Engineering of glycoside hydrolase family 7 cellobiohydrolases directed by natural diversity screening

Protein engineering and screening of processive fungal cellobiohydrolases (CBHs) remain challenging due to limited expression hosts, synergy-dependency, and recalcitrant substrates. In particular, glycoside hydrolase family 7 (GH7) CBHs are critically important for the bioeconomy and typically difficult to engineer. Here, we target the discovery of highly active natural GH7 CBHs and engineering of variants with improved activity. Using experimentally assayed activities of genome mined CBHs, we applied sequence and structural alignments to top performers to identify key point mutations linked to improved activity. From ∼1500 known GH7 sequences, an evolutionarily diverse subset of 57 GH7 CBH genes was expressed in Trichoderma reesei and screened using a multiplexed activity screening assay. Ten catalytically enhanced natural variants were identified, produced, purified, and tested for efficacy using industrially relevant conditions and substrates. Three key amino acids in CBHs with performance comparable or superior to Penicillium funiculosum Cel7A were identified and combinatorially engineered into P. funiculosum cel7a, expressed in T. reesei, and assayed on lignocellulosic biomass. The top performer generated using this combined approach of natural diversity genome mining, experimental assays, and computational modeling produced a 41% increase in conversion extent over native P. funiculosum Cel7A, a 55% increase over the current industrial standard T. reesei Cel7A, and 10% improvement over Aspergillus oryzae Cel7C, the best natural GH7 CBH previously identified in our laboratory.

Distinct lignocellulolytic enzymes produced by Trichoderma harzianum in response to different pretreated substrates

In order to optimize the composition of enzyme cocktail for improving the hydrolytic efficiency of lignocellulose, different substrates were tested as inducers for producing lignocellulolytic enzymes by Trichoderma harzianum EM0925 in this study. As results, ultrafine grinding or steam explosion pretreated substrates can induce T. harzianum EM0925 to secret holo lignocellulolytic enzymes; acid treated substrate can induce cellobiohydrolase; while alkali or sodium chlorite treated substrates can induce β-xylosidase specifically. Furthermore, the combination of enzyme cocktails with different hydrolysis characteristics can further improve the hydrolysis efficiency, since 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding treated corn stover at low enzyme dosage (1.2 mg proteins/g substrate). This study for the first time demonstrated an effective solution that specific-pretreated substrates can be used as inducers for specific enzyme production by T. harzianum, which provided new idea and potential strategy for the construction of highly-efficient lignocellulolytic enzyme cocktails.

Production of Polysaccharides and Single-Cell Protein by Some Local Isolates of Trichoderma spp

<b>Background and Objective:</b> Polysaccharides and Single-cell protein are one of the best essential natural products of microorganisms, they are excreted by different microorganisms such as yeast, fungi, bacteria and algae. This study was carried out to detect the ability of four local fungal isolates of <i>Trichoderma </i>spp. to produce polysaccharides and Single-cell protein. <b>Materials and Methods:</b> Standard Czapek Dox Broth Medium was used to detect the ability of fungal isolates to produce polysaccharides and Single-cell protein, with modified the components of medium for improved production using banana peels as a source of carbon and different nitrogen sources at different concentrations and the factorial experiment was carried out using a completely randomized design <b>Results:</b> The highest dry weight and polysaccharides production and protein content have been achieved for the fungus <i>T. reesei</i> with rates of (2.15, 0.276 and 0.94) g/100 mL, respectively, in comparison with the other treatments, the use of ammonium phosphate at concentration 0.6 g L<sup>1</sup> has given the highest dry weight and production of polysaccharides and protein content with rates of (3.75, 0.364 and 2.77) g/100 mL, respectively, also the use of banana peels extract at concentration 40 mL L<sup>1</sup> has given the highest dry weight and production of polysaccharides and protein content with rates of (5.21, 0.539 and 3.63) g/100 mL, respectively. <b>Conclusion:</b> The possibility of using the local isolate of <i>T. reesei</i> in the production of polysaccharides and Single-cell protein using some cheap agricultural waste such as banana peels as a carbon source instead of throwing them as waste and pollutants for the environment.

Trichoderma-Based Biopreparation with Prebiotics Supplementation for the Naturalization of Raspberry Plant Rhizosphere

The number of raspberry plants dying from a sudden outbreak of gray mold, verticillium wilt, anthracnosis, and phytophthora infection has increased in recent times, leading to crop failure. The plants suffer tissue collapse and black roots, symptoms similar to a Botrytis-Verticillium-Colletotrichum-Phytophthora disease complex. A sizeable number of fungal isolates were acquired from the root and rhizosphere samples of wild raspberries from different locations. Subsequent in vitro tests revealed that a core consortium of 11 isolates of selected Trichoderma spp. was the most essential element for reducing in phytopathogen expansion. For this purpose, isolates were characterized by the efficiency of their antagonistic properties against Botrytis, Verticillium, Colletotrichum and Phytophthora isolates and with hydrolytic properties accelerating the decomposition of organic matter in the soil and thus making nutrients available to plants. Prebiotic additive supplementation with a mixture of adonitol, arabitol, erythritol, mannitol, sorbitol, and adenosine was proven in a laboratory experiment to be efficient in stimulating the growth of Trichoderma isolates. Through an in vivo pathosystem experiment, different raspberry naturalization-protection strategies (root inoculations and watering with native Trichoderma isolates, applied separately or simultaneously) were tested under controlled phytotron conditions. The experimental application of phytopathogens attenuated raspberry plant and soil properties, while Trichoderma consortium incorporation exhibited a certain trend of improving these features in terms of a short-term response, depending on the pathosystem and naturalization strategy. What is more, a laboratory-scale development of a biopreparation for the naturalization of the raspberry rhizosphere based on the Trichoderma consortium was proposed in the context of two application scenarios. The first was a ready-to-use formulation to be introduced while planting (pellets, gel). The second was a variant to be applied with naturalizing watering (soluble powder).

Screening and evaluation of laccase produced by different Trichoderma species along with their phylogenetic relationship

Laccases have high biotechnological potential in industries since they catalyze the oxidation of many chemical compounds. The production of laccases by fungi has been extensively studied due to their secretion of enzymes and rapid growth using cheap substrates. Trichoderma; the versatile fungal genus includes species of great biotechnological value and considered as a magnificent industrial cell factory of enzymes. In this study, 10 Trichoderma species were screened for laccase enzyme production by submerged cultivation. The studied species were identified by internal transcribed spacer (ITS) gene sequences. Guaiacol (0.04%) as an enzyme substrate in plate medium was used for the selection of maximum laccase-enriched Trichoderma species by formation of visual color halo intensity. This activity was evaluated by liquid submersion (flask medium) also. The absorbance of laccase contained broth was measured by a spectrophotometer (450 nm). The highest laccase production was obtained by T. atroviride (2.62 U/mL). Trichoderma cremeum and T. longipile showed medium laccase potency, while T. beinartii exhibited weak laccase secretion ability. Laccase from T. atroviride was purified by SDS-PAGE and the molecular weight was determined (57 kDa). The laccase was confirmed by their respective amino acid sequences, and the phylogenetic tree was constructed for further analysis.

Enhancing PET hydrolytic enzyme activity by fusion of the cellulose-binding domain of cellobiohydrolase I from Trichoderma reesei

The large amounts of polyethylene terephthalate (PET) that enter and accumulate in the environment have posed a serious threat to global ecosystems and human health. A PET hydrolase from PET-assimilating bacterium Ideonella sakaiensis (IsPETase) that exhibits superior PET hydrolytic activity at mild conditions is attracting enormous attention in development of plastic biodegrading strategies. In order to enhance the PET hydrolysis capacity of IsPETase, we selected several polymer-binding domains that can adhere to a hydrophobic polymer surface and fused these to a previously engineered IsPETase^{S121E/D186H/R280A} (IsPETase^EHA) variant. We found that fusing a cellulose-binding domain (CBM) of cellobiohydrolase I from Trichoderma reesei onto the C-terminus of IsPETase^EHA showed a stimulatory effect on enzymatic hydrolysis of PET. Compared to the parental enzyme, IsPETase^EHA_CBM exhibited 71.5 % and 44.5 % higher hydrolytic activity at 30 ℃ and 40 ℃, respectively. The catalytic activity of IsPETase^EHA_CBM was increased by 86 % when the protein concentration was increased from 2.5 μg/mL to 20 μg/mL. These findings suggest that the fusion of polymer-binding module to IsPETase is a promising strategy to stimulate the enzymatic hydrolysis of PET.

