyme concentrations (up to 9.2 FPU/mL) that are common to proposed process designs.

Production and Characteristics of Avicel-Digesting and Non-Avicel-Digesting Cellobiohydrolases from Aspergillus ficum

Two immunologically related cellobiohydrolases, cellobiohydrolase I (CBH I) and cellobiohydrolase II (CBH II), were purified from Aspergillus ficum. The Avicel-adsorbable CBH I (molecular weight, 128,000) digested Avicel, cotton, and cellulose powder to cellobiose, but the Avicel-unadsorbable CBH II (molecular weight, 50,000) could not digest those substrates. Both enzymes hydrolyzed insoluble cellooligosaccharides (DP 25) to cellobiose. High-pressure liquid chromatographic analysis of soluble cellooligosaccharide hydrolysates revealed that both enzymes split off strictly cellobiose units from the nonreducing end of the cellulose chain with an exowise mechanism. CBH I showed glucosyltransferase activity, but CBH II did not. The N-bromosuccinimideoxidized CBH I was completely inactive but retained the ability to adsorb to Avicel. This suggested that CBH I has separate sites for binding to cellulose and for catalyzing cleavage of glycosidic linkages. Cellobiohydrolases were of two types, CBH I and CBH II. The former can adsorb to and digest Avicel, while the latter can do neither.

Enzymatic hydrolysis of cellulose: Visual characterization of the process

Cellulose from the Gram-negative bacterium Acetobacter xylinum has been used as a model substrate for visualizing the action of cellulase enzymes from the fungus Trichoderma reesei. High-resolution electron microscopy reveals that A. xylinum normally produces a ribbon of cellulose that is a composite of bundles of crystalline microfibrils. Visual patterns of the process of cellulose degradation have been established. Enzymes are initially observed bound to the cellulose ribbon. Within 10 min, the ribbon is split along its long axis into bundles of microfibrils which are subsequently thinned until they are completely dissolved within 30 min. Incubations with purified components of the cellulase enzyme system produced less dramatic changes in ribbon structure. Purified 1,4-beta-D-glucan cellobiohydrolase I (D) (EC 3.2.1.91) produced no visible change in cellulose structure. Purified endo-1,4-beta-D-glucanase IV (EC 3.2.1.4) produced some splaying of ribbons into microfibril bundles. In both cases, whole ribbons were present even after 60 min of incubation, visually confirming the synergistic mode of action of these enzymes.

Isolation of a Cellodextrinase from Bacteroides succinogenes

An enzyme which released the cellobiose group from p-nitrophenyl cellobioside was isolated from the periplasmic space of Bacteroides succinogenes grown on Avicel crystalline cellulose in a continuous cultivation system and separated from endoglucanases by column chromatography. The molecular weight of the enzyme was approximately 40,000, as estimated by gel filtration. The enzyme has an isoelectric point of 4.9. The enzyme exhibited low hydrolytic activity on acid-swollen cellulose and practically no activity on carboxymethyl cellulose, Avicel cellulose, and cellobiose, but it hydrolyzed p-nitrophenyl lactoside and released cellobiose from cellotriose and from higher cello-oligosaccharides. These data demonstrate that the enzyme is a cellodextrinase with an exotype of function.

Characterization and molecular cloning of a novel endoglucanase from Trichoderma sp. C-4

A fungal strain, C-4, was isolated from etiolated leaves. Based on taxonomic studies, the fungus C-4 can be classified as a strain of Trichoderma species. When strain C-4 was cultured in Mandels' medium at 28 degrees C for 6 days, the enzyme activities detected in the broth corresponded to 8.2 U/ml (28.1 U/mg) carboxymethylcellulase activity. An endoglucanase (EG; F-I-II) was purified from the culture filtrate of the strain through a four-step procedure-chromatography on Sephacryl S-200, DEAE-Sephadex A-50, Con A-Sepharose, and Chromatofocusing on Mono-P (HPLC). The molecular weight of this EG, which was called C4endoII, was determined to be about 51 kDa. The optimum temperature and pH of C4endoII were 50 degrees C and 5.0, respectively. Incubation at 50 degrees C for 24 h did not destroy the cellulose degradation activity. Amino acid sequence analysis revealed the N-terminal sequence of an internal peptide of C4endoII to be Phe-Ala-Gly-Ile-Asn-Ile-Ala-Gly-Phe-Asp-Phe, which is homologous to EGII from Trichoderma reesei. A C4endoII cDNA (C4endoII) was cloned from a cDNA library constructed using the mRNA of the strain cultivated in a cellulase-induction medium. The deduced protein sequence of C4endoII was 417 amino acids long and had a putative signal sequence of 21 amino acids with a predicted cleavage site after Ala-21. A single potential N-glycosylation site was present in the amino acid sequence.

Useful Byproducts from Cellulosic Wastes of Agriculture and Food Industry—A Critical Appraisal

Cellulose, an important cell wall polysaccharide, which is replenished constantly in nature by photosynthesis, goes waste in a lion's share in the form of pre-harvest and post-harvest agricultural losses and wastes of food processing industry. These cellulose wastes have an immense potential to be utilized for the production and recovery of several products and ingredients in food application. In this present study, a wide spectrum of researches in the arena of properties of cellulose, hemicellulose and lignin; their degradation; sources and composition of cellulosic and lignocellulosic wastes of agriculture and food industry; present status of converting them into value-added products of food applications; constraints in their conversions and future prospects therein has been reviewed in details. The study has encompassed production of biomass for various utilization and production and recovery of protein and amino acids, carbohydrates, lipids, organic acids, foods & feeds and other miscellaneous products.