Effects of supplementation of high-dosing Trichoderma reesei phytase in the corn-wheat-soybean meal-based diets on growth performance, nutrient digestibility, carcass traits, faecal gas emission, and meat quality in growing-finishing pigs

We conduct this study to investigate the effects of corn-wheat-soybean meal (SBM)-based diet supplemented with high-dosing Trichoderma reesei phytase on the growth performance, nutrient digestibility, carcass traits, faecal gas emission and meat quality in growing-finishing pigs (29.71-110.58 kg live weight; 70-day-old to 166-day-old). A total of 56 crossbred pigs [(Landrace × Yorkshire) × Duroc] were used in 96-day experiment with a completely randomized block design. The growing period was from day 0 to 42, and the finishing period was from day 43 to 96. Pigs were randomly allocated to one of two treatments with seven replicate pens and four pigs (two barrows and two gilts) per pen and fed corn-wheat-SBM-based nutrient adequate basal diet or the basal diet supplemented with 1500 FTU/kg diet Trichoderma reesei phytase. One phytase unit (FTU) was defined as the amount of enzyme that catalyses the release of one micromole phosphate from phytate per minute at 37°C and pH 5.5. Dietary supplement with Trichoderma reesei phytase had increased body weight on day 96 and average daily gain in days 0-96. Moreover, high apparent total tract digestibility (ATTD) of phosphorus (P) was observed in pigs fed with Trichoderma reesei phytase. However, the carcass traits, faecal gas emission and meat quality of pigs were unaffected by Trichoderma reesei phytase supplementation. In conclusion, supplementation of high-dosing Trichoderma reesei phytase (1500 FTU/kg diet) in the corn-wheat-SBM-based nutrient adequate basal diet increased body weight and the ATTD of P, while no adverse effects were observed on the production characteristics.

Method for the Production and Purification of Plant Immuno-Active Xylanase from Trichoderma

Plants lack a circulating adaptive immune system to protect themselves against pathogens. Therefore, they have evolved an innate immune system based upon complicated and efficient defense mechanisms, either constitutive or inducible. Plant defense responses are triggered by elicitors such as microbe-associated molecular patterns (MAMPs). These components are recognized by pattern recognition receptors (PRRs) which include plant cell surface receptors. Upon recognition, PRRs trigger pattern-triggered immunity (PTI). Ethylene Inducing Xylanase (EIX) is a fungal MAMP protein from the plant-growth-promoting fungi (PGPF)-Trichoderma. It elicits plant defense responses in tobacco (Nicotiana tabacum) and tomato (Solanum lycopersicum), making it an excellent tool in the studies of plant immunity. Xylanases such as EIX are hydrolytic enzymes that act on xylan in hemicellulose. There are two types of xylanases: the endo-1, 4-β-xylanases that hydrolyze within the xylan structure, and the β-d-xylosidases that hydrolyze the ends of the xylan chain. Xylanases are mainly synthesized by fungi and bacteria. Filamentous fungi produce xylanases in high amounts and secrete them in liquid cultures, making them an ideal system for xylanase purification. Here, we describe a method for cost- and yield-effective xylanase production from Trichoderma using wheat bran as a growth substrate. Xylanase produced by this method possessed xylanase activity and immunogenic activity, effectively inducing a hypersensitive response, ethylene biosynthesis, and ROS burst.

Influence of KCl Fertilizer and Trichoderma on the Growth and Yield of Upland Rice

<b>Background and Objective:</b> The rate of population growth is not balanced with the rate of increase in national rice production. The attention of the government and researchers in Southeast Sulawesi on upland rice is still very low, even though the potential for increased upland rice production is quite promising. The research aimed to study the influence of KCl fertilizer and <i>Trichoderma </i>spp. on the growth and yield of upland rice. <b>Materials and Methods:</b> The study was conducted in a Randomized Block Design (RBD) consisting of 6 treatments i.e.: without KCl fertilizer and <i>T. asperellum</i> (K<sub>0</sub>), KCl 0.15 g/polybag+<i>T. asperellum </i>50 g/polybag (K<sub>1</sub>), KCl 0.30 g/polybag+<i> T. asperellum </i>40 g/polybag (K<sub>2</sub>), KCl 0.45 g/polybag+<i>T. asperellum </i>30 g/polybag (K<sub>3</sub>), KCl 0.60 g/polybag+<i>T. asperellum </i>20 g/polybag (K<sub>4</sub>) and KCl 0.75 g/polybag+<i>T. asperellum </i>10 g/polybag (K<sub>5</sub>) with 4 replication for each treatment. The data obtained were analyzed by analysis of variance (ANOVA) and conducted further tests with the Duncan Multiple Range Test (DMRT) at a 95% confidence level. <b>Results:</b> The results of the research revealed KCl fertilizer combination with <i>T. asperellum</i> in general, can increase the growth and yield of upland local aromatic red rice. Application of KCl fertilizers as 0.45 g/polybag equivalent to 90 kg ha<sup>1</sup> (K<sub>3</sub>) can provide optimal potassium nutrients for vegetative growth of upland rice. <b>Conclusion:</b> The treatment of KCl fertilizer as 0.45 g/polybag with <i>T. asperellum </i>30 g/polybag (K<sub>3</sub>) provides growth and yield of upland rice with an average production of4.95 t ha<sup>1</sup>.

In-depth characterization of Trichoderma reesei cellobiohydrolase TrCel7A produced in Nicotiana benthamiana reveals limitations of cellulase production in plants by host-specific post-translational modifications

Sustainable production of biofuels from lignocellulose feedstocks depends on cheap enzymes for degradation of such biomass. Plants offer a safe and cost-effective production platform for biopharmaceuticals, vaccines and industrial enzymes boosting biomass conversion to biofuels. Production of intact and functional protein is a prerequisite for large-scale protein production, and extensive host-specific post-translational modifications (PTMs) often affect the catalytic properties and stability of recombinant enzymes. Here we investigated the impact of plant PTMs on enzyme performance and stability of the major cellobiohydrolase TrCel7A from Trichoderma reesei, an industrially relevant enzyme. TrCel7A was produced in Nicotiana benthamiana using a vacuum-based transient expression technology, and this recombinant enzyme (TrCel7Arec ) was compared with the native fungal enzyme (TrCel7Anat ) in terms of PTMs and catalytic activity on commercial and industrial substrates. We show that the N-terminal glutamate of TrCel7Arec was correctly processed by N. benthamiana to a pyroglutamate, critical for protein structure, while the linker region of TrCel7Arec was vulnerable to proteolytic digestion during protein production due to the absence of O-mannosylation in the plant host as compared with the native protein. In general, the purified full-length TrCel7Arec had 25% lower catalytic activity than TrCel7Anat and impaired substrate-binding properties, which can be attributed to larger N-glycans and lack of O-glycans in TrCel7Arec . All in all, our study reveals that the glycosylation machinery of N. benthamiana needs tailoring to optimize the production of efficient cellulases.

Low-Cost Cellulase-Hemicellulase Mixture Secreted by Trichoderma harzianum EM0925 with Complete Saccharification Efficacy of Lignocellulose

Fermentable sugars are important intermediate products in the conversion of lignocellulosic biomass to biofuels and other value-added bio-products. The main bottlenecks limiting the production of fermentable sugars from lignocellulosic biomass are the high cost and the low saccharification efficiency of degradation enzymes. Herein, we report the secretome of Trichoderma harzianum EM0925 under induction of lignocellulose. Numerously and quantitatively balanced cellulases and hemicellulases, especially high levels of glycosidases, could be secreted by T. harzianum EM0925. Compared with the commercial enzyme preparations, the T. harzianum EM0925 enzyme cocktail presented significantly higher lignocellulolytic enzyme activities and hydrolysis efficiency against lignocellulosic biomass. Moreover, 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding and alkali pretreated corn stover. These findings demonstrate a natural cellulases and hemicellulases mixture for complete conversion of biomass polysaccharide, suggesting T. harzianum EM0925 enzymes have great potential for industrial applications.

Rational molecular design for improving digestive enzyme resistance of beta-glucosidase from Trichoderma viride based on inhibition of bound state formation

Beta-glucosidase (BGL1) is widely used in animal feed industries. However, degradation caused by digestive enzymes in the intestine hampers its application. Improving the resistance of feed enzymes against proteases is crucial in livestock farming. To improve the resistance of beta-glucosidase against pepsin and trypsin, a rational molecular design based on the inhibition of bound-state formation and secondary design was developed. The strategy includes: (1) prediction of the interaction surface of the pepsin-BGL1 complex structure, (2) prediction of key amino acids affecting the formation of the complex, (3) optimization of pepsin-resistant mutants by structural evaluation, (4) secondary molecular design based on pepsin-resistant mutants, and optimization of pepsin and trypsin-resistant mutants. Two BGL1 protein mutants (BGL1^Q627C and BGL1^{Q627C/R543H/R646W}) were constructed, and then mutated and wild-type BGL1s were expressed in Pichia pastoris. The half-life of BGL1^Q627C and BGL1^{Q627C/R543H/R646W} were 1.36 and 1.51 times that of the wild type upon pepsin exposure, respectively. For trypsin resistance, the half-life were 0.93 and 1.53 times that of the wild type, respectively. Compare to those of the wild type, most of the basic enzymatic properties of both mutants were not significantly changed except for increased Michaelis constants. The rational design method can be used as a guide for modifying other feed enzymes.

The transcription factor ACE3 controls cellulase activities and lactose metabolism via two additional regulators in the fungus Trichoderma reesei

Fungi of the genus Trichoderma are a rich source of enzymes, such as cellulases and hemicellulases, that can degrade lignocellulosic biomass and are therefore of interest for biotechnological approaches seeking to optimize biofuel production. The essential transcription factor ACE3 is involved in cellulase production in Trichoderma reesei; however, the mechanism by which ACE3 regulates cellulase activities is unknown. Here, we discovered that the nominal ace3 sequence in the T. reesei genome available through the Joint Genome Institute is erroneously annotated. Moreover, we identified the complete ace3 sequence, the ACE3 Zn(II)2Cys6 domain, and the ACE3 DNA-binding sites containing a 5'-CGGAN(T/A)3-3' consensus. We found that in addition to its essential role in cellulase production, ace3 is required for lactose assimilation and metabolism in T. reesei Transcriptional profiling with RNA-Seq revealed that ace3 deletion down-regulates not only the bulk of the major cellulase, hemicellulase, and related transcription factor genes, but also reduces the expression of lactose metabolism-related genes. Additionally, we demonstrate that ACE3 binds the promoters of many cellulase genes, the cellulose response transporter gene crt1, and transcription factor-encoding genes, including xyr1 We also observed that XYR1 dimerizes to facilitate cellulase production and that ACE3 interacts with XYR1. Together, these findings uncover how two essential transcriptional activators mediate cellulase gene expression in T. reesei On the basis of these observations, we propose a model of how the interactions between ACE3, Crt1, and XYR1 control cellulase expression and lactose metabolism in T. reesei.

Purification and characterization of an endo-xylanase from Trichoderma sp., with xylobiose as the main product from xylan hydrolysis

Fungal endo-β-1,4-xylanases (endo-xylanases) can hydrolyze xylan into xylooligosaccharides (XOS), and have potential biotechnological applications for the exploitation of natural renewable polysaccharides. In the current study, we aimed to screen and characterize an efficient fungal endo-xylanase from 100 natural humus-rich soil samples collected in Guizhou Province, China, using extracted sugarcane bagasse xylan (SBX) as the sole carbon source. Initially, 182 fungal isolates producing xylanases were selected, among which Trichoderma sp. strain TP3-36 was identified as showing the highest xylanase activity of 295 U/mL with xylobiose (X2) as the main product when beechwood xylan was used as substrate. Subsequently, a glycoside hydrolase family 11 endo-xylanase, TXyn11A, was purified from strain TP3-36, and its optimal pH and temperature for activity against beechwood xylan were identified to be 5.0 and 55 °C, respectively. TXyn11A was stable across a broad pH range (3.0-10.0), and exhibited strict substrate specificity, including xylan from beechwood, wheat, rye, and sugarcane bagasse, with K_m and V_max values of 5 mg/mL and 1250 μmol/mg min, respectively, toward beechwood xylan. Intriguingly, the main product obtained from hydrolysis of beechwood xylan by TXyn11A was xylobiose, whereas SBX hydrolysis resulted in both X2 and xylotriose. Overall, these characteristics of the endo-xylanase TXyn11A indicate several potential industrial applications.

An Unusual Skeletal Rearrangement in the Biosynthesis of the Sesquiterpene Trichobrasilenol from Trichoderma

The skeletons of some classes of terpenoids are unusual in that they contain a larger number of Me groups (or their biosynthetic equivalents such as olefinic methylene groups, hydroxymethyl groups, aldehydes, or carboxylic acids and their derivatives) than provided by their oligoprenyl diphosphate precursor. This is sometimes the result of an oxidative ring-opening reaction at a terpene-cyclase-derived molecule containing the regular number of Me group equivalents, as observed for picrotoxan sesquiterpenes. In this study a sesquiterpene cyclase from Trichoderma spp. is described that can convert farnesyl diphosphate (FPP) directly via a remarkable skeletal rearrangement into trichobrasilenol, a new brasilane sesquiterpene with one additional Me group equivalent compared to FPP. A mechanistic hypothesis for the formation of the brasilane skeleton is supported by extensive isotopic labelling studies.

Definition of Liquid and Powder Cellulase Formulations Using Domestic Wastewater in Bubble Column Reactor

Raw domestic wastewater was used as a culture medium for cellulase production in a bubble column reactor (6.2 U_FP/mL, 64.6 U/L h) using the strain Trichoderma harzianum TRIC03-LPBII. Cellulases presented optimum pH and temperature between 4 and 5 and 50 and 70 °C, respectively. Enzymatic extract was concentrated through ultrafiltration and then a cellulolytic formulation was prepared with the addition of sorbitol (50% w/v) and benzoic acid (0.05% w/v). High cellulase stability of around 100% was reached after 30 days at 4 °C. The concentrated extract was also dried in a spray-dryer with the addition of maltodextrin at 20% (w/v), resulting in powder enzymatic formulation with 85% stability after 60 days. With these characteristics, the liquid and powder cellulase products have potential to be used in different industrial applications.

Glycosylation effects on the structure and dynamics of a full-length Cel7A cellulase

Fungi cellulases are used to degrade cellulose-containing biomass for bioethanol production. Industrial cellulases such as Cel7A from Trichoderma reesei (TrCel7A) are critical in this process. Thus, the understanding of structure and dynamics is crucial for engineering variants with improved cellulolytic activity. This cellulase consists of two domains connected by a flexible and highly glycosylated linker. However, the linker flexibility has hindered the determination of Cel7A complete structure. Herein, based on atomic and sparse data, we applied integrative modelling to build a model of the complete enzyme structure. Next, through simulations, we studied the glycosylation effects on the structure and dynamics of a solubilized TrCel7A. Essential dynamics analysis showed that O-glycosylation in the linker led to the stabilization of protein overall dynamics. O-linked glycans seem to restrict protein dihedral angles distribution in this region, selecting more elongated conformations. Besides the reduced flexibility, functional interdomain motions occurred in a more concerted way in the glycosylated system. In contrast, in the absence of glycosylation, we observed vast conformational plasticity with the functional domains frequently collapsing. We report here evidence that targeting Cel7A linker flexibility by point mutations including modification of glycosylation sites could be a promising design strategy to improve cellulase activity.