Cellulose degrading enzymes and their potential industrial applications

Bioconversion of cellulose to soluble sugars and glucose is catalyzed by a group of enzymes called cellulases. Microorganisms including fungi, bacteria and actinomycetes produce mainly three types of cellulase components--endo-1,4-beta-D-glucanase, exo-1,4-beta-D-glucanase and beta-glucosidase--either separately or in the form of a complex. Over the last several decades, cellulases have become better understood at a fundamental level; nevertheless, much remains to be learnt. The tremendous commercial potential of cellulases in a variety of applications remains the driving force for research in this area. This review summarizes the present state of knowledge on microbial cellulases and their applications.

Characterization of cellulase complex of Streptomyces albaduncus

Exoglucanase and endoglucanase (glucanases) enzymes of S. albaduncus were found to be very stable, showing only 36% and 8% loss in activities respectively after 3 days of incubation at 50 degrees C. In contrast, beta-glucosidase was significantly less stable retaining only 22.30% activity after 30 min incubation at 40 degrees C. The glucanases manifested maximum stability in pH range of 5.5-6.0 whereas beta-glucosidase was completely stable over a broad pH range of 6.5-9.0. Both glucanases were enhanced by some cations whereas beta-glucosidase did not require any cation for activity. K(m) values for crude exoglucanase, endoglucanase and beta-glucosidase were 40.00 mg/ml, 92.30 mg/ml and 1.714 mM with maximum reaction velocities (Vmax) of 0.606, 33.330 and 0.109 IU/mg of protein, respectively. The enzymes were subject to end-product inhibition, with exo- and endo-glucanases decreasing by 20% and 70% respectively, in the presence of 0.3% glucose. However, beta-glucosidase showed marked resistance to glucose inhibition, retaining 59% of residual activity even in the presence of 30% glucose in the reaction mixture. This characteristic may be advantageous in the commercial exploitation of enzyme system. An activation of beta-glucosidase at lower concentrations of glucose suggests competitive inhibition.

Cellulase: a perspective

Cellulose, a polymer of |3-1,4-linked D-glucose residues, is the World’s most abundant natural polymer. It occurs predominantly in plants, forming their main structural component, but also occurs widely in other organisms, such as bacteria, algae, fungi and animals. With annual production of around 1.8 x 10 12 tonnes, it has attracted considerable study encompassing its synthesis, biodegradation and utilization in several recent reviews (M. P. Goughian Biotechnol. Genetic Engng Rev. 3, 39-109 (1985); B. S. Montenecourt & D. E. Eveleigh in Gene manipulations in fungi (ed. J. M. Bennett & L. L. Lasure), pp. 491- 512, New York: Academic Press (1985); J. N. Saddler Microbiol. Sci . 3, 84-87 (1986)). With this wealth of data at hand, a perspective of fungal cellulase is presented with consideration of current models of action, nature of the enzyme complex, analytical methods and approaches for enhanced production.

Purification and characterization of cellulolytic enzymes produced by Aspergillus nidulans

Three exo-glucanases, two endo-glucanases and two beta-glucosidases were separated and purified from the culture medium of Aspergillus nidulans. The optimal assay conditions for all forms of cellulase components ranged from pH 5.0 to 6.0 and 50 degrees C and 65 degrees C for exo-glucanases and endo-glucanases but 35 degrees C and 65 degrees C for beta-glucosidases. A close relation of enzyme stability to their optimal pH range was observed. All the cellulase components were stable for 10 min at 40-50 degrees C. Exo-II and Exo-III (Km, 38.46 and 37.71 mg/ml) had greater affinity for the substrate than Exo-I (Km, 50.00 mg/ml). The Km values of Endo-I and Endo-II (5.0 and 4.0 mg/ml) and their maximum reaction velocities (Vmax, 12.0 and 10.0 IU/mg protein) were comparable. beta-Glucosidases exhibited Km values of 0.24 and 0.12 mmol and Vmax values of 8.00 and 0.67 IU/mg protein. The molecular weights recorded for various enzyme forms were: Exo-I, 29,000; Exo-II, 72,500; Exo-III, 138,000; Endo-I, 25,000; Endo-II, 32,500; beta-Gluco-I, 14,000 and beta-Gluco-II, 26,000. Exo- and endo-glucanases were found to require some metal ions as co-factors for their catalytic activities whereas beta-glucosidases did not. Hg2+ inhibited the activity of all the cellulase components. The saccharification studies demonstrated a high degree of synergism among all the three cellulase components for hydrolysis of dewaxed cotton.

Purification and characterization of a beta-glucosidase from Evernia prunastri

Intracellular beta-glucosidase from Evernia prunastri has been purified to homogeneity using anion exchange on DEAE-Sephadex A-50, and gel filtration chromatography on Sephadex G-100 and Sepharose 6B. The purified beta-glucosidase showed a single protein band on native electrophoresis and its isoelectric point was at pH 3.12. The molecular mass, calculated from its partition coefficient on the Sepharose 6B column, was 311 kDa, being composed of several subunits of 60 and 70 kDa. The highest activity of this enzyme was attained at pH 4.0 and 60 degrees C. The enzyme showed strong resistance to thermal inactivation. Its activation energy was about 15 kJ/mol. Cellobiose, salicin, and p-nitrophenyl beta-D-glucoside, but not carboxymethylcellulose, were hydrolyzed by the enzyme, following substrate inhibition kinetics. The purified beta-glucosidase was considered a true cellobiase because of its great affinity towards cellobiose. Cellobiose inhibition does not seem to be a physiological phenomenon. Glucose inhibited enzyme activity in a competitive way (Ki = 1.26 mM). Fe3+ and Co2+ inhibited activity notably. Hg2+, Cu2+ and EDTA were practically ineffective. Even 200 mM gluconolactone did not affect enzyme activity.