In-vitro bio-mineralization of arsenic and lead from aqueous solution and soil by wood rot fungus, Trichoderma sp

In the present study, we investigated the role of calcite, i.e., microbiologically-induced precipitate by ureolytic Trichoderma sp. MG, in remediation of soils contaminated with arsenic (As) and lead (Pb). The fungus tolerates high concentrations of As (500 mg/L) and Pb (650 mg/L). The effects of three factors, i.e., urea concentration, CaCl₂ concentration and pH, on urease production and bio-mineralization of As and Pb were investigated using Box-Behnken design. The maximum urease production (920 U/mL) and metal removal efficiency (68% and 59% for Pb and AS, respectively) were observed in the medium containing urea of 300 mM and CaCl₂ of 75 mM at pH 9.0. Fourier transform infrared spectroscopy result revealed the formation of metal carbonates by the isolate MG. Sequential extraction of metals revealed that the carbonate fractions of As and Pb were increased to 46.4% and 42.4% in bioremediated soil, whereas in control they were 35.5% and 32.5%, respectively. The X-ray powder diffraction result further confirmed the role of calcite precipitate in bioremediation of As- and Pb-contaminated soils. The results points out that the microbiologically-induced calcite precipitation is a feasible, eco-friendly technology for the bioremediation of As- and Pb-contaminated sites.

Bio-ionic liquid pretreatment and ultrasound-promoted enzymatic hydrolysis of black soybean okara

The effective processing method to produce fermentable sugars and modify the microstructure of black soybean okara using bio-ionic liquid (bio-IL) pretreatment and ultrasound-promoted enzymatic hydrolysis was investigated. The morphology and structural characteristics of okara before and after bio-IL pretreatment and enzymatic hydrolysis under different ultrasonic frequencies were analyzed by field emission scanning electron microscope (FE-SEM), X-ray energy dispersive spectrometer (EDS), and Fourier transform infrared spectroscopy (FTIR). Without pretreatment, the production of total reducing sugar (TRS) under ultrasound (40 kHz/300 W) was 3.4 times of that without ultrasound. Using the bio-IL choline acetate ([Ch][OAc]) in water for the pretreatment of black soybean okara, the TRS production of enzymatic hydrolysis was further increased to 5.2 times of that without ultrasound in 4 h of reaction. The analysis by FTIR and EDS showed that the highly structured matrix of okara was unfolded and broken by the action of combining ultrasound and choline acetate pretreatment, due to which the surface structures with large pores were presented to facilitate the reduction of unfavorable hindrance for enzymatic hydrolysis. The simplified kinetic model was proposed to describe the transport and reaction phenomena of enzymes in a solid-liquid system by using two kinetic parameters to show the impeded behavior of enzyme within the matrix of okara. The combination of bio-IL pretreatment and ultrasound-promoted enzymatic hydrolysis was able to make the efficient structural changes of black soybean okara to enhance the digestion of enzymes, and the okara could be valorized for use in foods.

Cellulolytic enzyme production from agricultural residues for biofuel purpose on circular economy approach

This study evaluated the production of cellulolytic enzymes from different agricultural residues. The crude enzyme extract produced was characterized and applied for saccharification of some agricultural residues. Maximum cellulolytic activities were obtained using soybean hulls. All enzymatic activities were highly stable at 40 °C at a pH range of 4.5-5.5. For stability at low temperatures, the enzyme extract was stored at freezing temperature and cooling for about 290 days without major loss of activity. The Km values found for total cellulase (FPase), endoglucanase (CMCase), and xylanase were 19.73 mg ml-1, 0.65 mg ml-1, and 22.64 mg ml-1, respectively, and Vmax values were 0.82 mol min-1 mg-1, 0.62 mol min-1 mg-1, and 104.17 mol min-1 mg-1 to cellulose, carboxymethyl cellulose, and xylan, respectively. In the saccharification tests, the total amount of total reducing sugars (TRS) released from 1 g of soybean hulls catalyzed by the enzymes present in the crude enzyme extract was 0.16 g g-1 dry substrate.

Trichoderma Histone Deacetylase HDA-2 Modulates Multiple Responses in Arabidopsis

Trichoderma spp. are a rich source of secondary metabolites and volatile organic compounds (VOCs), which may induce plant defenses and modulate plant growth. In filamentous fungi, chromatin modifications regulate secondary metabolism. In this study we investigated how the absence of histone deacetylase HDA-2 in the Trichoderma atroviride strain Δhda-2 impacts its effect on a host, Arabidopsis (Arabidopsis thaliana). The production of VOCs and their impact on plant growth and development were assessed as well. The Δhda-2 strain was impaired in its ability to colonize Arabidopsis roots, thus affecting the promotion of plant growth and modulation of plant defenses against foliar pathogens Botrytis cinerea and Pseudomonas syringae, which normally result from interaction with T. atroviride Furthermore, Δhda-2 VOCs were incapable of triggering plant defenses to counterattack foliar pathogens. The Δhda-2 overproduced the VOC 6-pentyl-2H-pyran-2-one (6-PP), which resulted in enhanced root branching and differentially regulated phytohormone-related genes. Analysis of ten VOCs (including 6-PP) revealed that three of them positively regulated plant growth, whereas six had the opposite effect. Assessment of secondary metabolites, detoxification, and communication with plant-related genes showed a dual role for HDA-2 in T. atroviride gene expression regulation during its interaction with plants. Chromatin immunoprecipitation of acetylated histone H3 on the promoters of plant-responsive genes in Δhda-2 showed, in the presence of Arabidopsis, low levels of epl-1 and abc-2 compared with that in the wild type; whereas ctf-1 presented high constitutive levels, supporting a dual role of HDA-2 in gene regulation. This work highlights the importance of HDA-2 as a global regulator in Trichoderma to modulate multiple responses in Arabidopsis.

Bridging the Micro-Macro Gap between Single-Molecular Behavior and Bulk Hydrolysis Properties of Cellulase

The microscopic kinetics of enzymes at the single-molecule level often deviate considerably from those expected from bulk biochemical experiments. Here, we propose a coarse-grained-model approach to bridge this gap, focusing on the unexpectedly slow bulk hydrolysis of crystalline cellulose by cellulase, which constitutes a major obstacle to mass production of biofuels and biochemicals. Building on our previous success in tracking the movements of single molecules of cellulase on crystalline cellulose, we develop a mathematical description of the collective motion and function of enzyme molecules hydrolyzing the surface of cellulose. Model simulations robustly explained the experimental findings at both the microscopic and macroscopic levels and revealed a hitherto-unknown mechanism causing a considerable slowdown of the reaction, which we call the crowding-out effect. The size of the cellulase molecule impacted significantly on the collective dynamics, whereas the rate of molecular motion on the surface did not.

Requirement of Two Acyltransferases for 4- O-Acylation during Biosynthesis of Harzianum A, an Antifungal Trichothecene Produced by Trichoderma arundinaceum

Trichothecenes are sesquiterpenoid toxins produced by multiple fungi, including plant pathogens, entomopathogens, and saprotrophs. Most of these fungi have the acyltransferase-encoding gene tri18. Even though its function has not been determined, tri18 is predicted to be involved in trichothecene biosynthesis because of its pattern of expression and its location near other trichothecene biosynthetic genes. Here, molecular genetic, precursor feeding, and analytical chemistry experiments indicate that in the saprotroph Trichoderma arundinaceum the tri18-encoded acyltransferase (TRI18) and a previously characterized acyltransferase (TRI3) are required for conversion of the trichothecene biosynthetic intermediate trichodermol to harzianum A, an antifungal trichothecene analog with an octa-2,4,6-trienedioyl acyl group. On the basis of the results, we propose that TRI3 catalyzes trichothecene 4- O-acetylation, and subsequently, TRI18 catalyzes replacement of the resulting acetyl group with octa-2,4,6-trienedioyl to form harzianum A. Thus, the findings provide evidence for a previously unrecognized two-step acylation process during trichothecene biosynthesis in T. arundinaceum and possibly other fungi.

Design, expression and functional characterization of a thermostable xylanase from Trichoderma reesei

Xylanases isolated from microorganisms such as the Trichoderma reesei have attracted considerable research interest because of their potential in various industrial applications. However, naturally isolated xylanases cannot withstand harsh conditions such as high temperature and basic pH. In this study, we performed structural analysis of the major T. reesei xylanase (Xyn2), and novel flexible regions of the enzyme were identified based on B-factor, a molecular dynamics (MD) parameter. To improve thermostability of the Xyn2, disulfide bonds were introduced into the unstable flexible region by using site-directed mutagenesis and two recombinant xylanases, XM1 (Xyn2Cys12-52) and XM2 (Xyn2Cys59-149) were successfully expressed in Pichia pastoris. Secreted recombinant Xyn2 was estimated by SDS-PAGE to be 24 kDa. Interestingly, the half-lives of XM1 and XM2 at 60°C were 2.5- and 1.8- fold higher, respectively than those of native Xyn2. The XM1 also exhibited improved pH stability and maintained more than 60% activity over pH values ranging from 2.0 to 10.0. However, the specific activity and catalytic efficiency of XM1 was decreased as compared to those of XM2 and native Xyn2. Our results will assist not only in elucidating of the interactions between protein structure and function, but also in rational target selection for improving the thermostability of enzymes.

Application of genetic algorithm in modelling and optimization of cellulase production

The aim of this work was to study the application of genetic algorithm (GA) in modelling and optimization of cellulose production by Trichoderma reesei from pea hull. Enzyme activity of cellulase was determined using Filter Paper Activity (FPA) assay. Optimization of process parameters was performed using mathematical (MO) and genetic optimizers to obtain combination of variables for highest possible enzyme activity. GA generated a higher value of cellulase activity (0.353 U/mL) as compared to MO (0.302 U/mL). The values of independent variables in set (GA, MO) were: agitation speed (127, 120 rpm), %H2O2 concentration (10.36, 5.0), cultivation time (112, 91 h). The investigation highlights that GA could be used as a potential optimizer for processes involving waste utilization.

Real-Time Adsorption of Exo- and Endoglucanases on Cellulose: Effect of pH, Temperature, and Inhibitors

Effective regulation of cellulase adsorption is key to improving the efficiencies of the two major bottlenecks of lignocellulose hydrolysis and cellulase recovery. In this work, we investigated the effect of inhibitors, pH, and temperature on the adsorption of exo- and endoglucanases (Cel7A and Cel7B, respectively) on cellulose using quartz crystal microgravimetry with dissipation. The addition of glucose and cellobiose can both inhibit the hydrolysis activity of Cel7A, whereas only cellobiose can inhibit that of Cel7B. Notably, the adsorption was favored by acidic conditions (pH ≤ 4.8) and low temperature, whereas alkaline conditions (pH 9 and 10) facilitated enzyme desorption, which is useful to guide the process of cellulase recovery. The adsorption and hydrolysis activity of Cel7A and Cel7B were both higher at 45 °C than at 25 °C. These findings pave the way to effective regulation of cellulase adsorption and thus improve lignocellulose conversion and cellulase recovery.

Potential of Trichoderma koningii to eliminate alachlor in the presence of copper ions

The filamentous fungus Trichoderma koningii is capable of fast and effective eliminate alachlor (90% after 72 h when added separately and 80-60% in the presence of 1-5 mM of copper). After 168 h over 99% elimination of alachlor resulted in detoxification and was connected with the mitigation of reactive oxygen species (ROS) production. Using MS/MS techniques, seven dechlorinated and hydroxylated metabolites were identified. Cytochrome P450 and laccase participate in biotransformation of the herbicide by this non-ligninolytic fungus. Laccase activity is stimulated both by copper and the mixture of copper and alachlor, which seems to be important for combined pollutants. T. koningii is characterized by high tolerance to copper (up to 7.5 mM). The metal content in mycelia reached 0.9-7.76 mg in 1 g of dry biomass. Our results suggest that T. koningii strain seems to be a promising tool for bioremediation of agricultural areas co-contaminated with copper-based fungicides and chloroacetanilide herbicides.

The cellulose binding region in Trichoderma reesei cellobiohydrolase I has a higher capacity in improving crystalline cellulose degradation than that of Penicillium oxalicum

Commercial cellulase preparations for lignocellulose bioconversion are mainly produced by the fungus Trichoderma reesei. The maximum cellulose conversion of T. reesei cellulase mixture was 15%-20% higher than that of Penicillium oxalicum in the hydrolysis of corncob residue and Avicel. Nevertheless, both preparations hydrolyzed more than 92% of cellulose in NaOH-mercerized Avicel. When added to Avicel hydrolysis residue that was less reactive to P. oxalicum cellulases, cellobiohydrolase I (CBH I) from T. reesei resulted in a higher cellulose conversion than its homologous proteins from P. oxalicum and Aspergillus niger at the same protein loadings. Further domain exchange experiment attributed the high hydrolytic efficiency of T. reesei CBH I to its inter-domain linker and cellulose-binding domain. The results in part explained the superior performance of T. reesei cellulases on the degradation of native crystalline cellulose, and highlighted the important role of cellulose-binding region in determining the degree of hydrolysis by cellulases.

Molecular characterization of β-endoglucanase from antagonistic Trichoderma saturnisporum isolate GITX-Panog (C) induced under mycoparasitic conditions

The endoglucanase belonging to glycoside hydrolase family 61 are little studied. In present study, a β-endoglucanase of ~37 kDa induced on autoclaved mycelium of Fusarium oxysporum was cloned and characterized. The molecular characterization of β-endoglucanase encoding gene revealed presence of a single intron and an open reading frame of 1044-bp which encoded a protein of 347 amino acid residues. The phylogenetic analysis of Eglu revealed its similarity to endo-β-glucanases of other Trichoderma spp. The catalytic site of β-endoglucanase contained Asp, Asn, His and Tyr residues. The cDNA encoding β-glucanase was cloned into E. coli and Pichia pastoris using pQUA-30 and pPIC9K vector system, respectively. The comparison of structure revealed that most similar structure to Eglu is Hypocrea jecorina template 5o2w.1.A of glycoside hydrolase family 61.The biochemical characterization of β-endoglucanase purified from T. saturnisporum isolate and the recombinant protein expressed in E. coli and P. pastoris was active under acidic conditions with a pH optima of 5 and temperature optima of 60 °C. The purified and expressed enzyme preparation was able to inhibit growth of F.oxysporum at 1 × 10⁵ spores/mL which clearly revealed its significance in plant pathogen suppression.

Screening and Identification of Trichoderma Strains Isolated from Natural Habitats with Potential to Cellulose and Xylan Degrading Enzymes Production

A total of 123 Trichoderma strains were isolated from different habitats and tested for their ability to degrade cellulose and xylan by simple plate screening method. Among strains, more than 34 and 45% respectively, exhibited higher cellulolytic and xylanolytic activity, compared to the reference strain T. reesei QM 9414. For strains efficiently degrading cellulose, a highest enzyme activity was confirmed using filter paper test, and it resulted in a range from 1.01 to 7.15 FPU/ml. Based on morphological and molecular analysis, the isolates were identified as Trichoderma. The most frequently identified strains belonged to Trichoderma harzianum species. Among all strains, the most effective in degradation of cellulose and xylose was T. harzianum and T. virens, especially those isolated from forest wood, forest soil or garden and mushroom compost. The results of this work confirmed that numerous strains from the Trichoderma species have high cellulose and xylan degradation potential and could be useful for lignocellulose biomass conversion e.g. for biofuel production.

Metabolic Engineering of Saccharomyces cerevisiae Using a Trifunctional CRISPR/Cas System for Simultaneous Gene Activation, Interference, and Deletion

Design and construction of an optimal microbial cell factory typically requires overexpression, knockdown, and knockout of multiple gene targets. In this chapter, we describe a combinatorial metabolic engineering strategy utilizing an orthogonal trifunctional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae. This strategy enables multiplexed perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. To implement this system, three orthogonal Cas proteins were utilized: dLbCpf1 fused to a transcriptional activator, dSpCas9 fused to a transcriptional repressor, and SaCas9 for gene deletion. Deletion was accomplished by the introduction of a 28bp frame-shift mutation using a homology donor on the guide RNA expression vector. This approach enables the application of metabolic engineering to systematically optimize phenotypes of interest through a combination of gain-, reduction-, and loss-of-function mutations. Finally, we describe the construction of the CRISPR-AID system and its application toward engineering an example phenotype, surface display of recombinant Trichoderma reesei endoglucanase II.

Autolytic enzymes are responsible for increased melanization of carbon stressed Aspergillus nidulans cultures

Melanization of carbon stressed Aspergillus nidulans cultures were studied. Melanin production showed strong positive correlation with the activity of the secreted chitinase and ß-1,3-glucanase. Deletion of either chiB encoding an autolytic endochitinase or engA encoding an autolytic ß-1,3-endoglucanase, or both, almost completely prevented melanization of carbon stressed cultures. In contrast, addition of Trichoderma lyticase to cultures induced melanin production. Synthetic melanin could efficiently inhibit the purified ChiB chitinase activity. It could also efficiently decrease the intensity of hyphal fragmentation and pellet disorganization in Trichoderma lyticase treated cultures. Glyphosate, an inhibitor of L-3,4-dihydroxyphenylalanine-type melanin synthesis, could prevent melanization of carbon-starved cultures and enhanced pellet disorganization, while pyroquilon, a 1,8-dihydroxynaphthalene-type melanin synthesis inhibitor, enhanced melanization, and prevented pellet disorganization. We concluded that cell wall stress induced by autolytic cell wall hydrolases was responsible for melanization of carbon-starved cultures. The produced melanin can shield the living cells but may not inhibit the degradation and reutilization of cell wall materials of dead hyphae. Controlling the activity of autolytic hydrolase production can be an efficient approach to prevent unwanted melanization in the fermentation industry, while applying melanin synthesis inhibitors can decrease the resistance of pathogenic fungi against the chitinases produced by the host organism.

Effect of β-mannanase domain from Trichoderma reesei on its biochemical characters and synergistic hydrolysis of sugarcane bagasse

BACKGROUND

β-mannanase is a key enzyme for hydrolyzing mannan, a major constituent of hemicellulose, which is the second most abundant polysaccharide in nature. Different structural domains greatly affect its biochemical characters and catalytic efficiency. However, the effects of linker and carbohydrate-binding module (CBM) on β-mannanase from Trichoderma reesei (Man1) have not yet been fully described. The present study aimed to determine the influence of different domains on the expression efficiency, biochemical characteristics and hemicellulosic deconstruction of Man1.

RESULTS

The expression efficiency was improved after truncating CBM. Activities of Man1 and Man1ΔCBM (CBM) in the culture supernatant after 168 h of induction were 34.5 and 42.9 IU mL^-1 , although a value of only 0.36 IU mL^-1 was detected for Man1ΔLCBM (lacking CBM and linker). Man1 showed higher thermostability than Man1ΔCBM at low temperature, whereas Man1ΔCBM had a higher specificity for galactomannan (K_m  = 2.5 mg mL^-1 ) than Man1 (K_m  = 4.0 mg mL^-1 ). Both Man1 and Man1ΔCBM could synergistically improve the hydrolysis of cellulose, galactomannan and pretreated sugarcane bagasse, with a 10-30% improvement of the reducing sugar yield.

CONCLUSION

Linker and CBM domains were vital for mannanase activity and expression efficiency. CBM affected the thermostability and adsorption ability of Man1. The results obtained in the present study should help guide the rational design and directional modification of Man with respect to improving its catalytic efficiency. © 2017 Society of Chemical Industry.

Efficient degradation of Azo dyes by a newly isolated fungus Trichoderma tomentosum under non-sterile conditions

A fast-growing fungus with remarkable ability to degrade several azo dyes under non-sterile conditions was isolated and identified. This fungus was identified as Trichoderma tomentosum. Textile effluent of ten-fold dilution could be decolorized by 94.9% within 72h before optimization. Acid Red 3R model wastewater with a concentration of 85.5mgL^-1 could be decolorized by 99.2% within the same time after optimization. High-level of manganese peroxidase and low-level of lignin peroxidase activities were detected during the process of decolorization from the culture supernatant, indicating the possible involvement of two enzymes in azo dye decolorization. No aromatic amine products were detected from the degradation products of Acid Red 3R by gas chromatography-mass spectrometry (GC/MS) analysis, indicating the possible involvement of a special symmetrical oxidative degradation pathway. Phytotoxicity assay confirmed the lower toxicity toward the test plant seeds of the degradation products when compared to the original dye.

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.

Individual fungi rely on particular host organisms or substrates for their nutrition. Therefore, the genomes of fungi feeding on plant biomass necessarily contain genes encoding plant cell wall-degrading enzymes, while animal parasites may depend on proteolytic activity. Molds in the genus Trichoderma (Ascomycota) display a unique nutritional versatility. They can feed on other fungi, attack animals, and degrade plant debris. The later property is so efficient that one species (T. reesei) is commercially used for the production of cellulolytic enzymes required for making biofuels and other industry. In this work, we have investigated the evolution of proteins required for plant cell wall degradation in nine Trichoderma genomes and found an unprecedented number of lateral gene transfer (LGT) events for genes encoding these enzymes. Interestingly, the transfers specifically occurred from Ascomycota molds that feed on plants. We detected no cases of LGT from other fungi (e.g., mushrooms or wood-rotting fungi from Basidiomycota) that are frequent hosts of Trichoderma. Therefore, we propose that LGT may be linked to the ability of Trichoderma to parasitize on related organisms. This is a characteristic ecological trait that distinguishes Trichoderma from other mycoparasitic fungi. In this report, we demonstrate that the lateral transfer of genes may result in a profound nutritional expansion and contribute to the emergence of a generalist capable of feeding on organic matter of any origin.

Advantages of a distant cellulase catalytic base

The inverting glycoside hydrolase Trichoderma reesei (Hypocrea jecorina) Cel6A is a promising candidate for protein engineering for more economical production of biofuels. Until recently, its catalytic mechanism had been uncertain: The best candidate residue to serve as a catalytic base, Asp-175, is farther from the glycosidic cleavage site than in other glycoside hydrolase enzymes. Recent unbiased transition path sampling simulations revealed the hydrolytic mechanism for this more distant base, employing a water wire; however, it is not clear why the enzyme employs a more distant catalytic base, a highly conserved feature among homologs across different kingdoms. In this work, we describe molecular dynamics simulations designed to uncover how a base with a longer side chain, as in a D175E mutant, affects procession and active site alignment in the Michaelis complex. We show that the hydrogen bond network is tuned to the shorter aspartate side chain, and that a longer glutamate side chain inhibits procession as well as being less likely to adopt a catalytically productive conformation. Furthermore, we draw comparisons between the active site in Trichoderma reesei Cel6A and another inverting, processive cellulase to deduce the contribution of the water wire to the overall enzyme function, revealing that the more distant catalytic base enhances product release. Our results can inform efforts in the study and design of enzymes by demonstrating how counterintuitive sacrifices in chemical reactivity can have worthwhile benefits for other steps in the catalytic cycle.

Functional Characterization of TvCyt2, a Member of the p450 Monooxygenases From Trichoderma virens Relevant During the Association With Plants and Mycoparasitism

Secondary metabolites are crucial for the establishment of interactions between plants and microbes, as in the case of Trichoderma-plant interactions. In the biosynthetic pathway of secondary metabolites, specific enzymes participate in the formation of hydroxyl and epoxy groups, belonging to the p450 monooxygenases family. Here, we show that the product of the gene TvCyt2 from Trichoderma virens encodes a new protein homologous to the cytochrome p450, which is down-regulated at the beginning of Trichoderma-Arabidopsis interaction. To investigate its role in the interactions established by Trichoderma spp., we analyzed the metabolic profile obtained from the overexpressing (OETvCyt2) and null mutant (Δtvcyt2) strains, observing that the OETvCyt2 strains produce a higher concentration of some metabolites than the wild-type (WT) strain. Δtvcyt2 strains showed a decreased antagonistic activity against Rhizoctonia solani in antibiosis assays. Arabidopsis plants cocultivated with the OETvCyt2 strains showed stronger induction of systemic acquired resistance than plants cocultivated with the WT strain, as well as increases in biomass and fitness. Our data suggest that the product of the TvCyt2 gene is involved in secondary metabolite biosynthesis, which can increase antagonistic activity with phytopathogenic fungi and the capacity to promote plant growth.

Ultrasound-ionic liquid enhanced enzymatic and acid hydrolysis of biomass cellulose

The purpose of this paper was to investigate the effect of ultrasound-ionic liquid (IL) pretreatment on the enzymatic and acid hydrolysis of the sugarcane bagasse and wheat straw. The lignocellulosic biomass was dissociated in ILs ([Bmim]Cl and [Bmim]AOC) aided by ultrasound waves. Sonication was performed at different frequencies (20, 28, 35, 40, and 50kHz), a power of 100W, a time of 30min and a temperature of 80°C. The changes in the structure and crystallinity of the cellulose were studied by Fourier transform infrared (FT-IR), X-ray diffraction (XRD) and thermal gravimetric analysis (TGA). The amounts of the total reducing sugars, glucose, cellobiose, xylose and arabinose in the hydrolysates were determined. The results of FT-IR, XRD and TGA revealed that the structure of cellulose of both biomass samples remained intact after the pretreatment, but the crystallinity decreased. The enzymatic and acid hydrolysis of the biomass samples pretreated with the ultrasound-IL result in higher yields of the reducing sugars compared with the IL-pretreated sample. Enzymatic hydrolysis of bagasse and wheat straw pretreated with [Bmim]Cl-ultrasound resulted in maximal yields of glucose at 20kHz (40.32% and 53.17%) and acid hydrolysis resulted in maximal yields of glucose at 40kHz (33.32% and 48.07%). Enzymatic hydrolysis of bagasse and wheat straw pretreated with [Bmim]OAc-ultrasound show maximal yields of glucose at 28kHz and acid hydrolysis at 50kHz. Combination of ultrasound with [Bmim]OAc is more effective than [Bmim]Cl in terms of the yields of reducing sugar.

An ascomycota coculture in batch bioreactor is better than polycultures for cellulase production

Efficient hydrolysis of holocellulose depends on a proper balance between cellulase (endoglucanase, exoglucanase, β-glucosidase) and xylanase activities. The present study aimed to induce the production of cellulases and xylanases using liquid cultures (one, two, three, and four fungal strains on the same bioreactor) of wild strains of Trichoderma harzianum, Aspergillus niger, and Fusarium oxysporum. The strains were identified by amplification and analysis of the ITS rDNA region and the obtained sequences were deposited in Genbank. Enzymes (endoglucanase, exoglucansae, β-glucosidase, and xylanase activities) and the profile of extracellular protein isoforms (SDS-PAGE) produced by different fungal combinations (N = 14) were analyzed by Pearson's correlation matrix and principal component analysis (PCA). According to our results, induction of endoglucanase (19.02%) and β-glucosidase (6.35%) were obtained after 4 days when A. niger and F. oxysporum were cocultured. The combination of A. niger-T. harzianum produced higher endoglucanase in a shorter time than monocultures. On the contrary, when more than two strains were cultured in the same reactor, the relationships of competition were established, trending to diminish the amount of enzymes and the extracellular protein isoforms produced. The xylanase production was sensible to stress produced by mixed cultures, decreasing their activity. This is important when the aim is to produce cellulase-free xylanase. In addition, exoglucanase activity did not change in the combinations tested.

Deactivation of Cellulase at the Air-Liquid Interface Is the Main Cause of Incomplete Cellulose Conversion at Low Enzyme Loadings

Amphiphilic additives such as bovine serum albumin (BSA) and Tween have been used to improve cellulose hydrolysis by cellulases. However, there has been a lack of clarity to explain their mechanism of action in enzymatic hydrolysis of pure or low-lignin cellulosic substrates. In this work, a commercial Trichoderma reesei enzyme preparation and the amphiphilic additives BSA and Tween 20 were applied for hydrolysis of pure Avicel cellulose. The results showed that these additives only had large effects on cellulose conversion at low enzyme to substrate ratios when the reaction flasks were shaken. Furthermore, changes in the air-liquid interfacial area profoundly affected cellulose conversion, but surfactants reduced or prevented cellulase deactivation at the air-liquid interface. Not shaking the flasks or adding low amounts of surfactant resulted in near theoretical cellulose conversion at low enzyme loadings given enough reaction time. At low enzyme loadings, hydrolysis of cellulose in lignocellulosic biomass with low lignin content suffered from enhanced enzyme deactivation at the air-liquid interface.

Genetic engineering of Trichoderma reesei cellulases and their production

Lignocellulosic biomass, which mainly consists of cellulose, hemicellulose and lignin, is the most abundant renewable source for production of biofuel and biorefinery products. The industrial use of plant biomass involves mechanical milling or chipping, followed by chemical or physicochemical pretreatment steps to make the material more susceptible to enzymatic hydrolysis. Thereby the cost of enzyme production still presents the major bottleneck, mostly because some of the produced enzymes have low catalytic activity under industrial conditions and/or because the rate of hydrolysis of some enzymes in the secreted enzyme mixture is limiting. Almost all of the lignocellulolytic enzyme cocktails needed for the hydrolysis step are produced by fermentation of the ascomycete Trichoderma reesei (Hypocreales). For this reason, the structure and mechanism of the enzymes involved, the regulation of their expression and the pathways of their formation and secretion have been investigated in T. reesei in considerable details. Several of the findings thereby obtained have been used to improve the formation of the T. reesei cellulases and their properties. In this article, we will review the achievements that have already been made and also show promising fields for further progress.

CO2-H2O based pretreatment and enzyme hydrolysis of soybean hulls

The high carbohydrate content of soybean hull makes it an attractive biorefinery resource. But hydrolyzing its complex structure requires concerted enzyme activities, at least cellulase, xylanase, pectinase and α-galactosidase. Effective pretreatment that generates minimal inhibitory products is important to facilitate enzymatic hydrolysis. Combined CO2-H2O pretreatment and enzymatic hydrolysis by Aspergillus niger and Trichoderma reesei enzyme broths was studied here. The pretreatment was evaluated at 80°C-180°C temperature and 750psi-1800psi pressure, with fixed moisture content (66.7%) and pretreatment time (30min). Ground hulls without and with different pretreatments were hydrolyzed by enzyme at 50°C and pH 4.8 and compared for glucose, xylose, galactose, arabinose, mannose and total reducing sugar release. CO2-H2O pretreatment at 1250psi and 130°C was found to be optimal. Compared to the unpretreated hulls hydrolyzed with 2.5-fold more enzyme, this pretreatment improved glucose, xylose, galactose, arabinose and mannose releases by 55%, 35%, 105%, 683% and 52%, respectively. Conversions of 97% for glucose, 98% for xylose, 41% for galactose, 59% for arabinose, 87% for mannose and 89% for total reducing sugar were achieved with Spezyme CP at 18FPU/g hull. Monomerization of all carbohydrate types was demonstrated. At the optimum pretreatment condition, generation of inhibitors acetic acid, furfural and hydroxymethylfurfural (HMF) was negligible, 1.5mg/g hull in total. The results confirmed the effective CO2-H2O pretreatment of soybean hulls at much lower pressure and temperature than those reported for biomass of higher lignin contents. The lower pressure requirement reduces the reactor cost and makes this new pretreatment method more practical and economical.

A comparative study on the activity of fungal lytic polysaccharide monooxygenases for the depolymerization of cellulose in soybean spent flakes

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes capable of the oxidative breakdown of polysaccharides. They are of industrial interest due to their ability to enhance the enzymatic depolymerization of recalcitrant substrates by glycoside hydrolases. In this paper, twenty-four lytic polysaccharide monooxygenases (LPMOs) expressed in Trichoderma reesei were evaluated for their ability to oxidize the complex polysaccharides in soybean spent flakes, an abundant and industrially relevant substrate. TrCel61A, a soy-polysaccharide-active AA9 LPMO from T. reesei, was used as a benchmark in this evaluation. In total, seven LPMOs demonstrated activity on pretreated soy spent flakes, with the products from enzymatic treatments evaluated using mass spectrometry and high performance anion exchange chromatography. The hydrolytic boosting effect of the top-performing enzymes was evaluated in combination with endoglucanase and beta-glucosidase. Two enzymes (TrCel61A and Aspte6) showed the ability to release more than 36% of the pretreated soy spent flake glucose - a greater than 75% increase over the same treatment without LPMO addition.

Expression, Docking, and Molecular Dynamics of Endo-β-1,4-xylanase I Gene of Trichoderma virens in Pichia stipitis

It is essential that major carbohydrate polymers in the lignocellulosic biomass are converted into fermentable sugars for the economical production of energy. Xylan, the major component of hemicelluloses, is the second most naturally abundant carbohydrate polymer comprising 20-40% of the total biomass. Endoxylanase (EXN) hydrolyzes xylan into mixtures of xylooligosaccharides. The objective of this study was to genetically modify Pichia stipitis, a pentose sugar fermenting yeast species, to hydrolyze xylan into xylooligosaccharides via cloning and heterologous extracellular expression of EXNI gene from locally isolated Trichoderma virens species. Pichia stipitis was engineered to carry the EXNI gene of T. virens using pGAPZα expression vector. The open reading frame encodes 191 amino acids and SDS-PAGE analysis revealed a 24 kDA recombinant protein. The EXNI activity expressed by recombinant P. stipitis clone under standard conditions using 1% beechwood xylan was 31.7 U/ml. Molecular docking and molecular dynamics simulations were performed to investigate EXNI-xylan interactions. Free EXNI and xylan bound EXNI exhibited similar stabilities and structural behavior in aqueous medium. Furthermore, this in silico work opens avenues for the development of newer generation EXN proteins that can perform better and have enhanced catalytic activity.

Effect of ultrasound and enzymatic pre-treatment on yield and properties of banana juice

Effect of ultrasound and enzymatic pre-treatments with cellulase and pectinase on yield and properties of banana juice were investigated. A two-level full factorial design was employed. The factors selected were ultrasonication time (0 and 30min), cellulase concentration (0 and 0.2%) and pectinase concentration (0 and 0.2%). The responses studied were yield, viscosity, clarity, total soluble solids (TSS) and pH. It was observed that pectinase was more effective in increasing the yield of juice compared to cellulase. Ultrasonic pre-treatment alone did not significantly increase the yield of juice. When ultrasound was combined with pre-treatment with both the enzymes maximum yield of 89.40% was obtained compared to 47.30% in the control. The viscosity of the juice decreased with addition of enzymes and with application of ultrasound. The clarity of the juice was not affected by cellulase treatment, but improved with pectinase treatment. Ultrasonication alone was found to be more effective than pectinase or cellulase treatment in improving the clarity of the juice. The TSS increased with enzymatic treatment, ultrasonication and their combination. pH was not affected by treatment type, but was found to be lower for the treated juices. Significant correlations were observed between the various responses.

Red rot resistant transgenic sugarcane developed through expression of β-1,3-glucanase gene

Sugarcane (Saccharum spp.) is a commercially important crop, vulnerable to fungal disease red rot caused by Colletotrichum falcatum Went. The pathogen attacks sucrose accumulating parenchyma cells of cane stalk leading to severe losses in cane yield and sugar recovery. We report development of red rot resistant transgenic sugarcane through expression of β-1,3-glucanase gene from Trichoderma spp. The transgene integration and its expression were confirmed by quantitative reverse transcription-PCR in first clonal generation raised from T₀ plants revealing up to 4.4-fold higher expression, in comparison to non-transgenic sugarcane. Bioassay of transgenic plants with two virulent C. falcatum pathotypes, Cf 08 and Cf 09 causing red rot disease demonstrated that some plants were resistant to Cf 08 and moderately resistant to Cf 09. The electron micrographs of sucrose storing stalk parenchyma cells from these plants displayed characteristic sucrose-filled cells inhibiting Cf 08 hyphae and lysis of Cf 09 hyphae; in contrast, the cells of susceptible plants were sucrose depleted and prone to both the pathotypes. The transgene expression was up-regulated (up to 2.0-fold in leaves and 5.0-fold in roots) after infection, as compared to before infection in resistant plants. The transgene was successfully transmitted to second clonal generation raised from resistant transgenic plants. β-1,3-glucanase protein structural model revealed that active sites Glutamate 628 and Aspartate 569 of the catalytic domain acted as proton donor and nucleophile having role in cleaving β-1,3-glycosidic bonds and pathogen hyphal lysis.

Trichoderma virens β-glucosidase I (BGLI) gene; expression in Saccharomyces cerevisiae including docking and molecular dynamics studies

BACKGROUND

Cellulose, a linear polymer of β 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and β-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions. Therefore, S.cerevisiae was genetically modified with the objective of heterologous extracellular expression of the BGLI gene of Trichoderma virens making it capable of utilizing cellobiose to produce ethanol.

RESULTS

The cDNA and a genomic sequence of the BGLI gene of Trichoderma virens was cloned in the yeast expression vector pGAPZα and separately transformed to Saccharomyces cerevisiae. The size of the BGLI cDNA clone was 1363 bp and the genomic DNA clone contained an additional 76 bp single intron following the first exon. The gene was 90% similar to the DNA sequence and 99% similar to the deduced amino acid sequence of 1,4-β-D-glucosidase of T. atroviride (AC237343.1). The BGLI activity expressed by the recombinant genomic clone was 3.4 times greater (1.7 x 10-3 IU ml-1) than that observed for the cDNA clone (5 x 10-4 IU ml-1). Furthermore, the activity was similar to the activity of locally isolated Trichoderma virens (1.5 x 10-3 IU ml-1). The estimated size of the protein was 52 kDA. In fermentation studies, the maximum ethanol production by the genomic and the cDNA clones were 0.36 g and 0.06 g /g of cellobiose respectively. Molecular docking results indicated that the bare protein and cellobiose-protein complex behave in a similar manner with considerable stability in aqueous medium. The deduced binding site and the binding affinity of the constructed homology model appeared to be reasonable. Moreover, it was identified that the five hydrogen bonds formed between the amino acid residues of BGLI and cellobiose are mainly involved in the integrity of enzyme-substrate association.

CONCLUSIONS

The BGLI activity was remarkably higher in the genomic DNA clone compared to the cDNA clone. Cellobiose was successfully fermented into ethanol by the recombinant S.cerevisiae genomic DNA clone. It has the potential to be used in the industrial production of ethanol as it is capable of simultaneous saccharification and fermentation of cellobiose. Homology modeling, docking studies and molecular dynamics simulation studies will provide a realistic model for further studies in the modification of active site residues which could be followed by mutation studies to improve the catalytic action of BGLI.

Microelectric Current Treatment Enhanced Biodegradation of Pumpkin Lignocelluloses by Trichoderma reesei RUT-C30

A homemade microcurrent reactor was used to treat the fermentation of Trichoderma reesei. Results indicated that the yield of saccharides for T. reesei RUT-C30 cultivated in pumpkin lignocellulose broth reaches 38.86% (w/w) when a microcurrent treatment (20 mA, at the 48th hour for 60 min) was carried out, which is significantly higher than the control group (p < 0.05). Additionally, activities of endoglucanase, cellobiohydrolase, xylanase, and pectinase were significantly increased in days 3-7. Furthermore, the fungal growth was facilitated by microelectric treatment, showing a 0.57-fold increase of spore numbers at the sixth day of cultivation. Besides, the monosaccharide composition, including glucose (1.03 mg/mL), xylose (0.12 mg/mL), arabinose (0.31 mg/mL), and fructose (0.13 mg/mL), extracted from the reactor was higher than that without the current treatment. In this work, we improved the biodegradation of lignocellulosic wastes by applying a microcurrent to lignocellulose-degrading fungal cultures and provided a new idea for the lignocellulose material pretreatment and bioconversion.

Production of rice straw hydrolysis enzymes by the fungi Trichoderma reesei and Humicola insolens using rice straw as a carbon source

Rice straw was evaluated as a carbon source for the fungi, Trichoderma reesei and Humicola insolens, to produce enzymes for rice straw hydrolysis. The enzyme activity of T. reesei and H. insolens cultivated in medium containing non-treated rice straw were almost equivalent to the enzyme of T. reesei cultivated in Avicel medium, a form of refined cellulose. The enzyme activity of T. reesei cultivated in medium containing NH₄OH-treated rice straw was 4-fold higher than enzyme from cultures grown in Avicel medium. In contrast, H. insolens enzyme from cultures grown in NH₄OH-treated rice straw had significantly lower activity compared with non-treated rice straw or Avicel. The combined use of T. reesei and H. insolens enzymes resulted in a significant synergistic enhancement in enzymatic activity. Our data suggest that rice straw is a promising low-cost carbon source for fungal enzyme production for rice straw hydrolysis.